Faculty Scholarship
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AMGSEFLamide, a member of a broadly conserved peptide family, modulates multiple neural networks in Homarus americanus
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.
Characterization of the mature form of a β-defensin-like peptide, Hoa-D1, in the lobster Homarus americanus
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.
Characterization of plexinA and two distinct semaphorin1a transcripts in the developing and adult cricket Gryllus bimaculatus
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.
Multiple transcriptome mining coupled with tissue specific molecular cloning and mass spectrometry provide insights into agatoxin-like peptide conservation in decapod crustaceans
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.
SIFamide peptides modulate cardiac activity differently in two species of Cancer crab
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.
Mass spectrometric identification of pEGFYSQRYamide: A crustacean peptide hormone possessing a vertebrate neuropeptide Y (NPY)-like carboxy-terminus
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.
APPSSAT: Approximate probabilistic planning using stochastic satisfiability
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.
The Rubble of Culture: Debris of an Extinct Thought
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.
Maximally rotating supermassive stars at the onset of collapse: Effects of gas pressure
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.
Study of D0 decays into K̄0 and K̄*0
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.