Browsing by Author "Nelson, David R."

Now showing 1 - 7 of 7
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    Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest
    Sparks, Michael E.; Bansal, Raman; Benoit, Joshua B.; Blackburn, Michael B.; Chao, Hsu; Chen, Mengyao; Cheng, Sammy; Childers, Christopher; Dinh, Huyen; Doddapaneni, Harsha V.; Dugan, Shannon; Elpidina, Elena N.; Farrow, David W.; Friedrich, Markus; Gibbs, Richard A.; Hall, Brantley; Han, Yi; Hardy, Richard W.; Holmes, Christopher J.; Hughes, Daniel S. T.; Ioannidis, Panagiotis; Cheatle Jarvela, Alys M.; Johnston, J. Spencer; Jones, Jeffery W.; Kronmiller, Brent A.; Kung, Faith; Lee, Sandra L.; Martynov, Alexander G.; Masterson, Patrick; Maumus, Florian; Munoz-Torres, Monica; Murali, Shwetha C.; Murphy, Terence D.; Muzny, Donna M.; Nelson, David R.; Oppert, Brenda; Panfilio, Kristen A.; Paula, Débora P.; Pick, Leslie; Poelchau, Monica F.; Qu, Jiaxin; Reding, Katie; Rhoades, Joshua H.; Rhodes, Adelaide; Richards, Stephen; Richter, Rose; Robertson, Hugh M.; Rosendale, Andrew J.; Tu, Zhijian Jake; Velamuri, Arun S.; Waterhouse, Robert M.; Weirauch, Matthew T.; Wells, Jackson T.; Werren, John H.; Worley, Kim C.; Zdobnov, Evgeny M.; Gundersen-Rindal, Dawn E. (2020-03-14)
    Background Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species’ feeding and habitat traits, defining potential targets for pest management strategies. Results Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys’ capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications. Conclusions Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls.
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    Genomic insights into the Ixodes scapularis tick vector of Lyme disease
    Gulia-Nuss, Monika; Nuss, Andrew B.; Meyer, Jason M.; Sonenshine, Daniel E.; Roe, R. Michael; Waterhouse, Robert M.; Sattelle, David B.; de la Fuente, Jose; Ribeiro, Jose M.; Megy, Karine; Thimmapuram, Jyothi; Miller, Jason R.; Walenz, Brian P.; Koren, Sergey; Hostetler, Jessica B.; Thiagarajan, Mathangi; Joardar, Vinita S.; Hannick, Linda I.; Bidwell, Shelby; Hammond, Martin P.; Young, Sarah; Zeng, Qiandong; Abrudan, Jenica L.; Almeida, Francisca C.; Ayllon, Nieves; Bhide, Ketaki; Bissinger, Brooke W.; Bonzon-Kulichenko, Elena; Buckingham, Steven D.; Caffrey, Daniel R.; Caimano, Melissa J.; Croset, Vincent; Driscoll, Timothy; Gilbert, Don; Gillespie, Joseph J.; Giraldo-Calderon, Gloria I.; Grabowski, Jeffrey M.; Jiang, David; Khalil, Sayed M. S.; Kim, Donghun; Kocan, Katherine M.; Koci, Juraj; Kuhn, Richard J.; Kurtti, Timothy J.; Lees, Kristin; Lang, Emma G.; Kennedy, Ryan C.; Kwon, Hyeogsun; Perera, Rushika; Qi, Yumin; Radolf, Justin D.; Sakamoto, Joyce M.; Sanchez-Gracia, Alejandro; Severo, Maiara S.; Silverman, Neal; Simo, Ladislav; Tojo, Marta; Tornador, Cristian; Van Zee, Janice P.; Vazquez, Jesus; Vieira, Filipe G.; Villar, Margarita; Wespiser, Adam R.; Yang, Yunlong; Zhu, Jiwei; Arensburger, Peter; Pietrantonio, Patricia V.; Barker, Stephen C.; Shao, Renfu; Zdobnov, Evgeny M.; Hauser, Frank; Grimmelikhuijzen, Cornelis J. P.; Park, Yoonseong; Rozas, Julio; Benton, Richard; Pedra, Joao H. F.; Nelson, David R.; Unger, Maria F.; Tubio, Jose M. C.; Tu, Zhijian Jake; Robertson, Hugh M.; Shumway, Martin; Sutton, Granger; Wortman, Jennifer R.; Lawson, Daniel; Wikel, Stephen K.; Nene, Vishvanath M.; Fraser, Claire M.; Collins, Frank H.; Birren, Bruce; Nelson, Karen E.; Caler, Elisabet; Hill, Catherine A. (Springer Nature, 2016-02)
    Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing similar to 57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.
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    Interactions and pinning energies in the Bose glass phase of vortices in superconductors
    Täuber, Uwe C.; Nelson, David R. (1995-12-01)
    We study the ground state and low energy excitations of vortices pinned to columnar defects in superconductors, taking into account the long–range interaction between the fluxons. We consider the “underfilled” situation in the Bose glass phase, where each flux line is attached to one of the defects, while some pins remain unoccupied. By exploiting an analogy with disordered semiconductors, we calculate the spatial configurations in the ground state, as well as the distribution of pinning energies, using a zero–temperature Monte Carlo algorithm minimizing the total energy with respect to all possible one–vortex transfers. Intervortex repulsion leads to strong correlations whenever the London penetration depth exceeds the fluxon spacing. A pronounced peak appears in the static structure factor S(q) for low filling fractions f 0.3. Interactions lead to a broad Coulomb gap in the distribution of pinning energies g(ǫ) near the chemical potential μ, separating the occupied and empty pins. The vanishing of g(ǫ) at μ leads to a considerable reduction of variable–range hopping vortex transport by correlated flux line pinning.
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    One thousand plant transcriptomes and the phylogenomics of green plants
    Leebens-Mack, James H.; Barker, Michael S.; Carpenter, Eric J.; Deyholos, Michael K.; Gitzendanner, Matthew A.; Graham, Sean W.; Grosse, Ivo; Li, Zheng; Melkonian, Michael; Mirarab, Siavash; Porsch, Martin; Quint, Marcel; Rensing, Stefan A.; Soltis, Douglas E.; Soltis, Pamela S.; Stevenson, Dennis W.; Ullrich, Kristian K.; Wickett, Norman J.; DeGironimo, Lisa; Edger, Patrick P.; Jordon-Thaden, Ingrid E.; Joya, Steve; Liu, Tao; Melkonian, Barbara; Miles, Nicholas W.; Pokorny, Lisa; Quigley, Charlotte; Thomas, Philip; Villarreal, Juan Carlos; Augustin, Megan M.; Barrett, Matthew D.; Baucom, Regina S.; Beerling, David J.; Benstein, Ruben Maximilian; Biffin, Ed; Brockington, Samuel F.; Burge, Dylan O.; Burris, Jason N.; Burris, Kellie P.; Burtet-Sarramegna, Valerie; Caicedo, Ana L.; Cannon, Steven B.; Cebi, Zehra; Chang, Ying; Chater, Caspar; Cheeseman, John M.; Chen, Tao; Clarke, Neil D.; Clayton, Harmony; Covshoff, Sarah; Crandall-Stotler, Barbara J.; Cross, Hugh; dePamphilis, Claude W.; Der, Joshua P.; Determann, Ron; Dickson, Rowan C.; Di Stilio, Veronica S.; Ellis, Shona; Fast, Eva; Feja, Nicole; Field, Katie J.; Filatov, Dmitry A.; Finnegan, Patrick M.; Floyd, Sandra K.; Fogliani, Bruno; Garcia, Nicolas; Gateble, Gildas; Godden, Grant T.; Goh, Falicia (Qi Yun); Greiner, Stephan; Harkess, Alex; Heaney, James Mike; Helliwell, Katherine E.; Heyduk, Karolina; Hibberd, Julian M.; Hodel, Richard G. J.; Hollingsworth, Peter M.; Johnson, Marc T. J.; Jost, Ricarda; Joyce, Blake; Kapralov, Maxim V.; Kazamia, Elena; Kellogg, Elizabeth A.; Koch, Marcus A.; Von Konrat, Matt; Konyves, Kalman; Kutchan, Toni M.; Lam, Vivienne; Larsson, Anders; Leitch, Andrew R.; Lentz, Roswitha; Li, Fay-Wei; Lowe, Andrew J.; Ludwig, Martha; Manos, Paul S.; Mavrodiev, Evgeny; McCormick, Melissa K.; McKain, Michael; McLellan, Tracy; McNeal, Joel R.; Miller, Richard E.; Nelson, Matthew N.; Peng, Yanhui; Ralph, Paula E.; Real, Daniel; Riggins, Chance W.; Ruhsam, Markus; Sage, Rowan F.; Sakai, Ann K.; Scascitella, Moira; Schilling, Edward E.; Schlosser, Eva-Marie; Sederoff, Heike; Servick, Stein; Sessa, Emily B.; Shaw, A. Jonathan; Shaw, Shane W.; Sigel, Erin M.; Skema, Cynthia; Smith, Alison G.; Smithson, Ann; Stewart, C. Neal, Jr.; Stinchcombe, John R.; Szovenyi, Peter; Tate, Jennifer A.; Tiebel, Helga; Trapnell, Dorset; Villegente, Matthieu; Wang, Chun-Neng; Weller, Stephen G.; Wenzel, Michael; Weststrand, Stina; Westwood, James H.; Whigham, Dennis F.; Wu, Shuangxiu; Wulff, Adrien S.; Yang, Yu; Zhu, Dan; Zhuang, Cuili; Zuidof, Jennifer; Chase, Mark W.; Pires, J. Chris; Rothfels, Carl J.; Yu, Jun; Chen, Cui; Chen, Li; Cheng, Shifeng; Li, Juanjuan; Li, Ran; Li, Xia; Lu, Haorong; Ou, Yanxiang; Sun, Xiao; Tan, Xuemei; Tang, Jingbo; Tian, Zhijian; Wang, Feng; Wang, Jun; Wei, Xiaofeng; Xu, Xun; Yan, Zhixiang; Yang, Fan; Zhong, Xiaoni; Zhou, Feiyu; Zhu, Ying; Zhang, Yong; Ayyampalayam, Saravanaraj; Barkman, Todd J.; Nam-Phuong Nguyen; Matasci, Naim; Nelson, David R.; Sayyari, Erfan; Wafula, Eric K.; Walls, Ramona L.; Warnow, Tandy; An, Hong; Arrigo, Nils; Baniaga, Anthony E.; Galuska, Sally; Jorgensen, Stacy A.; Kidder, Thomas I.; Kong, Hanghui; Lu-Irving, Patricia; Marx, Hannah E.; Qi, Xinshuai; Reardon, Chris R.; Sutherland, Brittany L.; Tiley, George P.; Welles, Shana R.; Yu, Rongpei; Zhan, Shing; Gramzow, Lydia; Theissen, Gunter; Wong, Gane Ka-Shu (2019-10-31)
    Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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    Superfluid bosons and flux liquids: disorder, thermal fluctuations, and finite-size effects
    Täuber, Uwe C.; Nelson, David R. (1997-10)
    The influence of different types of disorder (both uncorrelated and correlated) on the superfluid properties of a weakly interacting or dilute Bose gas, as well as on the corresponding quantities for flux line liquids in high–temperature superconductors at low magnetic fields are reviewed, investigated and compared. We exploit the formal analogy between superfluid bosons and the statistical mechanics of directed lines, and explore the influence of the different ”imaginary time” boundary conditions appropriate for a flux line liquid. For superfluids, we discuss the density and momentum correlations, the condensate fraction, and the normal–fluid density as function of temperature for two– and three–dimensional systems subject to a space– and time–dependent random potential as well as conventional point–, line–, and plane–like defects. In the case of vortex liquids subject to point disorder, twin boundaries, screw dislocations, and various configurations of columnar damage tracks, we calculate the corresponding quantities, namely density and tilt correlations, the “boson” order parameter, and the tilt modulus. The finite–size corrections due to periodic vs. open ”imaginary time” boundary conditions differ in interesting and important ways. Experimental implications for vortex lines are
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    A Transcriptome Survey Spanning Life Stages and Sexes of the Harlequin Bug, Murgantia histrionica
    Sparks, Michael E.; Rhoades, Joshua H.; Nelson, David R.; Kuhar, Daniel; Lancaster, Jason; Lehner, Bryan; Tholl, Dorothea; Weber, Donald C.; Gundersen-Rindal, Dawn E. (MDPI, 2017-05-25)
    The harlequin bug, Murgantia histrionica (Hahn), is an agricultural pest in the continental United States, particularly in southern states. Reliable gene sequence data are especially useful to the development of species-specific, environmentally friendly molecular biopesticides and effective biolures for this insect. Here, mRNAs were sampled from whole insects at the 2nd and 4th nymphal instars, as well as sexed adults, and sequenced using Illumina RNA-Seq technology. A global assembly of these data identified 72,540 putative unique transcripts bearing high levels of similarity to transcripts identified in other taxa, with over 99% of conserved single-copy orthologs among insects being detected. Gene ontology and protein family analyses were conducted to explore the functional potential of the harlequin bug’s gene repertoire, and phylogenetic analyses were conducted on gene families germane to xenobiotic detoxification, including glutathione S-transferases, carboxylesterases and cytochrome P450s. Genic content in harlequin bug was compared with that of the closely related invasive pest, the brown marmorated stink bug, Halyomorpha halys (Stål). Quantitative analyses of harlequin bug gene expression levels, experimentally validated using quantitative real-time PCR, identified genes differentially expressed between life stages and/or sexes.
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    Unique features of a global human ectoparasite identified through sequencing of the bed bug genome
    Benoit, Joshua B.; Adelman, Zach N.; Reinhardt, Klaus; Dolan, Amanda M.; Poelchau, Monica; Jennings, Emily C.; Szuter, Elise M.; Hagan, Richard W.; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M.; Nelson, David R.; Rosendale, Andrew J.; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M.; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R.; Ioannidis, Panagiotis; Waterhouse, Robert M.; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J. Spencer; Gondhalekar, Ameya D.; Scharf, Michael E.; Peterson, Brittany F.; Raje, Kapil R.; Hottel, Benjamin A.; Armisen, David; Crumiere, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Severine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S. T.; Duncan, Elizabeth J.; Murali, Shwetha C.; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L.; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C.; Muzny, Donna M.; Wheeler, David; Panfilio, Kristen A.; Jentzsch, Iris M. Vargas; Vargo, Edward L.; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T.; Anderson, Michelle A. E.; Jones, Jeffery W.; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D.; Attardo, Geoffrey M.; Robertson, Hugh M.; Zdobnov, Evgeny M.; Ribeiro, Jose M. C.; Gibbs, Richard A.; Werren, John H.; Palli, Subba R.; Schal, Coby; Richards, Stephen (Nature, 2016-02-02)
    The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite