Showing 451 - 500 of 733 Items

Date: 2000-01-01

Creator: Jack Bateman, Huidy Shu, David Van Vactor

Access: Open access

Recent analysis of Rho subfamily GTPases in Drosophila revealed roles for Rac and Cdc42 during axonogenesis. Here, we describe the identification and characterization of the Drosophila counterpart of Trio, a guanine nucleotide exchange factor (GEF) that associates with the receptor phosphatase LAR and regulates GTPase activation in vertebrate cells. Mutants deficient in trio activity display defects in both central and peripheral axon pathways reminiscent of pheno-types observed in embryos deficient in small GTPase function. Double mutant analysis shows that trio interacts with Rac in a dose-sensitive manner but not with Rho. Moreover, reduction of trio activity potentiates the phenotype of mutations in the LAR homolog Dlar, suggesting that these proteins collaborate in orchestrating the cytoskeletal events that underlie normal axonogenesis.

Date: 2016-07-26

Creator: Richard S. Dodd, Vladimir Douhovnikoff

Access: Open access

The earth is experiencing major changes in global and regional climates and changes are predicted to accelerate in the future. Many species will be under considerable pressure to evolve, to migrate, or be faced with extinction. Clonal plants would appear to be at a particular disadvantage due to their limited mobility and limited capacity for adaptation. However, they have outlived previous environmental shifts and clonal species have persisted for millenia. Clonal spread offers unique ecological advantages, such as resource sharing, risk sharing, and economies of scale among ramets within genotypes. We suggest that ecological attributes of clonal plants, in tandem with variation in gene regulation through epigenetic mechanisms that facilitate and optimize phenotype variation in response to environmental change may permit them to be well suited to projected conditions.

Date: 2019-03-01

Creator: Dawn M. Blitz, Andrew E. Christie, Aaron P. Cook, Patsy S. Dickinson, Michael P., Nusbaum

Access: Open access

Similarities and differences in circuit responses to applied Gly 1 -SIFamide and peptidergic (Gly 1 -SIFamide) neuron stimulation. J Neurophysiol 121: 950 –972, 2019. First published January 16, 2019; doi:10.1152/jn.00567.2018.—Microcircuit modulation by peptides is well established, but the cellular/synaptic mechanisms whereby identified neurons with identified peptide transmitters modulate microcircuits remain unknown for most systems. Here, we describe the distribution of GYRKPPFNGSIFamide (Gly 1 -SIFamide) immunoreactivity (Gly 1 -SIFamide-IR) in the stomatogastric nervous system (STNS) of the crab Cancer borealis and the Gly 1 -SIFamide actions on the two feeding-related circuits in the stomatogastric ganglion (STG). Gly 1 -SIFamide-IR localized to somata in the paired commissural ganglia (CoGs), two axons in the nerves connecting each CoG with the STG, and the CoG and STG neuropil. We identified one Gly 1 -SIFamide-IR projection neuron innervating the STG as the previously identified modulatory commissural neuron 5 (MCN5). Brief (~10 s) MCN5 stimulation excites some pyloric circuit neurons. We now find that bath applying Gly 1 -SIFamide to the isolated STG also enhanced pyloric rhythm activity and activated an imperfectly coordinated gastric mill rhythm that included unusually prolonged bursts in two circuit neurons [inferior cardiac (IC), lateral posterior gastric (LPG)]. Furthermore, longer duration (±30 s) MCN5 stimulation activated a Gly 1 -SIFamide-like gastric mill rhythm, including prolonged IC and LPG bursting. The prolonged LPG bursting decreased the coincidence of its activity with neurons to which it is electrically coupled. We also identified local circuit feedback onto the MCN5 axon terminals, which may contribute to some distinctions between the responses to MCN5 stimulation and Gly 1 -SIFamide application. Thus, MCN5 adds to the few identified projection neurons that modulate a well-defined circuit at least partly via an identified neuropeptide transmitter and provides an opportunity to study peptide regulation of electrical coupled neurons in a functional context. NEW & NOTEWORTHY Limited insight exists regarding how identified peptidergic neurons modulate microcircuits. We show that the modulatory projection neuron modulatory commissural neuron 5 (MCN5) is peptidergic, containing Gly 1 -SIFamide. MCN5 and Gly 1 -SIFamide elicit similar output from two well-defined motor circuits. Their distinct actions may result partly from circuit feedback onto the MCN5 axon terminals. Their similar actions include eliciting divergent activity patterns in normally coactive, electrically coupled neurons, providing an opportunity to examine peptide modulation of electrically coupled neurons in a functional context.

Date: 2001-09-04

Creator: Jack Bateman, R. Srekantha Reddy, Haruo Saito, David Van Vactor

Access: Open access

Background: Regulation of actin structures is instrumental in maintaining proper cytoarchitecture in many tissues. In the follicular epithelium of Drosophila ovaries, a system of actin filaments is coordinated across the basal surface of cells encircling the oocyte. These filaments have been postulated to regulate oocyte elongation; however, the molecular components that control this cytoskeletal array are not yet understood. Results: We find that the receptor tyrosine phosphatase (RPTP) Dlar and integrins are involved in organizing basal actin filaments in follicle cells. Mutations in Dlar and the common β-integrin subunit mys cause a failure in oocyte elongation, which is correlated with a loss of proper actin filament organization. Immunolocalization shows that early in oogenesis Dlar is polarized to membranes where filaments terminate but becomes generally distributed late in development, at which time β-integrin and Enabled specifically associate with actin filament terminals. Rescue experiments point to the early period of polar Dlar localization as critical for its function. Furthermore, clonal analysis shows that loss of Dlar or mys influences actin filament polarity in wild-type cells that surround mutant tissues, suggesting that communication between neighboring cells regulates cytoskeletal organization. Finally, we find that two integrin α subunits encoded by mew and if are required for proper oocyte elongation, implying that multiple components of the ECM are instructive in coordinating actin fiber polarity. Conclusions: Dlar cooperates with integrins to coordinate actin filaments at the basal surface of the follicular epithelium. To our knowledge, this is the first direct demonstration of an RPTP's influence on the actin cytoskeleton.

Date: 2003-10-01

Creator: Neil X. Krueger, R. Sreekantha Reddy, Karl Johnson, Jack Bateman, Nancy, Kaufmann, Daniella Scalice, David Van Vactor, Haruo Saito

Access: Open access

The receptor protein tyrosine phosphatase (PTPase) Dlar has an ectodomain consisting of three immunoglobulin (Ig)-like domains and nine fibronectin type III (FnIII) repeats and a cytoplasmic domain consisting of two PTPase domains, membrane-proximal PTP-D1 and C-terminal PTP-D2. A series of mutant Dlar transgenes were introduced into the Drosophila genome via P-element transformation and were then assayed for their capacity to rescue phenotypes caused by homozygous loss-of-function genotypes. The Ig-like domains, but not the FnIII domains, are essential for survival. Conversely, the FnIII domains, but not the Ig-like domains, are required during oogenesis, suggesting that different domains of the Dlar ectodomain are involved in distinct functions during Drosophila development. All detectable PTPase activity maps to PTP-D1 in vitro. The catalytically inactive mutants of Dlar were able to rescue Dlar -/- lethality nearly as efficiently as wild-type Dlar transgenes, while this ability was impaired in the PTP-D2 deletion mutants DlarΔPTP-D2 and Dlarbypass. Dlar-C1929S, in which PTP-D2 has been inactivated, increases the frequency of bypass phenotype observed in Dlar-/- genotypes, but only if PTP-D1 is catalytically active in the transgene. These results indicate multiple roles for PTP-D2, perhaps by acting as a docking domain for downstream elements and as a regulator of PTP-D1.

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.

Date: 2008-07-22

Creator: R. R. Thompson, P. S. Dickinson, J. D. Rose, K. A. Dakin, G. M., Civiello, A. Segerdahl, R. Bartlett

Access: Open access

We tested whether the sex pheromones that stimulate courtship clasping in male roughskin newts do so, at least in part, by amplifying the somatosensory signals that directly trigger the motor pattern associated with clasping and, if so, whether that amplification is dependent on endogenous vasotocin (VT). Female olfactory stimuli increased the number of action potentials recorded in the medulla of males in response to tactile stimulation of the cloaca, which triggers the clasp motor reflex, as well as to tactile stimulation of the snout and hindlimb. That enhancement was blocked by exposing the medulla to a V1a receptor antagonist before pheromone exposure. However, the antagonist did not affect medullary responses to tactile stimuli in the absence of pheromone exposure, suggesting that pheromones amplify somatosensory signals by inducing endogenous VT release. The ability of VT to couple sensory systems together in response to social stimulation could allow this peptide to induce variable behavioural outcomes, depending on the immediate context of the social interaction and thus on the nature of the associated stimuli that are amplified. If widespread in vertebrates, this mechanism could account for some of the behavioural variability associated with this and related peptides both within and across species. © 2008 The Royal Society.

Date: 2001-09-15

Creator: Adi Mizrahi, Patsy S. Dickinson, Peter Kloppenburg, Valerie Fénelon, Deborah J., Baro, Ronald M. Harris-Warrick, Pierre Meyrand, John Simmers

Access: Open access

Organotypic cultures of the lobster (Homarus gammarus) stomatogastric nervous system (STNS) were used to assess changes in membrane properties of neurons of the pyloric motor pattern-generating network in the long-term absence of neuromodulatory inputs to the stomatogastric ganglion (STG). Specifically, we investigated decentralization-induced changes in the distribution and density of the transient outward current, IA, which is encoded within the STG by the shal gene and plays an important role in shaping rhythmic bursting of pyloric neurons. Using an antibody against lobster shal K+ channels, we found shal immunoreactivity in the membranes of neuritic processes, but not somata, of STG neurons in 5 d cultured STNS with intact modulatory inputs. However, in 5 d decentralized STG, shal immunoreactivity was still seen in primary neurites but was likewise present in a subset of STG somata. Among the neurons displaying this altered shal localization was the pyloric dilator (PD) neuron, which remained rhythmically active in 5 d decentralized STG. Two-electrode voltage clamp was used to compare IA in synaptically isolated PD neurons in long-term decentralized STG and nondecentralized controls. Although the voltage dependence and kinetics of IA changed little with decentralization, the maximal conductance of IA in PD neurons increased by 43.4%. This increase was consistent with the decentralization-induced increase in shal protein expression, indicating an alteration in the density and distribution of functional A-channels. Our results suggest that, in addition to the short-term regulation of network function, modulatory inputs may also play a role, either directly or indirectly, in controlling channel number and distribution, thereby maintaining the biophysical character of neuronal targets on a long-term basis.

Date: 2013-09-27

Creator: Alexandra Pfister, Amy Johnson, Olaf Ellers, Hadley W. Horch

Access: Open access

Dendrite and axon growth and branching during development are regulated by a complex set of intracellular and external signals. However, the cues that maintain or influence adult neuronal morphology are less well understood. Injury and deafferentation tend to have negative effects on adult nervous systems. An interesting example of injury-induced compensatory growth is seen in the cricket, Gryllus bimaculatus. After unilateral loss of an ear in the adult cricket, auditory neurons within the central nervous system (CNS) sprout to compensate for the injury. Specifically, after being deafferented, ascending neurons (AN-1 and AN-2) send dendrites across the midline of the prothoracic ganglion where they receive input from auditory afferents that project through the contralateral auditory nerve (N5). Deafferentation also triggers contralateral N5 axonal growth. In this study, we quantified AN dendritic and N5 axonal growth at 30 h, as well as at 3, 5, 7, 14, and 20 days after deafferentation in adult crickets. Significant differences in the rates of dendritic growth between males and females were noted. In females, dendritic growth rates were non-linear; a rapid burst of dendritic extension in the first few days was followed by a plateau reached at 3 days after deafferentation. In males, however, dendritic growth rates were linear, with dendrites growing steadily over time and reaching lengths, on average, twice as long as in females. On the other hand, rates of N5 axonal growth showed no significant sexual dimorphism and were linear. Within each animal, the growth rates of dendrites and axons were not correlated, indicating that independent factors likely influence dendritic and axonal growth in response to injury in this system. Our findings provide a basis for future study of the cellular features that allow differing dendrite and axon growth patterns as well as sexually dimorphic dendritic growth in response to deafferentation. © 2013 Pfister, Johnson, Ellers and Horch.

Date: 2019-01-01

Creator: Patsy S. Dickinson, Evyn S. Dickinson, Emily R. Oleisky, Cindy D. Rivera, Meredith E., Stanhope, Elizabeth A. Stemmler, J. Joe Hull, Andrew E. Christie

Access: Open access

Recent genomic/transcriptomic studies have identified a novel peptide family whose members share the carboxyl terminal sequence –GSEFLamide. However, the presence/identity of the predicted isoforms of this peptide group have yet to be confirmed biochemically, and no physiological function has yet been ascribed to any member of this peptide family. To determine the extent to which GSEFLamides are conserved within the Arthropoda, we searched publicly accessible databases for genomic/transcriptomic evidence of their presence. GSEFLamides appear to be highly conserved within the Arthropoda, with the possible exception of the Insecta, in which sequence evidence was limited to the more basal orders. One crustacean in which GSEFLamides have been predicted using transcriptomics is the lobster, Homarus americanus. Expression of the previously published transcriptome-derived sequences was confirmed by reverse transcription (RT)-PCR of brain and eyestalk ganglia cDNAs; mass spectral analyses confirmed the presence of all six of the predicted GSEFLamide isoforms – IGSEFLamide, MGSEFLamide, AMGSEFLamide, VMGSEFLamide, ALGSEFLamide and AVGSEFLamide – in H. americanus brain extracts. AMGSEFLamide, of which there are multiple copies in the cloned transcripts, was the most abundant isoform detected in the brain. Because the GSEFLamides are present in the lobster nervous system, we hypothesized that they might function as neuromodulators, as is common for neuropeptides. We thus asked whether AMGSEFLamide modulates the rhythmic outputs of the cardiac ganglion and the stomatogastric ganglion. Physiological recordings showed that AMGSEFLamide potently modulates the motor patterns produced by both ganglia, suggesting that the GSEFLamides may serve as important and conserved modulators of rhythmic motor activity in arthropods.

Date: 2018-09-01

Creator: Giap H. Vu, Daniel Do, Cindy D. Rivera, Patsy S. Dickinson, Andrew E., Christie, Elizabeth A. Stemmler

Access: Open access

We report on the characterization of the native form of an American lobster, Homarus americanus, β-defensin-like putative antimicrobial peptide, H. americanus defensin 1 (Hoa-D1), sequenced employing top-down and bottom-up peptidomic strategies using a sensitive, chip-based nanoLC-QTOF-MS/MS instrument. The sequence of Hoa-D1 was determined by mass spectrometry; it was found to contain three disulfide bonds and an amidated C-terminus. The sequence was further validated by searching publicly-accessible H. americanus expressed sequence tag (EST) and transcriptome shotgun assembly (TSA) datasets. Hoa-D1, SYVRScSSNGGDcVYRcYGNIINGAcSGSRVccRSGGGYamide (with c representing a cysteine participating in a disulfide bond), was shown to be related to β-defensin-like peptides previously reported from Panulirus japonicas and Panulirus argus. We found Hoa-D1 in H. americanus hemolymph, hemocytes, the supraoesophageal ganglion (brain), eyestalk ganglia, and pericardial organ extracts, as well as in the plasma of some hemolymph samples. Using discontinuous density gradient separations, we fractionatated hemocytes and localized Hoa-D1 to hemocyte sub-populations. While Hoa-D1 was detected in semigranulocytes and granulocytes using conventional proteomic strategies for analysis, the direct analysis of cell lysates exposed evidence of Hoa-D1 processing, including truncation of the C-terminal tyrosine residue, in the granulocytes, but not semigranulocytes. These measurements demonstrate the insights regarding post-translational modifications and peptide processing that can be revealed through the MS analysis of intact peptides. The identification of Hoa-D1 as a widely-distributed peptide in the lobster suggests the possibility that it may be pleiotropic, with functions in addition to its proposed role as an antimicrobial molecule in the innate immune system.

Date: 2020-03-01

Creator: Hadley W. Horch, Sara B. Spicer, Isabel I.C. Low, Colby T. Joncas, Eleanor D., Quenzer, Hikmah Okoya, Lisa M. Ledwidge, Harrison P. Fisher

Access: Open access

Guidance cues act during development to guide growth cones to their proper targets in both the central and peripheral nervous systems. Experiments in many species indicate that guidance molecules also play important roles after development, though less is understood about their functions in the adult. The Semaphorin family of guidance cues, signaling through Plexin receptors, influences the development of both axons and dendrites in invertebrates. Semaphorin functions have been extensively explored in Drosophila melanogaster and some other Dipteran species, but little is known about their function in hemimetabolous insects. Here, we characterize sema1a and plexA in the cricket Gryllus bimaculatus. In fact, we found two distinct predicted Sema1a proteins in this species, Sema1a.1 and Sema1a.2, which shared only 48% identity at the amino acid level. We include a phylogenetic analysis that predicted that many other insect species, both holometabolous and hemimetabolous, express two Sema1a proteins as well. Finally, we used in situ hybridization to show that sema1a.1 and sema1a.2 expression patterns were spatially distinct in the embryo, and both roughly overlap with plexA. All three transcripts were also expressed in the adult brain, mainly in the mushroom bodies, though sema1a.2 was expressed most robustly. sema1a.2 was also expressed strongly in the adult thoracic ganglia while sema1a.1 was only weakly expressed and plexA was undetectable.

Date: 2020-12-01

Creator: Andrew E. Christie, Cindy D. Rivera, Catherine M. Call, Patsy S. Dickinson, Elizabeth A., Stemmler, J. Joe Hull

Access: Open access

Over the past decade, in silico genome and transcriptome mining has led to the identification of many new crustacean peptide families, including the agatoxin-like peptides (ALPs), a group named for their structural similarity to agatoxin, a spider venom component. Here, analysis of publicly accessible transcriptomes was used to expand our understanding of crustacean ALPs. Specifically, transcriptome mining was used to investigate the phylogenetic/structural conservation, tissue localization, and putative functions of ALPs in decapod species. Transcripts encoding putative ALP precursors were identified from one or more members of the Penaeoidea (penaeid shrimp), Sergestoidea (sergestid shrimps), Caridea (caridean shrimp), Astacidea (clawed lobsters and freshwater crayfish), Achelata (spiny/slipper lobsters), and Brachyura (true crabs), suggesting a broad, and perhaps ubiquitous, conservation of ALPs in decapods. Comparison of the predicted mature structures of decapod ALPs revealed high levels of amino acid conservation, including eight identically conserved cysteine residues that presumably allow for the formation of four identically positioned disulfide bridges. All decapod ALPs are predicted to have amidated carboxyl-terminals. Two isoforms of ALP appear to be present in most decapod species, one 44 amino acids long and the other 42 amino acids in length, both likely generated by alternative splicing of a single gene. In carideans, a gene or terminal exon duplication appears to have occurred, with alternative splicing producing four ALPs, two 44 and two 42 amino acid isoforms. The identification of ALP precursor-encoding transcripts in nervous system-specific transcriptomes (e.g., Homarus americanus brain, eyestalk ganglia, and cardiac ganglion assemblies, finding confirmed using RT-PCR) suggests that members of this peptide family may serve as locally-released and/or hormonally-delivered neuromodulators in decapods. Their detection in testis- and hepatopancreas-specific transcriptomes suggests that members of the ALP family may also play roles in male reproduction and innate immunity/detoxification.

Date: 2019-10-01

Creator: Patsy S. Dickinson, Heidi M. Samuel, Elizabeth A. Stemmler, Andrew E. Christie

Access: Open access

The SIFamides are a broadly conserved arthropod peptide family characterized by the C-terminal motif –SIFamide. In decapod crustaceans, two isoforms of SIFamide are known, GYRKPPFNGSIFamide (Gly1-SIFamide), which is nearly ubiquitously conserved in the order, and VYRKPPFNGSIFamide (Val1-SIFamide), known only from members of the astacidean genus Homarus. While much work has focused on the identification of SIFamide isoforms in decapods, there are few direct demonstrations of physiological function for members of the peptide family in this taxon. Here, we assessed the effects of Gly1- and Val1-SIFamide on the cardiac neuromuscular system of two closely related species of Cancer crab, Cancer borealis and Cancer irroratus. In each species, both peptides were cardioactive, with identical, dose-dependent effects elicited by both isoforms in a given species. Threshold concentrations for bioactivity are in the range typically associated with hormonal delivery, i.e., 10−9 to 10−8 M. Interestingly, and quite surprisingly, while the predicted effects of SIFamide on cardiac output are similar in both C. borealis and C. irroratus, frequency effects predominate in C. borealis, while amplitude effects predominate in C. irroratus. These findings suggest that, while SIFamide is likely to increase cardiac output in both crabs, the mechanism through which this is achieved is different in the two species. Immunohistochemical/mass spectrometric data suggest that SIFamide is delivered to the heart hormonally rather than locally, with the source of hormonal release being midgut epithelial endocrine cells in both Cancer species. If so, midgut-derived SIFamide may function as a regulator of cardiac output during the process of digestion.

Date: 2007-05-15

Creator: Elizabeth A. Stemmler, Emily A. Bruns, Noah P. Gardner, Patsy S. Dickinson, Andrew E., Christie

Access: Open access

In invertebrates, peptides possessing the carboxy (C)-terminal motif -RXRFamide have been proposed as the homologs of vertebrate neuropeptide Y (NPY). Using matrix assisted laser desorption/ionization mass spectrometry, in combination with sustained off-resonance irradiation collision-induced dissociation and chemical and enzymatic reactions, we have identified the peptide pEGFYSQRYamide from the neuroendocrine pericardial organ (PO) of the crab Pugettia producta. This peptide is likely the same as that previously reported, but misidentified, as PAFYSQRYamide in several earlier reports (e.g. [Li, L., Kelley, W.P., Billimoria, C.P., Christie, A.E., Pulver, S.R., Sweedler, J.V., Marder, E. 2003. Mass spectrometric investigation of the neuropeptide complement and release in the pericardial organs of the crab, Cancer borealis. J. Neurochem. 87, 642-656; Fu, Q., Kutz, K.K., Schmidt, J.J., Hsu, Y.W., Messinger, D.I., Cain, S.D., de la Iglesia, H.O., Christie, A.E., Li, L. 2005. Hormone complement of the Cancer productus sinus gland and pericardial organ: an anatomical and mass spectrometric investigation. J. Comp. Neurol. 493, 607-626.]). The -QRYamide motif contained in pEGFYSQRYamide is identical to that present in many vertebrate members of the NPY superfamily. Mass spectrometric analysis conducted on the POs of several other decapods showed that pEGFYSQRYamide is present in three other brachyurans (Cancer borealis, Cancer irroratus and Cancer productus) as well as in one species from another decapod infraorder (Lithodes maja, an anomuran). Thus, our findings show that at least some invertebrates possess NPY-like peptides in addition to those exhibiting an -RXRFamide C-terminus, and raise the question as to whether the invertebrate -QRYamides are functionally and/or evolutionarily related to the NPY superfamily. © 2007 Elsevier Inc. All rights reserved.

Date: 2007-07-01

Creator: Stephen M. Majercik

Access: Open access

We describe appssat, an anytime probabilistic contingent planner based on zander, a probabilistic contingent planner that operates by converting the planning problem to a stochastic satisfiability (Ssat) problem and solving that problem instead [S.M. Majercik, M.L. Littman, Contingent planning under uncertainty via stochastic satisfiability, Artificial Intelligence 147 (2003) 119-162]. The values of some of the variables in an Ssat instance are probabilistically determined; appssat considers the most likely instantiations of these variables (the most probable situations facing the agent) and attempts to construct an approximation of the optimal plan that succeeds under those circumstances, improving that plan as time permits. Given more time, less likely instantiations/situations are considered and the plan is revised as necessary. In some cases, a plan constructed to address a relatively low percentage of possible situations will succeed for situations not explicitly considered as well, and may return an optimal or near-optimal plan. We describe experimental results showing that appssat can find suboptimal plans in cases in which zander is unable to find the optimal (or any) plan. Although the test problems are small, the anytime quality of appssat means that it has the potential to efficiently derive suboptimal plans in larger, time-critical domains in which zander might not have sufficient time to calculate any plan. We also suggest further work needed to bring appssat closer to attacking real-world problems. © 2006 Elsevier Inc. All rights reserved.

Date: 2023-01-01

Creator: David A. Collings

Access: Open access

Humanity now faces the possibility that it will become extinct over the next few decades or so. This is not simply a reality about the biological fate of the species; it also raises the prospect of thought’s own extinction. But what does it mean for thought that it, too, might disappear? Thought’s possible disappearance shatters the assumption, at work across all the institutions and disciplines of the West, that one version or another of thought is enduring and will survive. As it turns out, no familiar practice rests on a secure ground; under the sign of the terminus - the prospect of humanity’s extinction - each one is shattered and undone. The cultural legacy becomes a field of rubble. In dozens of short essays, this book moves through this field. It takes up a host of specific inheritances and traces how each is shattered and transformed by an extinct thought. It engages with religion, philosophy, history, literature, ethics, studies of political power and resistance, and depictions of humanity’s place in the nonhuman world. It reconsiders the emergence of capitalism and of biopower, the science of climate change, the import of mediation and technology, and philosophies of temporality. Moreover, it contends with many innovative waves of thought over the past two centuries, from German idealism to deconstruction, from psychoanalysis to queer theory, from decolonizing theory to Afropessimism, and from the critique of ideology to speculative realism. It concludes by assessing what it is like for thought, having confronted its extinction, to live on in this debris, to dance with its own oblivion.

Date: 2019-09-21

Creator: Kenneth A. Dennison, Thomas W. Baumgarte, Stuart L. Shapiro

Access: Open access

The ‘direct collapse’ scenario has emerged as a promising evolutionary track for the formation of supermassive black holes early in the Universe. In an idealized version of such a scenario, a uniformly rotating supermassive star spinning at the mass-shedding (Keplerian) limit collapses gravitationally after it reaches a critical configuration. Under the assumption that the gas is dominated by radiation pressure, this critical configuration is characterized by unique values of the dimensionless parameters J/M2 and Rp/M, where J is the angular momentum, Rp the polar radius, and M the mass. Motivated by a previous perturbative treatment, we adopt a fully non-linear approach to evaluate the effects of gas pressure on these dimensionless parameters for a large range of masses. We find that gas pressure has a significant effect on the critical configuration even for stellar masses as large as M ~ 106 MO. We also calibrate two approximate treatments of the gas pressure perturbation in a comparison with the exact treatment, and find that one commonly used approximation in particular results in increasing deviations from the exact treatment as the mass decreases, and the effects of gas pressure increase. The other approximation, however, proves to be quite robust for all masses M >~ 104 MO.

Date: 1993-01-01

Creator: M. Procario, S. Yang, D. S. Akerib, B. Barish, M., Chadha, S. Chan, D. F. Cowen, G. Eigen, J. S. Miller, J. Urheim, A. J. Weinstein, D. Acosta, M. Athanas, G. Masek, B. Ong, H. Paar, M. Sivertz, A. Bean, J. Gronberg, R. Kutschke, S. Menary, R. J. Morrison, S. Nakanishi, H. N. Nelson, T. K. Nelson, J. D. Richman, H. Tajima, D. Schmidt, D. Sperka, M. S. Witherell, R. Ballest

Access: Open access

Using the CLEO II detector at CESR we have studied D0 decays into final states with a K̄0 or K̄*0, and have measured branching ratios for the decay modes D0→(K̄0K̄*0)π0,η, η′. These results are compared with predictions of various charm decay models, and contributions of final-state interactions are discussed. © 1993 The American Physical Society.

Date: 1993-01-01

Creator: S. Sanghera, T. Skwarnicki, R. Stroynowski, M. Artuso, M., Goldberg, N. Horwitz, R. Kennett, G. C. Moneti, F. Muheim, S. Playfer, Y. Rozen, P. Rubin, S. Stone, M. Thulasidas, W. M. Yao, G. Zhu, A. V. Barnes, J. Bartelt, S. E. Csorna, Z. Egyed, V. Jain, P. Sheldon, D. S. Akerib, B. Barish, M. Chadha, D. F. Cowen, G. Eigen, J. S. Miller, J. Urheim, A. J. Weinstein, D. Acosta

Access: Open access

We present a measurement of the lepton decay asymmetry Afb in the reaction B̄→D*l-ν̄l using data collected with the CLEO II detector at the Cornell Electron Storage Ring (CESR). The value of Afb confirms that the chirality of the weak interaction is predominantly left-handed in b→c transitions as expected in the standard model, if it is assumed that the lepton current is also left-handed. Using Afb and the previously determined branching ratio, q2 distribution, and D* polarization, we obtain the first measurement of the form-factor ratios that are used to describe this semileptonic decay. © 1993 The American Physical Society.

Date: 2014-09-01

Creator: Stephen G. Naculich

Access: Open access

Abstract: We generalize the scattering equations to include both massless and massive particles. We construct an expression for the tree-level n-point amplitude with n − 2 gluons or gravitons and a pair of massive scalars in arbitrary spacetime dimension as a sum over the (n − 3)! solutions of the scattering equations, à la Cachazo, He, and Yuan. We derive the BCJ relations obeyed by these massive amplitudes.

Date: 2003-08-01

Creator: Mark Battle, Michael Bender, Melissa B. Hendricks, David T. Ho, Robert, Mika, Galen McKinley, Song Miao Fan, Tegan Blaine, Ralph F. Keeling

Access: Open access

The Ar/N2 ratio of air measured at 6 globally distributed sites shows annual cycles with amplitudes of 12 to 37 parts in 106. Summertime maxima reflect the atmospheric Ar enrichment driven by seasonal warming and degassing of the oceans. Paired models of air-sea heat fluxes and atmospheric tracer transport predict seasonal cycles in the Ar/N2 ratio that agree with observations, within uncertainties.

Date: 2010-01-01

Creator: Johannes M. Henn, Stephen G. Naculich, Howard J. Schnitzer, Marcus Spradlin

Access: Open access

We extend the analysis of Higgs-regulated planar amplitudes of N = 4 supersymmetric Yang-Mills theory to four loops for the four-gluon amplitude and to two loops for the five-gluon amplitude. Our calculations are consistent with a proposed all-loop ansatz for planar MHV n-gluon amplitudes that is the analog of the BDS ansatz in dimensional regularization. In all cases considered, we have verified that the IR-finite parts of the logarithm of the amplitudes have the same dependence on kinematic variables as the corresponding functions in dimensionally-regulated amplitudes (up to overall additive constants, which we determine). We also study various Regge limits of N = 4 SYM planar n-gluon amplitudes. Euclidean Regge limits of Higgs-regulated n ≥ 4 amplitudes yield results similar in form to those found using dimensional regularization, but with different expressions for the gluon trajectory and Regge vertices resulting from the different regulator scheme. We also show that the Regge limit of the four-gluon amplitude is dominated at next-to-leading-log order by vertical ladder diagrams together with the class of vertical ladder diagrams with a single H-shaped insertion. © 2010 SISSA, Trieste, Italy.

Date: 1999-06-01

Creator: Yves Balkanski, Patrick Monfray, Mark Battle, Martin Heimann

Access: Open access

Recently, very precise measurements have detected the seasonal variability in the atmospheric O2/N2 ratio at several sites in the northern and southern hemispheres. In this paper, we derive marine primary productivity (PP) from satellite ocean color data. To infer air-sea oxygen fluxes, a simple one-dimensional diagnostic model of ocean biology has been developed that depends on only two parameters: a time delay between organic production and oxidation (set to 2 weeks) and an export scale length (50 m). This model gives a global net community production of 4.3 mol C m-2 yr-1 in the euphotic zone and 3.2 mol C m-2 yr-1 in the mixed layer. This last value corresponds to a global f ratio (net community production (NCP)/PP) at the base of the mixed layer of 0.37. The air-sea fluxes derived from this model are then used at the base of a three-dimensional atmospheric model to compare the atmospheric seasonal cycle of O2/N2 at five sites: Cape Grim (40.6S, 144.6E), Baring Head (41.3S, 174.8E), Mauna Loa (19.5N,154.8W), La Jolla (32.9N, 117.3W), and Barrow (71.3N, 156.6W). The agreement between model and observations is very encouraging. We infer from the agreement that the seasonal variations in O2/N2 are largely controlled by the photosynthesis rate but also by the remineralization linked to the deepening and shoaling of the mixed layer. Lateral ventilation to high latitudes may also be an important factor controlling the amplitude of the seasonal cycle.

Date: 2011-01-01

Creator: Stephen G. Naculicha, Howard J. Schnitzerb

Access: Open access

We apply factorization and eikonal methods from gauge theories to scattering amplitudes in gravity. We hypothesize that these amplitudes factor into an IR-divergent soft function and an IR-finite hard function, with the former given by the expectation value of a product of gravitational Wilson line operators. Using this approach, we show that the IR-divergent part of the n-graviton scattering amplitude is given by the exponential of the one-loop IR divergence, as originally discovered byWeinberg, with no additional subleading IR-divergent contributions in dimensional regularization. © SISSA 2011.

Date: 1993-04-12

Creator: Stephen G. Naculich, Harold A. Riggs, Howard J. Schnitzer

Access: Open access

A previously proposed two-step algorithm for calculating the expectation values of arbitrary Chern-Simons graphs fails to determine certain crucial signs. The step which involves calculating tetrahedra by solving certain non-linear equations is repaired by introducing additional linear equations. The step which involves reducing arbitrary graphs to sums of products of tetrahedra remains seriously disabled, apart from a few exceptional cases. As a first step towards a new algorithm for general graphs we find useful linear equations for those special graphs which support knots and links. Using the improved set of equations for tetrahedra we examine the symmetries between tetrahedra generated by arbitrary simple currents. Along the way we describe the simple, classical origin of simple-current charges. The improved skein relations also lead to exact identities between planar tetrahedra in level K G(N) and level N G(K) Chern-Simons theories, where G(N) denotes a classical group. These results are recast as WZW braid-matrix identities and as identities between quantum 6-jsymbols at appropriate roots of unity. We also obtain the transformation properties of arbitrary graphs, knots, and links under simple-current symmetries and rank-level duality. For links with knotted components this requires precise control of the braid eigenvalue permutation signs, which we obtain from plethysm and an explicit expression for the (multiplicity-free) signs, valid for all compact gauge groups and all fusion products. © 1993.

Date: 1997-11-17

Creator: Stephen G. Naculich, Howard J. Schnitzer

Access: Open access

We construct a one-to-one map between the primary fields of the N = 2 superconformal Kazama-Suzuki models G(m, n, k) and G(k, n, m) based on complex Grassmannian cosets, using level-rank duality of Wess-Zumino-Witten models. We then show that conformal weights, superconformal U(1) charges, modular transformation matrices, and fusion rules are preserved under this map, providing strong evidence for the equivalence of these coset models. © 1997 Elsevier Science B.V.

Date: 1995-01-01

Creator: Stephen G. Naculich, Harold A. Riggs

Access: Open access

Compact string expressions are found for nonintersecting Wilson loops in SU(N) Yang-Mills theory on any surface (orientable or nonorientable) as a weighted sum over covers of the surface. All terms from the coupled chiral sectors of the 1/N expansion of the Wilson loop expectation values are included. © 1995 The American Physical Society.

Date: 2006-10-30

Creator: Stephen G. Naculich, Howard J. Schnitzer

Access: Open access

We analyze the level-rank duality of ωc-twisted D-branes of over(su, ̂) (N)K (when N and K > 2). When N or K is even, the duality map involves Z2-cominimal equivalence classes of twisted D-branes. We prove the duality of the spectrum of an open string stretched between ωc-twisted D-branes, and ascertain the relation between the charges of level-rank-dual ωc-twisted D-branes. © 2006 Elsevier B.V. All rights reserved.

Date: 2003-02-24

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

Access: Open access

We perform a completely perturbative matrix model calculation of the physical low-energy quantities of the N = 2 U(N) gauge theory. Within the matrix model framework we propose a perturbative definition of the periods a i in terms of certain tadpole diagrams, and check our conjecture up to first order in the gauge theory instanton expansion. The prescription does not require knowledge of the Seiberg-0Witten differential or curve.We also compute the N = 2 prepotential F(a) perturbatively up to the first-instanton level, finding agreement with the known result. 2002 Elsevier Science B.V. All rights reserved.

Date: 1994-01-01

Creator: D. N. Brown, J. Fast, R. L. McIlwain, T. Miao, D. H., Miller, M. Modesitt, D. Payne, E. I. Shibata, I. P.J. Shipsey, P. N. Wang, M. Battle, J. Ernst, Y. Kwon, S. Roberts, E. H. Thorndike, C. H. Wang, J. Dominick, M. Lambrecht, S. Sanghera, V. Shelkov, T. Skwarnicki, R. Stroynowski, I. Volobouev, G. Wei, P. Zadorozhny, M. Artuso, M. Goldberg, D. He, N. Horwitz, R. Kennett, R. Mountain

Access: Open access

We have measured the vector-pseudoscalar mass splitting M(Ds*+)-M(Ds+)=144.220.470.37 MeV significantly more precisely than the previous world average. We minimize the systematic errors by also measuring the vector-pseudoscalar mass difference M(D*0)-M(D0) using the radiative decay D*0D0, obtaining [M(Ds*+)-M(Ds+)]-[M(D*0)-M(D0)] =2.090.470.37 MeV. This is then combined with our previous high-precision measurement of M(D*0)-M(D0), which used the decay D*0D00. We also measure the mass difference M(Ds+)-M(D+)=99.50.60.3 MeV, using the + decay modes of the Ds+ and D+ mesons. © 1994 The American Physical Society.

Date: 1993-01-01

Creator: A. Bean, J. Gronberg, R. Kutschke, S. Menary, R. J., Morrison, H. N. Nelson, J. D. Richman, H. Tajima, D. Schmidt, D. Sperka, M. S. Witherell, M. Procario, S. Yang, R. Ballest, 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, H. A. Cho, D. M. Coffman, P. S. Drell, R. Ehrlich

Access: Open access

Using a sample of 935 000 BB̄ pairs collected with the CLEO-II detector at the Cornell Electron Storage Ring, we have obtained upper limits on the branching ratios for the b→ul-ν̄ processes B-→ωl- ν̄, B-→ρ0l-ν̄, and B̄0→ρ+l-ν̄. The combined result using the relationships among the widths for these three modes is B(B-→ρ0l-ν̄)<(1.6-2.7)×10-4 at 90% C.L., where the range of values is due to model dependence of the detection efficiencies. These measurements yield the limits Vub/Vcb<0.08-0.13. © 1993 The American Physical Society.

Date: 2019-08-01

Creator: Luke Carberry, Collin Roesler, Susan Drapeau

Access: Open access

Chlorophyll fluorometry is one of the most commonly implemented approaches for estimating phytoplankton biomass in situ, despite documented sources of natural variability and instrumental uncertainty in the relationship between in vivo fluorescence and chlorophyll concentration. A number of strategies are employed to minimize errors and quantify natural variability in this relationship in the open ocean. However, the assumptions underlying these approaches are unsupported in coastal waters due to the short temporal and small spatial scales of variability, as well as the optical complexity. The largest source of variability in the in situ chlorophyll fluorometric signal is nonphotochemical quenching (NPQ). Typically, unquenched nighttime observations are interpolated over the quenched daytime interval, but this assumes a spatial homogeneity not found in tidally impacted coastal waters. Here, we present a model that provides a tidally resolved correction for NPQ in moored chlorophyll fluorescence measurements. The output of the model is a time series of unquenched chlorophyll fluorescence in tidal endmembers (high and low tide extremes), and thus a time series of phytoplankton biomass growth and loss in these endmember populations. Comparison between modeled and measured unquenched time series yields quantification of nonconservative variations in phytoplankton biomass. Tidally modeled interpolation between these endmember time series yields a highly resolved time series of unquenched daytime chlorophyll fluorescence values at the location of the moored sensor. Such data sets provide a critical opportunity for validating the satellite remotely sensed ocean color chlorophyll concentration data product in coastal waters.

Date: 2002-01-01

Creator: Eric Chown, Randolph M. Jones, Amy E. Henninger

Access: Open access

Our research focuses on complex agents that are capable of interacting with their environments in ways that are increasingly similar to individual humans. In this article we describe a cognitive architecture for an interactive decision-making agent with emotions. The primary goal of this work is to make the decision-making process of complex agents more realistic with regard to the behavior moderators, including emotional factors that affect humans. Instead of uniform agents that rely entirely on a deterministic body of expertise to make their decisions, the decision making process of our agents will vary according to select emotional factors affecting the agent as well as the agent's parameterized emotional profile. The premise of this model is that emotions serve as a kind of automatic assessment system that can guide or otherwise influence the more deliberative decision making process. The primary components of this emotional system are pleasure/pain and clarity/confusion subsystems that differentiate between positive and negative states. These, in turn, feed into an arousal system that interfaces with the decision-making system. We are testing our model using synthetic special-forces agents in a reconnaissance simulation.

Date: 2015-01-01

Creator: Elizabeth Mamantov, William Silver, William Dawson, Eric Chown

Access: Open access

RoboGrams is a lightweight and efficient message passing architecture that we designed for the RoboCup domain and that has been successfully used by the Northern Bites SPL team. This unique architecture provides a framework for separating code into strongly decoupled modules, which are combined into configurable dataflow graphs. We present several different architecture types and preexisting message passing implementations, but among all of these, we contend that Robo-Grams' features make it particularly well suited for use in RoboCup. As a success story, we describe the Northern Bites' use of RoboGrams and the benefits it has provided to a single team, but we also suggest that it could help SPL teams collaborate in the future.

Date: 2019-01-01

Creator: Justin W. Henry, Sree Padma

Access: Open access

The five articles which make up this special issue of South Asia explore the role of the Ramayana in Sri Lankan art, literature, religious ritual and political discourse in shaping Sinhala Buddhist and Tamil Saiva perceptions of the island’s distant past. Contributors work to answer the question as to when and how Sri Lanka came to be equated with the mythic ‘Lankapura’ of Valmiki’s epic, exploring both positive and negative portrayals of Ravana (ruler of Lanka antagonist of the Ramayana) in Sinhala and Tamil literature from the late medieval period to the present day. Authors work to account for the politicisation and historicisation of the Ramayana in twenty-first century Sri Lanka (including similarities to and differences from the contemporary Indian situation), along with the appropriation of Ravana as a Sinhala Buddhist cultural hero, and the incorporation of Vibhishana as a ‘guardian deity’ in the Sinhala Buddhist pantheon.

Date: 2020-08-24

Creator: Mary Alta Rogalski, Meghan A. Duffy

Access: Open access

Date: 2014-04-29

Creator: Stephen Polasky, David J. Lewis, Andrew J. Plantinga, Erik Nelson

Access: Open access

Many ecosystem services are public goods whose provision depends on the spatial pattern of land use. The pattern of land use is often determined by the decisions of multiple private landowners. Increasing the provision of ecosystem services, though beneficial for society as a whole, may be costly to private landowners. A regulator interested in providing incentives to landowners for increased provision of ecosystem services often lacks complete information on landowners' costs. The combination of spatially dependent benefits and asymmetric cost information means that the optimal provision of ecosystem services cannot be achieved using standard regulatory or payment for ecosystem services approaches. Here we show that an auction that sets payments between landowners and the regulator for the increased value of ecosystem services with conservation provides incentives for landowners to truthfully reveal cost information, and allows the regulator to implement the optimal provision of ecosystem services, even in the case with spatially dependent benefits and asymmetric information.

Date: 2022-04-01

Creator: Syanah C. Wynn, Erika Nyhus

Access: Open access

The primary aim of this review is to examine the brain activity patterns that are related to subjectively perceived memory confidence. We focus on the main brain regions involved in episodic memory: the medial temporal lobe (MTL), prefrontal cortex (PFC), and posterior parietal cortex (PPC), and relate activity in their subregions to memory confidence. How this brain activity in both the encoding and retrieval phase is related to (subsequent) memory confidence ratings will be discussed. Specifically, encoding related activity in MTL regions and ventrolateral PFC mainly shows a positive linear increase with subsequent memory confidence, while dorsolateral and ventromedial PFC activity show mixed patterns. In addition, encoding-related PPC activity seems to only have indirect effects on memory confidence ratings. Activity during retrieval in both the hippocampus and parahippocampal cortex increases with memory confidence, especially during high-confident recognition. Retrieval-related activity in the PFC and PPC show mixed relationships with memory confidence, likely related to post-retrieval monitoring and attentional processes, respectively. In this review, these MTL, PFC, and PPC activity patterns are examined in detail and related to their functional roles in memory processes. This insight into brain activity that underlies memory confidence is important for our understanding of brain–behaviour relations and memory-guided decision making. © 2022 The Authors. European Journal of Neuroscience published by Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Date: 2014-08-01

Creator: P. Jeremy Werdell, Collin S. Roesler, Joaquim I. Goes

Access: Open access

Ocean reflectance inversion models (ORMs) provide a mechanism for inverting the color of the water observed by a satellite into marine inherent optical properties (IOPs), which can then be used to study phytoplankton community structure. Most ORMs effectively separate the total signal of the collective phytoplankton community from other water column constituents; however, few have been shown to effectively identify individual contributions by multiple phytoplankton groups over a large range of environmental conditions. We evaluated the ability of an ORM to discriminate between Noctiluca miliaris and diatoms under conditions typical of the northern Arabian Sea. We: (1) synthesized profiles of IOPs that represent bio-optical conditions for the Arabian Sea; (2) generated remote-sensing reflectances from these profiles using Hydrolight; and (3) applied the ORM to the synthesized reflectances to estimate the relative concentrations of diatoms and N. miliaris. By comparing the estimates from the inversion model with those from synthesized vertical profiles, we identified those conditions under which the ORM performs both well and poorly. Even under perfectly controlled conditions, the absolute accuracy of ORM retrievals degraded when further deconstructing the derived total phytoplankton signal into subcomponents. Although the absolute magnitudes maintained biases, the ORM successfully detected whether or not Noctiluca miliaris appeared in the simulated water column. This quantitatively calls for caution when interpreting the absolute magnitudes of the retrievals, but qualitatively suggests that the ORM provides a robust mechanism for identifying the presence or absence of species.

Date: 2010-03-01

Creator: Michael M. Franz, Travis N. Ridout

Access: Open access

The 2008 presidential election was historic in many respects. The campaign included the first African American major-party candidate, and neither candidate was an incumbent president or vice president. In addition, one candidate took public funding and the other candidate did not. This latter disparity resulted in an imbalance of resources across the two campaigns, especially in the purchase of political advertising. But did that imbalance matter for who won? Did advertising move voters, and if so, by how much? This article examines patterns of presidential ad buys in 2008 and compares them with presidential ad buys in 2004. It also examines the impact of advertising on county-level vote returns in both years. The results demonstrate some important differences in advertising patterns across years, especially in terms of ad sponsorship and market-level advertising advantages. We also find significant and strong advertising persuasion effects in 2008. © The Author(s) 2010.

Date: 2016-10-01

Creator: Erik J. Nelson, Matthew R. Helmus, Jeannine Cavender-Bares, Stephen Polasky, Jesse R., Lasky, Amy E. Zanne, William D. Pearse, Nathan J.B. Kraft, Daniela A. Miteva

Access: Open access

Increasing trade between countries and gains in income have given consumers around the world access to a richer and more diverse set of commercial plant products (i.e., foods and fibers produced by farmers). According to the economic theory of comparative advantage, countries open to trade will be able to consume more-in termsof volume and diversity-if they concentrate production on commodities that they can most cost-effectively produce, while importing goods that are expensive to produce, relative to other countries. Here, we performa global analysis of traded commercial plant products and find little evidence that increasing globalization has incentivized agricultural specialization. Instead, a country's plant production and consumption patterns are still largely determined by local evolutionary legacies of plant diversification. Because tropical countries harbor a greater diversity of lineages across the tree of life than temperate countries, tropical countries produce and consume a greater diversity of plant products than do temperate countries. In contrast, the richer and more economically advanced temperate countries have the capacity to produce and consume more plant species than the generally poorer tropical countries, yet this collection of plant species is drawn from fewer branches on the tree of life. Why have countries not increasingly specialized in plant production despite the theoretical financial incentive to do so? Potential explanations include the persistence of domestic agricultural subsidies that distort production decisions, cultural preferences for diverse local food production, and that diverse food production protects rural households in developing countries from food price shocks. Less specialized production patterns will make crop systems more resilient to zonal climatic and social perturbations,but this may come at the expense of global crop production efficiency, an important step in making the transition to a hotter and more crowded world.

Date: 2016-11-01

Creator: Erik Nelson, Virginia Matzek

Access: Open access

Nascent US carbon markets reward farmers for reforesting agricultural land, with consequent ecological co-benefits. We use a dynamic optimization model to determine the likelihood of an orchard farmer in northern California converting to forest under 90 plausible future scenarios. We find reforestation to be a highly unlikely outcome, occurring only 4.0% of the time under current economic, biophysical, and policy conditions, and only 18.5% of the time under a set of assumptions that make carbon offset production more economically viable. Conversion to "carbon farming" was more sensitive to changes in orchard production costs and yields than to carbon offset policy changes. In the absence of other changes, the price of a carbon offset would have to increase nearly a hundredfold to make reforestation compete economically with orchard agriculture. Our results partly explain low participation in the reforestation sector of US carbon markets. We conclude that farmers will not be interested in forest conversion unless their land has limited agricultural potential or they are motivated by social, rather than economic, rewards.

Date: 2013-04-01

Creator: Chaiyaboot Ariyachet, Norma V. Solis, Yaoping Liu, Nemani V. Prasadarao, Scott G., Filler, Anne E. McBride

Access: Open access

Candida albicans causes both mucosal and disseminated infections, and its capacity to grow as both yeast and hyphae is a key virulence factor. Hyphal formation is a type of polarized growth, and members of the SR (serine-arginine) family of RNA-binding proteins influence polarized growth of both Saccharomyces cerevisiae and Aspergillus nidulans. Therefore, we investigated whether SR-like proteins affect filamentous growth and virulence of C. albicans. BLAST searches with S. cerevisiae SR-like protein Npl3 (ScNpl3) identified two C. albicans proteins: CaNpl3, an apparent ScNpl3 ortholog, and Slr1, another SR-like RNAbinding protein with no close S. cerevisiae ortholog. Whereas ScNpl3 was critical for growth, deletion of NPL3 in C. albicans resulted in few phenotypic changes. In contrast, the slr1δ/δ mutant had a reduced growth rate in vitro, decreased filamentation, and impaired capacity to damage epithelial and endothelial cells in vitro. Mice infected intravenously with the slr1δ/δ mutant strain had significantly prolonged survival compared to that of mice infected with the wild-type or slr1δ/δ mutant complemented with SLR1 (slr1δ/δ+SLR1) strain, without a concomitant decrease in kidney fungal burden. Histopathology, however, revealed differential localization of slr1δ/δ hyphal and yeast morphologies within the kidney. Mice infected with slr1δ/δ cells also had an increased brain fungal burden, which correlated with increased invasion of brain, but not umbilical vein, endothelial cells in vitro. The enhanced brain endothelial cell invasion was likely due to the increased surface exposure of the Als3 adhesin on slr1δ/δ cells. Our results indicate that Slr1 is an SR-like protein that influences C. albicans growth, filamentation, host cell interactions, and virulence. © 2013, American Society for Microbiology.

Date: 2019-11-04

Creator: Jack R. Bateman, Judith A. Kassis

Access: Open access

Homologous chromosomes pair in somatic cells in Drosophila, but how this occurs is poorly understood. In this issue of Developmental Cell, Viets et al. (2019) show that proteins and chromatin structure mediate pairing and argue against a DNA sequence-based mechanism.

Date: 2008-04-03

Creator: Michael M. Franz

Access: Open access

Has the most recent campaign finance reform failed relative to interest groups? More broadly, what's next in the realm of interest group electioneering? This paper explores the role of interest groups in two areas: as contributors to candidates and parties and as candidate and issue advocates. Overall, the numbers reported here show that direct interest group influence with candidates and parties likely declined in the wake of reform. On the other hand, recent uncertainty in the regulatory environment should foster the expansion of interest group advocacy efforts (and has already done so in this year's presidential primary elections). On this score, the attempts of reformers to reduce interest group electioneering have likely failed. Instead of concluding that such a development is bad for American elections, however, this paper argues that such discontent is misplaced. Copyright ©2008 The Berkeley Electronic Press. All rights reserved.

Date: 2019-07-01

Creator: David K. Hecht

Access: Open access

Rachel Carson's Silent Spring is justly remembered as a landmark in the history of modern environmentalism. It is, however, a more complicated text than cultural memory tends to acknowledge. Blending conservative and traditional elements with more progressive and pioneering ones, Silent Spring is marked by a complexity that extends to its reception and legacy. This article argues that-in a seeming paradox-it was the more conservative elements of Silent Spring that allowed it to be considered a revolutionary book. Carson carefully constructed her argument in ways that facilitated its initial acceptance. But those same decisions made it easier for supporters to de-emphasize its more radical implications, even as they granted it revolutionary status.

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.

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.

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.