110 results on '"J. Nolen"'
Search Results
2. Symmetry-based design of fragment separator optics
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B. Erdelyi, J. Maloney, and J. Nolen
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Nuclear and particle physics. Atomic energy. Radioactivity ,QC770-798 - Abstract
Next-generation high-intensity large acceptance fragment separators require a careful design due to the large high order aberrations induced by the large aperture superconducting magnets needed to collect rare isotopes obtained from a high energy primary heavy-ion beam hitting a target. In this paper we propose a fragment separator layout based on various symmetries that satisfies the baseline requirements. Analytical calculations based on symmetry theories simplify the design to numerical optimization of a basic cell with only a few magnetic elements. The insight provided by these calculations resulted in the specification of a simple layout with large acceptance, transmission, and resolution. The design method may be easily adapted to project-specific needs. The important effects of energy degraders necessary for full fragment separator design will be addressed in a future publication.
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- 2007
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3. The intrinsically disordered cytoplasmic tail of a dendrite branching receptor uses two distinct mechanisms to regulate the actin cytoskeleton
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Daniel A Kramer, Heidy Y Narvaez-Ortiz, Urval Patel, Rebecca Shi, Kang Shen, Brad J Nolen, Julien Roche, and Baoyu Chen
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dendrite branching ,actin cytoskeleton ,capping protein ,intrinsically disordered protein ,neuronal receptor ,Arp2/3 complex ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Dendrite morphogenesis is essential for neural circuit formation, yet the molecular mechanisms underlying complex dendrite branching remain elusive. Previous studies on the highly branched Caenorhabditis elegans PVD sensory neuron identified a membrane co-receptor complex that links extracellular signals to intracellular actin remodeling machinery, promoting high-order dendrite branching. In this complex, the claudin-like transmembrane protein HPO-30 recruits the WAVE regulatory complex (WRC) to dendrite branching sites, stimulating the Arp2/3 complex to polymerize actin. We report here our biochemical and structural analysis of this interaction, revealing that the intracellular domain (ICD) of HPO-30 is intrinsically disordered and employs two distinct mechanisms to regulate the actin cytoskeleton. First, HPO-30 ICD binding to the WRC requires dimerization and involves the entire ICD sequence, rather than a short linear peptide motif. This interaction enhances WRC activation by the GTPase Rac1. Second, HPO-30 ICD directly binds to the sides and barbed end of actin filaments. Binding to the barbed end requires ICD dimerization and inhibits both actin polymerization and depolymerization, resembling the actin capping protein CapZ. These dual functions provide an intriguing model of how membrane proteins can integrate distinct mechanisms to fine-tune local actin dynamics.
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- 2023
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4. Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline
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Michael R. Hoopmann, David D. Shteynberg, Alex Zelter, Michael Riffle, Andrew S. Lyon, David A. Agard, Qing Luan, Brad J. Nolen, Michael J. MacCoss, Trisha N. Davis, and Robert L. Moritz
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General Chemistry ,Biochemistry - Published
- 2023
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5. The genomic landscape of adaptation to a new host plant
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Kalle J Nilsson, Rachel A Steward, Jesús Ortega Giménez, Zachary J Nolen, Chao Yan, Yajuan Huang, Julio Ayala López, and Anna Runemark
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Adaptation to novel ecological niches is known to be rapid. However, how ecological divergence translates into reproductive isolation remains a consequential question in speciation research. It is still unclear how coupling of ecological divergence loci and reproductive isolation loci occurs at the genomic level, ultimately enabling the formation of persistent species. Here, we investigate the genomic underpinning colonization of a new niche and formation of two host races inTephritis conurapeacock flies that persist in sympatry. To uncover the genomic differences underlying host plant adaptation, we take advantage of two independent sympatric zones, where host plant specialists using the thistle speciesCirsium heterophyllumandC. oleraceumco-occur, and address what regions of the genome that diverge between the host races in a parallel fashion. Using Population Branch Statistics, dxy and BayPass we identify 2996 and 3107 outlier regions associated with host use among western and eastern Baltic populations, respectively, with 82% overlap. The majority of outliers are located within putative inversions, adding to the growing body of evidence that structural changes to the genome are important for adaptations to persist in face of gene flow. Potentially, the high contents of repetitive elements could have given rise to the inversions, but this remains to be tested. The outlier regions were enriched for genes involved in e.g. metabolism and morphogenesis, potentially due to the selection for processing different metabolites, and changes in size and ovipositor length respectively. In conclusion, this study suggests that structural changes in the genome, and divergence in independent ecological functions may facilitate the formation of persistent host races in face of gene flow.
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- 2023
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6. Identification of an ATP-controlled allosteric switch that controls actin filament nucleation by Arp2/3 complex
- Author
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Max Rodnick-Smith, Su-Ling Liu, Connor J. Balzer, Qing Luan, and Brad J. Nolen
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Science - Abstract
Arp2/3 complex nucleates branched actin filaments, and is inactive in the absense of activators. Here the authors present a model of Arp2/3 autoinhibition, whereby the Arp3 C-terminal tail acts as a structural switch that blocks movement of Arp2 and Arp3 into an activated filament-like conformation.
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- 2016
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7. Genomic methods reveal independent demographic histories despite strong morphological conservatism in fish species
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Ricardo José Garcia Pereira, Nidia Noemi Fabré, Tamí Mott, Zachary J. Nolen, and Jessika M. M. Neves
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0106 biological sciences ,0301 basic medicine ,Sympatry ,Species complex ,Demographic history ,Speciation ,Population ,Biology ,DNA, Mitochondrial ,010603 evolutionary biology ,01 natural sciences ,Article ,03 medical and health sciences ,Species Specificity ,Effective population size ,Genetics ,Animals ,Humans ,Genetic variation ,education ,Ecosystem ,Phylogeny ,Genetics (clinical) ,Demography ,education.field_of_study ,Genetic diversity ,Genomics ,Phylogenetics ,030104 developmental biology ,Evolutionary biology ,Sympatric speciation ,Genetic isolate - Abstract
Human overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, especially in regards to highly vulnerable marine ecosystems. In this context, cryptic species are particularly challenging to conserve because they are hard to distinguish based on morphology alone, and thus it is often unclear how many species coexist in sympatry, what are their phylogenetic relationships and their demographic history. We answer these questions using morphologically similar species of the genus Mugil that are sympatric in the largest coastal Marine Protected Area in the Tropical Southwestern Atlantic marine province. Using a sub-representation of the genome, we show that individuals are assigned to five highly differentiated genetic clusters that are coincident with five mitochondrial lineages, but discordant with morphological information, supporting the existence of five species with conserved morphology in this region. A lack of admixed individuals is consistent with strong genetic isolation between sympatric species, but the most likely species tree suggests that in one case speciation has occurred in the presence of interspecific gene flow. Patterns of genetic diversity within species suggest that effective population sizes differ up to two-fold, probably reflecting differences in the magnitude of population expansions since species formation. Together, our results show that strong morphologic conservatism in marine environments can lead to species that are difficult to distinguish morphologically but that are characterized by an independent evolutionary history, and thus that deserve species-specific management strategies.
- Published
- 2021
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8. The intrinsically disordered cytoplasmic tail of a dendrite branching receptor uses two distinct mechanisms to regulate the actin cytoskeleton
- Author
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Daniel A. Kramer, Heidy Y. Narvaez-Ortiz, Urval Patel, Rebecca Shi, Kang Shen, Brad J. Nolen, Julien Roche, and Baoyu Chen
- Abstract
Dendrite morphogenesis is essential for neural circuit formation, yet the molecular mechanisms underlying complex dendrite branching remain elusive. Previous studies on the highly branchedC. elegansPVD sensory neuron identified a membrane co-receptor complex that links extracellular signals to intracellular actin remodeling machinery, promoting high-order dendrite branching. In this complex, the claudin-like transmembrane protein HPO-30 recruits the WAVE regulatory complex (WRC) to dendrite branching sites, stimulating the Arp2/3 complex to polymerize actin. We report here our biochemical and structural analysis of this interaction, revealing that the intracellular domain (ICD) of HPO-30 is intrinsically disordered and employs two distinct mechanisms to regulate the actin cytoskeleton. First, HPO-30 ICD binding to the WRC requires dimerization and involves the entire ICD sequence, rather than a short linear peptide motif. This interaction enhances WRC activation by the GTPase Rac1. Second, HPO-30 ICD directly binds to the sides and barbed end of actin filaments. Binding to the barbed end requires ICD dimerization and inhibits both actin polymerization and depolymerization, resembling the actin capping protein CapZ. These dual functions provide an intriguing model of how membrane proteins can integrate distinct mechanisms to fine-tune local actin dynamics.
- Published
- 2022
- Full Text
- View/download PDF
9. Analysis of functional surfaces on the actin nucleation promoting factor Dip1 required for Arp2/3 complex activation and endocytic actin network assembly
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Su-Ling Liu, Heidy Y. Narvaez-Ortiz, Matt Miner, Jack Kiemel, Nicholas Oberhelman, April Watt, Andrew R. Wagner, Qing Luan, Luke A. Helgeson, and Brad J. Nolen
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Actin Cytoskeleton ,Schizosaccharomyces ,Cell Biology ,Pseudopodia ,Schizosaccharomyces pombe Proteins ,Molecular Biology ,Biochemistry ,Actin-Related Protein 2-3 Complex ,Actins - Abstract
Arp2/3 complex nucleates branched actin filaments that drive processes like endocytosis and lamellipodial protrusion. WISH/DIP/SPIN90 (WDS) proteins form a class of Arp2/3 complex activators or nucleation promoting factors (NPFs) that, unlike WASP family NPFs, activate Arp2/3 complex without requiring preformed actin filaments. Therefore, activation of Arp2/3 complex by WDS proteins is thought to produce the initial actin filaments that seed branching nucleation by WASP-bound Arp2/3 complexes. However, whether activation of Arp2/3 complex by WDS proteins is important for the initiation of branched actin assembly in cells has not been directly tested. Here, we used structure-based point mutations of the Schizosaccharomyces pombe WDS protein Dip1 to test the importance of its Arp2/3-activating activity in cells. Six of thirteen Dip1 mutants caused severe defects in Arp2/3 complex activation in vitro, and we found a strong correlation between the ability of mutants to activate Arp2/3 complex and to rescue endocytic actin assembly defects caused by deleting Dip1. These data support a model in which Dip1 activates Arp2/3 complex to produce actin filaments that initiate branched actin assembly at endocytic sites. Dip1 mutants that synergized with WASP in activating Arp2/3 complex in vitro showed milder defects in cells compared to those that did not, suggesting that in cells the two NPFs may coactivate Arp2/3 complex to initiate actin assembly. Finally, the mutational data reveal important complementary electrostatic contacts at the Dip1-Arp2/3 complex interface and corroborate the previously proposed wedge model, which describes how Dip1 binding triggers structural changes that activate Arp2/3 complex.
- Published
- 2022
10. Preinvasion Assessment of Exotic Bark Beetle-Vectored Fungi to Detect Tree-Killing Pathogens
- Author
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Wisut Sittichaya, Jianghua Sun, Andrew Johnson, Zvi Mendel, Zachary J. Nolen, Michelle A. Jusino, Miroslav Kolařík, Min Lu, Pham Hong Thai, Adam Black, Damian C. Adams, Hou-Feng Li, Ji-Hyun Park, James Skelton, Lei Gao, Craig C. Bateman, Allan Gonzalez, Bo Wang, Stanley Freeman, Miloš Knížek, Masato Torii, Shin-ichiro Ito, You Li, Yin-Tse Huang, Chi-Yu Chen, Zhen Zhang, and Jiri Hulcr
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0106 biological sciences ,Bark beetle ,Ecology ,Fungi ,Plant Science ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Trees ,Coleoptera ,010602 entomology ,Tree (data structure) ,Forest pathology ,Forest ecology ,Plant Bark ,Animals ,Agronomy and Crop Science ,Ecosystem ,Plant Diseases - Abstract
Exotic diseases and pests of trees have caused continental-scale disturbances in forest ecosystems and industries, and their invasions are considered largely unpredictable. We tested the concept of preinvasion assessment of not yet invasive organisms, which enables empirical risk assessment of potential invasion and impact. Our example assesses fungi associated with Old World bark and ambrosia beetles and their potential to impact North American trees. We selected 55 Asian and European scolytine beetle species using host use, economic, and regulatory criteria. We isolated 111 of their most consistent fungal associates and tested their effect on four important southeastern American pine and oak species. Our test dataset found no highly virulent pathogens that should be classified as an imminent threat. Twenty-two fungal species were minor pathogens, which may require context-dependent response for their vectors at North American borders, while most of the tested fungi displayed no significant impact. Our results are significant in three ways; they ease the concerns over multiple overseas fungus vectors suspected of heightened potential risk, they provide a basis for the focus on the prevention of introduction and establishment of species that may be of consequence, and they demonstrate that preinvasion assessment, if scaled up, can support practical risk assessment of exotic pathogens.
- Published
- 2021
11. A COMPACT MULTI-ION LINAC WITH FLASH CAPABILITY
- Author
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B. Mustapha, A. Nassiri, J. Nolen, J. Noonan, S. Kutsaev, S. Boucher, R. Agustsson, and A. Smirnov
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Biophysics ,General Physics and Astronomy ,Radiology, Nuclear Medicine and imaging ,General Medicine - Published
- 2022
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12. Gender and Psychological Pressure in Competitive Environments
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Alison L. Booth and Patrick J. Nolen
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- 2021
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13. Gender and psychological pressure in competitive environments
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Patrick J. Nolen and Alison L. Booth
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Competition (economics) ,If and only if ,Psychological pressure ,Production (economics) ,Tournament ,Set (psychology) ,Psychology ,Piece work ,Social psychology ,Winner-take-all - Abstract
Gender differences in paid performance under competition have been found in many laboratory-based experiments, and it has been suggested that these may arise because men and women respond differently to psychological pressure in competitive environments. To explore this further, we conducted a laboratory experiment comprising 444 subjects, and measured gender differences in performance in four distinct competitive situations. These were as follows: (i) the standard tournament game where the subject competes with three other individuals and the winner takes all; (ii) an anonymized competition in which an individual competes against an imposed production target and is paid only if s/he exceeds it; (iii) a ‘personified’ competition where an individual competes against a target based on the previous performance of one anonymised person of unknown gender; and (iv) a ‘gendered’ competition where an individual competes against a target based on the previous performance of one anonymised person whose gender is known. We found that only men respond to pressure differently in each situation; women responded the same to pressure no matter the situation. Moreover, the personified target caused men to increase performance more than under an anonymized target and, when the gender of the person associated with the target was revealed, men worked even harder to outperform a woman but strived only to equal the target set by a male.
- Published
- 2021
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14. nuCARIBU : An upgrade for the CARIBU facility at the Argonne Tandem Linac Accelerator System
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J. McLain, C. A. Dickerson, M. Gott, J. Greene, J. Nolen, G. Savard, J. Song, and R. C. Vondrasek
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History ,Computer Science Applications ,Education - Abstract
The Californium Rare Isotope Breeder Upgrade (CARIBU) facility is changing the mechanism for creating neutron-rich fission products. Spontaneous fission from a 252Cf source has provided beams to support the low energy and accelerated-beams ATLAS programs. 252Cf has a 2.65-year half-life, requiring the source to be replaced every three years to maintain high beam intensities. Fabricating an appropriately thin 252Cf source to efficiently release the fission products has been challenging. The solution to these problems is nuCARIBU, a new system that provides neutron-induced fission on actinide foils. The Best Cyclotron B6P System (6-MeV proton beam at 0.5mA) is chosen, utilizing a multi-cusp negative ion source extracting into a cyclotron, which uses carbon foils to strip the H- ions to protons. These protons are delivered to a 7Li target to produce neutrons. The fast neutrons are moderated to thermal energies to induce fission in an actinide foil, providing neutron-rich fission products. These subsystems are described in detail along with comparisons between the current CARIBU facility and the presented nuCARIBU facility. This work was supported by the U.S. Department of Energy, Office of Nuclear Physics, under Contract No. DE-AC02-06CH11357
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- 2022
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15. Synergy between Wsp1 and Dip1 may initiate assembly of endocytic actin networks
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Connor J. Balzer, Vladimir Sirotkin, Brad J. Nolen, Michael L. James, Luke A Helgeson, and Heidy Y Narvaez-Ortiz
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QH301-705.5 ,Science ,Endocytic cycle ,Chemical biology ,Arp2/3 complex ,macromolecular substances ,Endocytosis ,Actin-Related Protein 2-3 Complex ,General Biochemistry, Genetics and Molecular Biology ,Protein filament ,Biochemistry and Chemical Biology ,Gene Expression Regulation, Fungal ,Schizosaccharomyces ,endocytosis ,Biology (General) ,Dip1 ,Actin ,Total internal reflection fluorescence microscope ,General Immunology and Microbiology ,biology ,Chemistry ,General Neuroscience ,Cell Biology ,General Medicine ,biology.organism_classification ,Actins ,Cell biology ,Schizosaccharomyces pombe ,biology.protein ,Medicine ,Schizosaccharomyces pombe Proteins ,Wsp1 ,actin ,Research Article ,S. pombe - Abstract
The actin filament nucleator Arp2/3 complex is activated at cortical sites inSchizosaccharomyces pombeto assemble branched actin networks that drive endocytosis. Arp2/3 complex activators Wsp1 and Dip1 are required for proper actin assembly at endocytic sites, but how they coordinately control Arp2/3-mediated actin assembly is unknown. Alone, Dip1 activates Arp2/3 complex without preexisting actin filaments to nucleate ‘seed’ filaments that activate Wsp1-bound Arp2/3 complex, thereby initiating branched actin network assembly. In contrast, because Wsp1 requires preexisting filaments to activate, it has been assumed to function exclusively in propagating actin networks by stimulating branching from preexisting filaments. Here we show that Wsp1 is important not only for propagation but also for initiation of endocytic actin networks. Using single molecule total internal reflection fluorescence microscopy we show that Wsp1 synergizes with Dip1 to co-activate Arp2/3 complex. Synergistic co-activation does not require preexisting actin filaments, explaining how Wsp1 contributes to actin network initiation in cells.
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- 2020
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16. Author response: Synergy between Wsp1 and Dip1 may initiate assembly of endocytic actin networks
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Vladimir Sirotkin, Luke A Helgeson, Heidy Y Narvaez-Ortiz, Brad J. Nolen, Michael L. James, and Connor J. Balzer
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Chemistry ,Endocytic cycle ,Actin ,Cell biology - Published
- 2020
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17. A Course In Business Fundamentals For Engineers
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Ofodike Ezekoye, John Doggett, J. Nolen, John Butler, and Steven Nichols
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- 2020
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18. Synergy between Wsp1 and Dip1 may initiate assembly of endocytic actin networks
- Author
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Brad J. Nolen, Vladimir Sirotkin, Connor J. Balzer, Luke A Helgeson, and Michael L. James
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Protein filament ,Total internal reflection fluorescence microscope ,Chemistry ,Endocytic cycle ,Biophysics ,macromolecular substances ,Endocytosis ,Actin - Abstract
The actin filament nucleator Arp2/3 complex is activated at cortical sites inS. pombeto assemble branched actin networks that drive endocytosis. Arp2/3 complex activators Wsp1 and Dip1 are required for proper actin assembly at endocytic sites, but how they coordinately control Arp2/3-mediated actin assembly is unknown. Alone, Dip1 activates Arp2/3 complex without preexisting actin filaments to nucleate “seed” filaments that activate Wsp1-bound Arp2/3 complex, thereby initiating branched actin network assembly. In contrast, because Wsp1 requires pre-existing filaments to activate, it has been assumed to function exclusively in propagating actin networks by stimulating branching from pre-existing filaments. Here we show that Wsp1 is important not only for propagation, but also for initiation of endocytic actin networks. Using single molecule TIRF microscopy we show that Wsp1 synergizes with Dip1 to co-activate Arp2/3 complex. Synergistic coactivation does not require pre-existing actin filaments, explaining how Wsp1 contributes to actin network initiation in cells.
- Published
- 2020
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19. Cryo-EM reveals the transition of Arp2/3 complex from inactive to nucleation-competent state
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Brad J. Nolen, Mohammed Shaaban, and Saikat Chowdhury
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Models, Molecular ,Cryo-electron microscopy ,Protein Conformation ,Dimer ,Nucleation ,Arp2/3 complex ,macromolecular substances ,Filamentous actin ,Actin-Related Protein 2-3 Complex ,Article ,Protein filament ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Structural Biology ,Schizosaccharomyces ,Molecular Biology ,Actin ,030304 developmental biology ,0303 health sciences ,biology ,Cryoelectron Microscopy ,biology.organism_classification ,Actin Cytoskeleton ,chemistry ,Schizosaccharomyces pombe ,biology.protein ,Biophysics ,Schizosaccharomyces pombe Proteins ,Protein Multimerization ,030217 neurology & neurosurgery ,Protein Binding - Abstract
Arp2/3 complex, a crucial actin filament nucleator, undergoes structural rearrangements during activation by nucleation-promoting factors (NPFs). However, the conformational pathway leading to the nucleation-competent state is unclear due to lack of high-resolution structures of the activated state. Here we report a ~3.9 A resolution cryo-EM structure of activated Schizosaccharomyces pombe Arp2/3 complex bound to the S. pombe NPF Dip1 and attached to the end of the nucleated actin filament. The structure reveals global and local conformational changes that allow the two actin-related proteins in Arp2/3 complex to mimic a filamentous actin dimer and template nucleation. Activation occurs through a clamp-twisting mechanism, in which Dip1 forces two core subunits in Arp2/3 complex to pivot around one another, shifting half of the complex into a new activated position. By showing how Dip1 stimulates activation, the structure reveals how NPFs can activate Arp2/3 complex in diverse cellular processes.
- Published
- 2020
20. Historical isolation facilitates species radiation by sexual selection: Insights from Chorthippus grasshoppers
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Shanlin Liu, M. Thomas P. Gilbert, Ricardo José Garcia Pereira, Daniel Buchvaldt Amby, Burcin Yildirim, Iker Irisarri, Clara Groot Crego, Zachary J. Nolen, Frieder Mayer, European Commission, Swedish National Infrastructure for Computing, and Ministerio de Economía y Competitividad (España)
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0301 basic medicine ,0106 biological sciences ,Gene Flow ,Male ,Reproductive Isolation ,Genetic Speciation ,Speciation ,Introgression ,Grasshoppers ,Biology ,010603 evolutionary biology ,01 natural sciences ,Coalescent theory ,Evolutionsbiologi ,03 medical and health sciences ,Genetics ,Animals ,Selection, Genetic ,Hybridization ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,Evolutionary Biology ,Natural selection ,Assortative mating ,Reproductive isolation ,biology.organism_classification ,Gene flow ,Chorthippus ,Sympatry ,030104 developmental biology ,Sexual selection ,Sympatric speciation ,Evolutionary biology ,Diversification ,Female - Abstract
Theoretical and empirical studies have shown that species radiations are facilitated when a trait under divergent natural selection is also involved in sexual selection. It is yet unclear how quick and effective radiations are where assortative mating is unrelated to the ecological environment and primarily results from sexual selection. We address this question using sympatric grasshopper species of the genus Chorthippus, which have evolved strong behavioural isolation while lacking noticeable ecomorphological divergence. Mitochondrial genomes suggest that the radiation is relatively recent, dating to the mid-Pleistocene, which leads to extensive incomplete lineage sorting throughout the mitochondrial and nuclear genomes. Nuclear data shows that hybrids are absent in sympatric localities but that all species have experienced gene flow, confirming that reproductive isolation is strong but remains incomplete. Demographic modelling is most consistent with a long period of geographic isolation, followed by secondary contact and extensive introgression. Such initial periods of geographic isolation might facilitate the association between male signaling and female preference, permitting the coexistence of sympatric species that are genetically, morphologically, and ecologically similar, but otherwise behave mostly as good biological species., RJP was funded by the European Union’s Horizon 2020 research and innovaion programme, under the Marie Sklodowska-Curie grant agreement No. 658706. II was supported by a Juan de la Cierva-Incorporación postdoctoral fellowship (IJCI-2016- 29566) from the Spanish Ministry for Science and Competitiveness (MINECO). Computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC) at Uppsala Multidisciplinary Centre for Advanced Computational Science (UPPMAX) under Project SNIC 2019/8-67.
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- 2020
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21. IT IS BETTER TO BE METEORITE THAN METEOR-WRONG:ANALYSIS AND CLASSIFICATION OF POTENTIAL IRON METEORITE SPECIMEN
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Daniel J. Nolen and Kevin Glenn Thaisen
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Meteor (satellite) ,Meteorite ,Iron meteorite ,Geology ,Astrobiology - Published
- 2020
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22. Is publicly-reported firm-level trade data reliable? Evidence from the UK
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Holger Breinlich, Patrick J. Nolen, and Greg C. Wright
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Asia ,Internationality ,Economics ,Political Science ,Science ,Social Sciences ,India ,Accounting ,Truth Disclosure ,Geographical locations ,Governments ,Germany ,Salaries ,Humans ,Industry ,Revenue ,European Union ,National Governments ,Multidisciplinary ,Majesty ,business.industry ,Commerce ,International Trade ,United Kingdom ,Europe ,Labor Economics ,Medicine ,Self Report ,Business ,People and places ,Ireland ,Finance ,Research Article - Abstract
In this paper we compare firms’ self-reported overseas sales, as reported in a commonly used UK financial reporting dataset, with their actual exports, as reported by Her Majesty’s Revenue and Customs (HMRC). Finding that these flows are in several dimensions quite different, we then explore the implications of these differences more formally. Since several studies within the international trade literature report findings based on the self-reported export values in financial datasets, we discuss these findings in light of the departure of financial dataset-based exports from “true” (HMRC) export values.
- Published
- 2020
23. Do single-sex classes affect academic achievement? An experiment in a coeducational university
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Patrick J. Nolen, Lina Cardona-Sosa, and Alison L. Booth
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Economics and Econometrics ,Single sex ,Higher education ,business.industry ,05 social sciences ,Academic achievement ,Quarter (United States coin) ,Affect (psychology) ,Educational attainment ,Drop out ,0502 economics and business ,Economics ,050207 economics ,business ,Finance ,050205 econometrics ,Demography - Abstract
We examine the effect of single-sex classes on the educational attainment of students within a coeducational university. Before students arrived on campus, we randomly assigned them to all-female, all-male, and coed classes, and thereby avoid the selection issues present in earlier studies on single-sex education of students in primary and secondary school. We find that 1 h a week of single-sex classes benefits women: females score a quarter of standard deviation better overall and are 7.7% more likely to pass their first year course. Furthermore, women assigned to all-females classes in their first year are roughly 57% less likely to drop out of university and are 61% more likely to get a top ranked degree under the UK system. There is evidence that single-sex classes cause women to adopt behaviors associated with better academic outcomes, such as attending more classes and doing optional assignments. However, these behavioral changes cannot explain much of the all-female effect.
- Published
- 2018
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24. Wood decay fungus Flavodon ambrosius (Basidiomycota: Polyporales) is widely farmed by two genera of ambrosia beetles
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Michelle A. Jusino, David Rabern Simmons, Craig C. Bateman, Zachary J. Nolen, James Skelton, Jiri Hulcr, and You Li
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0106 biological sciences ,Asia ,Fungus ,Ambrosia beetle ,DNA, Ribosomal ,010603 evolutionary biology ,01 natural sciences ,Symbiosis ,Phylogenetics ,DNA, Ribosomal Spacer ,RNA, Ribosomal, 28S ,Botany ,Genetics ,Animals ,Cluster Analysis ,Ambrosia ,Polyporales ,DNA, Fungal ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,biology ,Xyleborini ,Genes, rRNA ,RNA, Fungal ,Feeding Behavior ,Sequence Analysis, DNA ,biology.organism_classification ,RNA, Ribosomal, 5.8S ,Wood-decay fungus ,010602 entomology ,Infectious Diseases ,North America ,Weevils - Abstract
The ambrosia fungus Flavodon ambrosius is the primary nutritional mutualist of ambrosia beetles Ambrosiodmus and Ambrosiophilus in North America. F. ambrosius is the only known ambrosial basidiomycete, unique in its efficient lignocellulose degradation. F. ambrosius is associated with both native American beetle species and species introduced from Asia. It remains unknown whether F. ambrosius is strictly a North American fungus, or whether it is also associated with these ambrosia beetle genera on other continents. We isolated fungi from the mycangia and galleries of ambrosia beetles Ambrosiodmus rubricollis, Ambrosiodmus minor, Ambrosiophilus atratus, and Ambrosiophilus subnepotulus in China, South Korea, and Vietnam. Phylogenetic analyses suggest that all Asian and North American isolates represent a single haplotype. These results confirm Flavodon ambrosius as the exclusive mutualistic fungus of multiple Ambrosiodmus and Ambrosiophilus beetle species around the world, making it the most widespread known ambrosia fungus species, both geographically and in terms of the number of beetle species. The Flavodon-beetle symbiosis appears to employ an unusually strict mechanism for maintaining fidelity, compared to the symbioses of the related Xyleborini beetles, which mostly vector more dynamic fungal communities.
- Published
- 2017
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25. Seasonal resource value and male size influence male aggressive interactions in the leaf footed cactus bug, Narnia femorata
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Zachary J. Nolen, Pablo E. Allen, and Christine W. Miller
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Cactaceae ,Male ,0106 biological sciences ,0301 basic medicine ,Coreidae ,010603 evolutionary biology ,01 natural sciences ,Heteroptera ,03 medical and health sciences ,Behavioral Neuroscience ,medicine ,Animals ,Body Size ,biology ,Ecology ,Phenology ,Aggression ,General Medicine ,biology.organism_classification ,Hemiptera ,030104 developmental biology ,Fruit ,Sexual selection ,Cactus ,Animal Science and Zoology ,Seasons ,Resource holding potential ,medicine.symptom - Abstract
In animal contests, resource value (the quality of a given resource) and resource holding potential (a male's absolute fighting ability) are two important factors determining the level of engagement and outcome of contests. Few studies have tested these factors simultaneously. Here, we investigated whether natural, seasonal differences in cactus phenology (fruit quality) influence interactions between males in the leaf-footed cactus bug, Narnia femorata (Hemiptera: Coreidae). We also considered whether males were more likely to interact when they were similar in size, as predicted by theory. Finally, we examined if male size relative to the size of an opponent predicted competitive success. We found that males have more interactions on cactus with high value ripe fruit, as we predicted. Further, we found that males that were closer in size were more likely to interact, and larger males were more likely to become dominant.
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- 2017
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26. A Bayesian Approach for Estimating Branch-Specific Speciation and Extinction Rates
- Author
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Zachary J. Nolen, Sebastian Hoehna, William A. Freyman, Brian R. Moore, John P. Huelsenbeck, and Michael R. May
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0106 biological sciences ,0303 health sciences ,Extinction ,Phylogenetic tree ,Bayesian probability ,Diversification (marketing strategy) ,010603 evolutionary biology ,01 natural sciences ,Numerical integration ,03 medical and health sciences ,Prior probability ,Statistics ,Genetic algorithm ,Species richness ,030304 developmental biology ,Mathematics - Abstract
Species richness varies considerably among the tree of life which can only be explained by heterogeneous rates of diversification (speciation and extinction). Previous approaches use phylogenetic trees to estimate branch-specific diversification rates. However, all previous approaches disregard diversification-rate shifts on extinct lineages although 99% of species that ever existed are now extinct. Here we describe a lineage-specific birth-death-shift process where lineages, both extant and extinct, may have heterogeneous rates of diversification. To facilitate probability computation we discretize the base distribution on speciation and extinction rates intokrate categories. The fixed number of rate categories allows us to extend the theory of state-dependent speciation and extinction models (e.g.,BiSSE and MuSSE) to compute the probability of an observed phylogeny given the set of speciation and extinction rates. To estimate branch-specific diversification rates, we develop two independent and theoretically equivalent approaches: numerical integration with stochastic character mapping and data-augmentation with reversible-jump Markov chain Monte Carlo sampling. We validate the implementation of the two approaches in RevBayes using simulated data and an empirical example study of primates. In the empirical example, we show that estimates of the number of diversification-rate shifts are, unsurprisingly, very sensitive to the choice of prior distribution. Instead, branch-specific diversification rate estimates are less sensitive to the assumed prior distribution on the number of diversification-rate shifts and consistently infer an increased rate of diversification for Old World Monkeys. Additionally, we observe that as few as 10 diversification-rate categories are sufficient to approximate a continuous base distribution on diversification rates. In conclusion, our implementation of the lineage-specific birth-death-shift model in RevBayes provides biologists with a method to estimate branch-specific diversification rates under a mathematically consistent model.
- Published
- 2019
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27. Prospects for an advanced heavy ion therapy center in the Chicago area
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B. Mustapha, J. Robb, Bulent Aydogan, M. Pankuch, J. Nolen, J. Noonan, James S. Welsh, Reinhard W. Schulte, and A. Nassiri
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Accelerator physics ,Engineering ,Particle therapy ,Ion beam ,business.industry ,medicine.medical_treatment ,Linear particle accelerator ,Radiation therapy ,Systems engineering ,medicine ,Heavy ion therapy ,Center (algebra and category theory) ,business ,Research center - Abstract
Argonne National Laboratory (ANL) and the Department of Radiation and Cellular Oncology at the University of Chicago (UChicago) are investigating the feasibility of developing an innovative heavy ion therapy center by combining an advanced compact heavy ion linac (ACCIL) designed at Argonne with real-time image-guided therapy. The proposed technology will not only be the first linac-based heavy-ion therapy technology in the world, with the advantage of much desired fast energy and ion switching capability, but also the first real-time image-guided heavy ion therapy modality. ANL has a prime location to house such a development within existing infrastructure and radiation enclosure at the former Intense Pulsed Neutron Source (IPNS) site. The cost of developing the technology and building a linac-based ion therapy facility on the existing ANL site will be significantly lower than the “green field” carbon ion therapy centers proposed elsewhere. Such a facility would prove a unique platform to stage the development of pre-clinical studies to prepare for Federal Drug Administration (FDA) clearance for carbon and other ion beam therapies in the US, and pave the way to establishing a clinical therapy facility in the Chicago area. In addition to discovery science in high-gradient accelerator physics and the development of superconducting heavy-ion gantry for therapy delivery coupled with real-time guidance, the proposed facility will enable a breadth of research and applications, and as such, will serve as the advanced particle therapy research center in the US. Potential research topics include cellular radiobiology comparative studies of different ion beam therapies and the development of real-time imaging for precise and accurate dose delivery. The ANL/UChicago Advanced Heavy Ion Therapy Center initiative has recently grown to include the regional and nationwide interest, support and collaboration of Northwestern University, the Chicago Proton Center, the Hines Illinois branch of the Department of Veteran Affairs (VA), as well as the National Center for Particle Beam Radiation Therapy Research.
- Published
- 2019
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28. Structural Perspective into Activation of Arp2-3 Complex for Nucleating Linear and Branched Actin Assemblies
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Bojian Ding, Saikat Chowdhury, Heidy Narvaez Ortiz, and Brad J. Nolen
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biology ,Chemistry ,Perspective (graphical) ,Biophysics ,biology.protein ,Arp2/3 complex ,Actin - Published
- 2021
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29. Incentives and children's dietary choices: A field experiment in primary schools
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Patrick J. Nolen, Jonathan James, and Michèle Belot
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Male ,Economic growth ,Field experiment ,Health Promotion ,Age and gender ,Competition (economics) ,Food Preferences ,Habits ,03 medical and health sciences ,0302 clinical medicine ,Reward ,Incentives ,0502 economics and business ,Economics ,Humans ,030212 general & internal medicine ,050207 economics ,Child ,Child nutrition ,Consumption (economics) ,Motivation ,Schools ,Health Policy ,05 social sciences ,fiield experiments ,Food Services ,Public Health, Environmental and Occupational Health ,Field experiments ,Diet ,Test (assessment) ,Incentive ,England ,Health ,Female ,Demography - Abstract
We conduct a field experiment in 31 primary schools in England to test the effectiveness of different temporary incentives on increasing choice and consumption of fruit and vegetables at lunchtime. In each treatment, pupils received a sticker for choosing a fruit or vegetable at lunch. They were eligible for an additional reward at the end of the week depending on the number of stickers accumulated, either individually (individual scheme) or in comparison to others (competition). Overall, we find no significant effect of the individual scheme, but positive effects of competition. For children who had margin to increase their consumption, competition increases choice of fruit and vegetables by 33% and consumption by 48%. These positive effects generally carry over to the week immediately following the treatment, but are not sustained effects six months later. We also find large differences in effectiveness across demographic characteristics such as age and gender.
- Published
- 2016
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30. Cryo-EM Reveals Actin Filament Nucleation by Activated Arp2/3 Complex
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Brad J. Nolen, Saikat Chowdhury, and Mohammed Shaaban
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Materials science ,biology ,Cryo-electron microscopy ,Biophysics ,biology.protein ,Arp2/3 complex ,Actin filament nucleation - Published
- 2020
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31. Structure of the nucleation‐promoting factor <scp>SPIN</scp> 90 bound to the actin filament nucleator Arp2/3 complex
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Su-Ling Liu, Qing Luan, Luke A Helgeson, and Brad J. Nolen
- Subjects
0301 basic medicine ,Protein subunit ,Nucleation ,Muscle Proteins ,Arp2/3 complex ,macromolecular substances ,Endocytosis ,Actin-Related Protein 2-3 Complex ,General Biochemistry, Genetics and Molecular Biology ,Protein filament ,Structure-Activity Relationship ,03 medical and health sciences ,Protein Domains ,Animals ,Humans ,Protein Structure, Quaternary ,Molecular Biology ,Actin ,Adaptor Proteins, Signal Transducing ,General Immunology and Microbiology ,biology ,General Neuroscience ,Articles ,Actin Cytoskeleton ,030104 developmental biology ,Armadillo repeats ,Biophysics ,biology.protein ,Actin filament binding ,Cattle - Abstract
Unlike the WASP family of Arp2/3 complex activators, WISH/DIP/SPIN90 (WDS) family proteins activate actin filament nucleation by the Arp2/3 complex without the need for a preformed actin filament. This allows WDS proteins to initiate branched actin network assembly by providing seed filaments that activate WASP‐bound Arp2/3 complex. Despite their important role in actin network initiation, it is unclear how WDS proteins drive the activating steps that require both WASP and pre‐existing actin filaments during WASP‐mediated nucleation. Here, we show that SPIN90 folds into an armadillo repeat domain that binds a surface of Arp2/3 complex distinct from the two WASP sites, straddling a hinge point that may stimulate movement of the Arp2 subunit into the activated short‐pitch conformation. SPIN90 binds a surface on Arp2/3 complex that overlaps with actin filament binding, explaining how it could stimulate the same structural rearrangements in the complex as pre‐existing actin filaments. By revealing how WDS proteins activate the Arp2/3 complex, these data provide a molecular foundation to understand initiation of dendritic actin networks and regulation of Arp2/3 complex by its activators.
- Published
- 2018
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32. Dip1 Co-opts Features of Branching Nucleation to Create Linear Actin Filaments that Activate WASP-Bound Arp2/3 Complex
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Luke A Helgeson, Brad J. Nolen, Andrew R. Wagner, and Connor J. Balzer
- Subjects
0301 basic medicine ,Initial Seed ,Nucleation ,Arp2/3 complex ,macromolecular substances ,Endocytosis ,Branching (polymer chemistry) ,General Biochemistry, Genetics and Molecular Biology ,Actin-Related Protein 2-3 Complex ,Article ,Protein filament ,03 medical and health sciences ,0302 clinical medicine ,Schizosaccharomyces ,Actin ,Cytoskeleton ,Total internal reflection fluorescence microscope ,biology ,030104 developmental biology ,Biophysics ,biology.protein ,Schizosaccharomyces pombe Proteins ,biological phenomena, cell phenomena, and immunity ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery ,Protein Binding - Abstract
Summary When activated by Wiskott-Aldrich syndrome proteins (WASP), Arp2/3 complex nucleates branched actin filaments important for processes like cellular motility and endocytosis [ 1 ]. WASP-mediated activation of Arp2/3 complex requires a preformed actin filament, ensuring that activation by WASP creates branched instead of linear filaments. However, this biochemical requirement also means that assembly of branched actin networks must be primed with an initial seed filament [ 2 , 3 , 4 ]. We recently described a class of activators called WISH/DIP/SPIN90 (WDS) proteins, which, unlike WASP, activate Arp2/3 complex without a preformed filament [ 4 ]. Although this property may allow WDS proteins to serve as seed filament generators, it is unknown whether actin filaments nucleated by WDS-activated Arp2/3 complex can activate WASP-bound Arp2/3 complex. Further, despite their potential importance as branched actin network initiators, little is known about how WDS proteins turn on Arp2/3 complex. Here, we use two-color single-molecule total internal reflection fluorescence (TIRF) microscopy to show that Dip1, the S. pombe WDS protein [ 5 ], co-opts features of branching nucleation to activate Arp2/3 complex. Specifically, it activates Arp2/3 complex to nucleate linear filaments analogous to the branch created by WASP-mediated activation. The barbed ends of Dip1-Arp2/3 nucleated filaments are free to elongate, and their pointed ends remain anchored to Dip1-bound Arp2/3 complex. The linear filaments nucleated by Dip1-bound Arp2/3 complex activate WASP-bound Arp2/3 complex as potently as spontaneously nucleated or branched actin filaments. These observations provide important insights into the regulation of Arp2/3 complex by its activators and the molecular basis for initiation of branched actin networks.
- Published
- 2018
33. Identification of Wiskott-Aldrich syndrome protein (WASP) binding sites on the branched actin filament nucleator Arp2/3 complex
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Trisha N. Davis, Michael J. MacCoss, Alex Zelter, Qing Luan, and Brad J. Nolen
- Subjects
0301 basic medicine ,Saccharomyces cerevisiae Proteins ,Protein Conformation ,Protein subunit ,Arp2/3 complex ,Sequence Homology ,macromolecular substances ,Saccharomyces cerevisiae ,Actin-Related Protein 2-3 Complex ,Protein filament ,03 medical and health sciences ,0302 clinical medicine ,Protein Interaction Mapping ,Amino Acid Sequence ,Binding site ,Actin ,Multidisciplinary ,Binding Sites ,biology ,Chemistry ,Wiskott–Aldrich syndrome protein ,Actin Cytoskeleton ,030104 developmental biology ,Förster resonance energy transfer ,PNAS Plus ,Docking (molecular) ,biology.protein ,Biophysics ,030217 neurology & neurosurgery ,Wiskott-Aldrich Syndrome Protein ,Protein Binding - Abstract
Arp2/3 complex nucleates branched actin filaments important for cellular motility and endocytosis. WASP family proteins are Arp2/3 complex activators that play multiple roles in branching nucleation, but little is known about the structural bases of these WASP functions, owing to an incomplete understanding of how WASP binds Arp2/3 complex. Recent data show WASP binds two sites, and biochemical and structural studies led to models in which the WASP C segment engages the barbed ends of the Arp3 and Arp2 subunits while the WASP A segment binds the back side of the complex on Arp3. However, electron microscopy reconstructions showed density for WASP inconsistent with these models on the opposite (front) side of Arp2/3 complex. Here we use chemical cross-linking and mass spectrometry (XL-MS) along with computational docking and structure-based mutational analysis to map the two WASP binding sites on the complex. Our data corroborate the barbed end and back side binding models and show one WASP binding site on Arp3, on the back side of the complex, and a second site on the bottom of the complex, spanning Arp2 and ARPC1. The XL-MS-identified cross-links rule out the front side binding model and show that the A segment of WASP binds along the bottom side of the ARPC1 subunit, instead of at the Arp2/ARPC1 interface, as suggested by FRET experiments. The identified binding sites support the Arp3 tail release model to explain WASP-mediated activating conformational changes in Arp2/3 complex and provide insight into the roles of WASP in branching nucleation.
- Published
- 2018
34. The Effect of Health Insurance Reform: Evidence from China
- Author
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Patrick J. Nolen and Huajing He
- Subjects
Economics and Econometrics ,business.industry ,050204 development studies ,05 social sciences ,Causal effect ,Instrumental variable ,Health outcomes ,Preventive care ,Double difference ,Environmental health ,0502 economics and business ,Health care ,Health insurance ,Business ,050207 economics ,China ,Finance - Abstract
This paper estimates the impact of a health insurance reform on health outcomes in urban China. Using the China Health and Nutrition Survey 1 we find that this reform increases the rate of health insurance coverage significantly among workers in Non-State Owned Enterprises. The double difference (DD) estimations show that the reform also leads to better health outcomes: workers are less likely to get sick and more likely to use preventive care. Using an instrumental variable (IV) approach to look at the causal effect of health insurance, we find those with health insurance use more preventive care but do not report significantly better health outcomes, an increase in health care utilisation, or an increase in out-of-pocket medical expenditure.
- Published
- 2018
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35. 8. Will The Real Family-Friendly Employer Please Stand Up: Who Permits Work Hour Reductions For Childcare?
- Author
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Kathleen Christensen, Patrick J. Nolen, Barbara Schneider, and Robert M. Hutchens
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Labour economics ,Work (electrical) ,Business ,Family-friendly - Published
- 2017
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36. Single-Turnover Activation of Arp2/3 Complex by Dip1 May Balance Nucleation of Linear versus Branched Actin Filaments
- Author
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Luke A Helgeson, Brad J. Nolen, Andrew R. Wagner, and Connor J. Balzer
- Subjects
0301 basic medicine ,Total internal reflection fluorescence microscope ,biology ,Activator (genetics) ,Cellular differentiation ,Endocytic cycle ,Arp2/3 complex ,macromolecular substances ,Endocytosis ,Actin-Related Protein 2-3 Complex ,Article ,General Biochemistry, Genetics and Molecular Biology ,Protein filament ,Actin Cytoskeleton ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Schizosaccharomyces ,Biophysics ,biology.protein ,Schizosaccharomyces pombe Proteins ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery ,Actin ,Protein Binding - Abstract
Summary Arp2/3 complex nucleates branched actin filaments important for cellular motility, endocytosis, meiosis, and cellular differentiation [ 1 , 2 , 3 , 4 ]. Wiskott-Aldrich syndrome proteins (WASPs), the prototypical Arp2/3 complex activators, activate Arp2/3 complex only once it is bound to the side of an actin filament [ 5 , 6 ]. This ensures WASP-activated Arp2/3 complex only nucleates branched actin filaments but means branched actin networks must be seeded with an initial preformed filament. Dip1 and other WISH/DIP/SPIN90 family proteins activate Arp2/3 complex without preformed filaments [ 7 ], creating seed filaments that activate WASP-bound Arp2/3 complex [ 8 ]. Importantly, Dip1-mediated activation of Arp2/3 complex creates linear filaments instead of branches [ 7 ]. Cells may therefore need to limit Dip1 activity relative to WASP to preserve the dendritic nature of actin networks, although it is unclear whether such regulatory mechanisms exist. Here, we use total internal reflection fluorescence (TIRF) microscopy to show that Dip1 causes actin assembled with WASP and Arp2/3 complex to form disconnected networks with many linear filaments rather than highly branched arrays. We discover a key biochemical difference between Dip1 and WASP that may limit linear filament nucleation in cells; although WASP must be released for nucleation, Dip1 stays associated with Arp2/3 complex on the pointed ends of nucleated actin filaments, so Dip1 is consumed in the reaction. Using live-cell imaging of fission yeast, we provide evidence that Dip1 is a single-turnover activator of Arp2/3 complex in vivo, revealing a mechanism by which Dip1 can initiate branched actin networks at endocytic sites without disrupting their branched architectures.
- Published
- 2019
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37. Developments towards an Advanced Ion Therapy Research Center in the US
- Author
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Bulent Aydogan, J. Nolen, B. Mustapha, J. Noonan, M. Pankuch, J.S. Welsh, and A. Nassiri
- Subjects
Cancer Research ,medicine.medical_specialty ,Radiation ,Therapy research ,Oncology ,business.industry ,Medicine ,Radiology, Nuclear Medicine and imaging ,Medical physics ,Center (algebra and category theory) ,business - Published
- 2019
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38. Photonuclear production of high specific activity copper-67 and scandium-47
- Author
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D. Ehst, David A. Rotsch, Roman Gromov, W. Henning, Nicholas A. Smith, Th. Brossard, J. Nolen, M.A. Brown, J. Song, J. Greene, and Sergey D. Chemerisov
- Subjects
Cancer Research ,High specific activity ,Chemistry ,Radiochemistry ,Molecular Medicine ,chemistry.chemical_element ,Radiology, Nuclear Medicine and imaging ,Scandium ,Copper - Published
- 2019
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39. Dip1 Defines a Class of Arp2/3 Complex Activators that Function without Preformed Actin Filaments
- Author
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Brad J. Nolen, Andrew R. Wagner, Qing Luan, and Su-Ling Liu
- Subjects
0303 health sciences ,Agricultural and Biological Sciences(all) ,Actin-Related Protein 2-3 Complex ,Biochemistry, Genetics and Molecular Biology(all) ,Actin remodeling ,Arp2/3 complex ,macromolecular substances ,Biology ,Actin cytoskeleton ,General Biochemistry, Genetics and Molecular Biology ,Cell biology ,03 medical and health sciences ,0302 clinical medicine ,Treadmilling ,biology.protein ,Actin-binding protein ,MDia1 ,General Agricultural and Biological Sciences ,Cytoskeleton ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Summary Background Arp2/3 complex is a key actin cytoskeletal regulator that creates branched actin filament networks in response to cellular signals. WASP-activated Arp2/3 complex assembles branched actin networks by nucleating new filaments from the sides of pre-existing ones. WASP-mediated activation requires seed filaments, to which the WASP-bound Arp2/3 complex can bind to form branches, but the source of the first substrate filaments for branching is unknown. Results Here we show that Dip1, a member of the WISH/DIP/SPIN90 family of actin regulators, potently activates Arp2/3 complex without preformed filaments. Unlike other Arp2/3 complex activators, Dip1 does not bind actin monomers or filaments, and it interacts with the complex using a non-WASP-like binding mode. In addition, Dip1-activated Arp2/3 complex creates linear instead of branched actin filament networks. Conclusions Our data show the mechanism by which Dip1 and other WISH/DIP/SPIN90 proteins can provide seed filaments to Arp2/3 complex to serve as master switches in initiating branched actin assembly. This mechanism is distinct from other known activators of Arp2/3 complex.
- Published
- 2013
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40. Unemployment and household values: Distribution sensitive measures of unemployment
- Author
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Patrick J. Nolen
- Subjects
Organizational Behavior and Human Resource Management ,Economics and Econometrics ,Labour economics ,Poverty ,business.industry ,media_common.quotation_subject ,Public policy ,Distribution (economics) ,Literacy ,Argument ,Unemployment ,Economics ,business ,Externality ,media_common - Abstract
Headcount measures have been criticized as potentially inadequate when looking at changes in poverty or literacy over time or in determining the success of particular public policies. In this paper I argue that using the headcount measure of unemployment can be misleading as well. I utilize an externality argument similar to the one used in the literacy debate and provide a class of measures that capture externalities of employment.
- Published
- 2013
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41. Structural basis for regulation of Arp2/3 complex by GMF
- Author
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Brad J. Nolen and Qing Luan
- Subjects
Glia Maturation Factor ,Models, Molecular ,Protein subunit ,Molecular Sequence Data ,Arp2/3 complex ,macromolecular substances ,Glia maturation factor ,Biology ,Crystallography, X-Ray ,Actin-Related Protein 2-3 Complex ,Article ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Structural Biology ,Animals ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Cytoskeleton ,Molecular Biology ,Actin ,030304 developmental biology ,Actin nucleation ,0303 health sciences ,Sequence Homology, Amino Acid ,Actin cytoskeleton ,Actins ,Recombinant Proteins ,Wiskott-Aldrich Syndrome Protein Family ,3. Good health ,Protein Subunits ,Crystallography ,Multiprotein Complexes ,Biophysics ,biology.protein ,Cattle ,biological phenomena, cell phenomena, and immunity ,030217 neurology & neurosurgery - Abstract
The Arp2/3 complex mediates formation of complex cellular structures such as lamellipodia by nucleating branched actin filaments. Arp2/3-complex activity is precisely controlled by over a dozen regulators, yet the structural mechanism by which regulators interact with the complex is unknown. GMF is a recently discovered regulator of the Arp2/3 complex that can inhibit nucleation and disassemble branches. We solved the structure of the 240-kDa assembly of Mus musculus GMF and Bos taurus Arp2/3 complex and found that GMF binds the barbed end of Arp2, overlapping with the proposed binding site of WASP-family proteins. The structure suggests that GMF can bind branch junctions in the manner that cofilin binds filament sides, consistent with a modified cofilin-like mechanism for debranching by GMF. The GMF-Arp2 interface reveals how the ADF-H actin-binding domain in GMF is exploited to specifically recognize Arp2/3 complex and not actin.
- Published
- 2013
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42. Anaemia in CKD 5D
- Author
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A. Mikhail, M. Kaplan, I. Macdougall, R. J. Schmidt, A. Rastogi, W. Wang, S. Tong, M. Mayo, N. Oestreicher, B. Schiller, J. M. Green, R. Verma, K. Leu, R. B. Mortensen, P. R. Young, P. Schatz, D. M. Wojchowski, Y. Shimonaka, Y. Sasaki, K. Yorozu, M. N. Sasaki, K. Ikuta, Y. Kohgo, Y. M. Omori, M. Hiramatsu, N. Momoki, Y. Kakio, N. Shibuto, H. Takeuchi, M. Fukumoto, K. Maruyama, Y. Matsuo, Y. Omori, B. M. Robinson, M. Larkina, D. A. Goodkin, Y. Li, F. Locatelli, J. Nolen, W. Kleophas, R. L. Pisoni, S. Sibbel, S. Brunelli, M. Krishnan, M. Horie, E. Hasegawa, K.-i. Minoshima, C. Ambrus, L. Kerkovits, J. Szegedi, A. Benke, E. Toth, L. Nagy, B. Borbas, A. Rozinka, J. Nemeth, G. Varga, I. Kulcsar, L. Gergely, S. Szakony, I. Kiss, K. Danielson, A. R. Qureshi, O. Heimburger, P. Stenvinkel, B. Lindholm, B. Hylander-Rossner, G. Germanis, M. Hansson, S. Beshara, P. Barany, J.-M. Dueymes, A. Kolko, C. Couchoud, C. Combe, A. Covic, D. Goldsmith, P. Zaoui, L. Gesualdo, G. London, F. Dellanna, J. Mann, M. Turner, M. Muenzberg, K. MacDonald, K. Denhaerynck, I. Abraham, M. B. Sanchez, R. C. Casero, R. V. Ortiz, I. G. Carmelo, S. C. Munoz, E. R. Gomez, C. S. Rodriguez, T. Kuji, T. Fujikawa, M. Kakimoto-Shino, K. Shibata, Y. Toya, S. Umemura, N. Topuzovic, I. Mihaljevic, V. Rupcic, G. Sterner, N. Clyne, J. Toblli, F. Di Gennaro, M. Chmielewski, P. Jagodzinski, M. Lichodziejewska-Niemierko, B. Rutkowski, K. Takasawa, C. Takaeda, H. Ueda, M. Higuchi, T. Maeda, N. Tomosugi, T. F. Moghazy, M. Jakic, L. Zibar, G. Romei Longhena, W. Beck, A. Liebchen, U. Teatini, J. B. Rottembourg, A. Guerin, M. Diaconita, A. Dansaert, K. Koike, K. Fukami, K. Shimamatsu, A. Kawaguchi, and S. Okuda
- Subjects
Transplantation ,medicine.medical_specialty ,Nephrology ,business.industry ,Internal medicine ,medicine ,business - Published
- 2013
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43. Small Molecules CK-666 and CK-869 Inhibit Actin-Related Protein 2/3 Complex by Blocking an Activating Conformational Change
- Author
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Brad J. Nolen, Luke A Helgeson, Min Suk Han, and Byron Hetrick
- Subjects
Models, Molecular ,Conformational change ,Indoles ,Protein Conformation ,Stereochemistry ,Clinical Biochemistry ,macromolecular substances ,Crystallography, X-Ray ,Biochemistry ,Actin-Related Protein 2-3 Complex ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Adenosine Triphosphate ,0302 clinical medicine ,Protein structure ,Organoselenium Compounds ,Drug Discovery ,Animals ,Organosilicon Compounds ,Protein Interaction Maps ,Actin-binding protein ,Binding site ,Molecular Biology ,Actin ,030304 developmental biology ,Pharmacology ,0303 health sciences ,Binding Sites ,biology ,General Medicine ,Small molecule ,Actins ,3. Good health ,chemistry ,Biophysics ,biology.protein ,Molecular Medicine ,Cattle ,Adenosine triphosphate ,030217 neurology & neurosurgery - Abstract
SummaryActin-related protein 2/3 (Arp2/3) complex is a seven-subunit assembly that nucleates branched actin filaments. Small molecule inhibitors CK-666 and CK-869 bind to Arp2/3 complex and inhibit nucleation, but their modes of action are unknown. Here, we use biochemical and structural methods to determine the mechanism of each inhibitor. Our data indicate that CK-666 stabilizes the inactive state of the complex, blocking movement of the Arp2 and Arp3 subunits into the activated filament-like (short pitch) conformation, while CK-869 binds to a serendipitous pocket on Arp3 and allosterically destabilizes the short pitch Arp3-Arp2 interface. These results provide key insights into the relationship between conformation and activity in Arp2/3 complex and will be critical for interpreting the influence of the inhibitors on actin filament networks in vivo.
- Published
- 2013
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44. Identification of an ATP-controlled allosteric switch that controls actin filament nucleation by Arp2/3 complex
- Author
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Brad J. Nolen, Su-Ling Liu, Max Rodnick-Smith, Connor J. Balzer, and Qing Luan
- Subjects
0301 basic medicine ,Saccharomyces cerevisiae Proteins ,Protein Conformation ,Science ,Allosteric regulation ,General Physics and Astronomy ,Arp2/3 complex ,macromolecular substances ,Actin-Related Protein 2-3 Complex ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Adenosine Triphosphate ,Schizosaccharomyces ,Amino Acid Sequence ,Actin-binding protein ,Conserved Sequence ,Actin ,Multidisciplinary ,biology ,Protein Stability ,Chemistry ,Actin remodeling ,General Chemistry ,Actin cytoskeleton ,Actin Cytoskeleton ,030104 developmental biology ,Biochemistry ,Actin-Related Protein 3 ,Actin-Related Protein 2 ,biology.protein ,Biophysics ,Schizosaccharomyces pombe Proteins ,Protein Multimerization ,biological phenomena, cell phenomena, and immunity - Abstract
Nucleation of branched actin filaments by Arp2/3 complex is tightly regulated to control actin assembly in cells. Arp2/3 complex activation involves conformational changes brought about by ATP, Nucleation Promoting Factor (NPF) proteins, actin filaments and NPF-recruited actin monomers. To understand how these factors promote activation, we must first understand how the complex is held inactive in their absence. Here we demonstrate that the Arp3 C-terminal tail is a structural switch that prevents Arp2/3 complex from adopting an active conformation. The interaction between the tail and a hydrophobic groove in Arp3 blocks movement of Arp2 and Arp3 into an activated filament-like (short pitch) conformation. Our data indicate ATP binding destabilizes this interaction via an allosteric link between the Arp3 nucleotide cleft and the hydrophobic groove, thereby promoting the short-pitch conformation. Our results help explain how Arp2/3 complex is locked in an inactive state without activators and how autoinhibition is relieved., Arp2/3 complex nucleates branched actin filaments, and is inactive in the absense of activators. Here the authors present a model of Arp2/3 autoinhibition, whereby the Arp3 C-terminal tail acts as a structural switch that blocks movement of Arp2 and Arp3 into an activated filament-like conformation.
- Published
- 2016
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45. Role and structural mechanism of WASP-triggered conformational changes in branched actin filament nucleation by Arp2/3 complex
- Author
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Brad J. Nolen, Su-Ling Liu, Qing Luan, and Max Rodnick-Smith
- Subjects
0301 basic medicine ,Conformational change ,Stereochemistry ,Saccharomyces cerevisiae ,Molecular Sequence Data ,Molecular Conformation ,Arp2/3 complex ,macromolecular substances ,Biology ,Actin-Related Protein 2-3 Complex ,03 medical and health sciences ,Schizosaccharomyces ,Amino Acid Sequence ,Peptide sequence ,Actin ,Multidisciplinary ,fungi ,Wiskott–Aldrich syndrome protein ,biology.organism_classification ,Actin cytoskeleton ,Actin Cytoskeleton ,030104 developmental biology ,Cross-Linking Reagents ,PNAS Plus ,biology.protein ,Biophysics ,Wiskott-Aldrich Syndrome Protein - Abstract
The Arp2/3 (Actin-related proteins 2/3) complex is activated by WASP (Wiskott–Aldrich syndrome protein) family proteins to nucleate branched actin filaments that are important for cellular motility. WASP recruits actin monomers to the complex and stimulates movement of Arp2 and Arp3 into a “short-pitch” conformation that mimics the arrangement of actin subunits within filaments. The relative contribution of these functions in Arp2/3 complex activation and the mechanism by which WASP stimulates the conformational change have been unknown. We purified budding yeast Arp2/3 complex held in or near the short-pitch conformation by an engineered covalent cross-link to determine if the WASP-induced conformational change is sufficient for activity. Remarkably, cross-linked Arp2/3 complex bypasses the need for WASP in activation and is more active than WASP-activated Arp2/3 complex. These data indicate that stimulation of the short-pitch conformation is the critical activating function of WASP and that monomer delivery is not a fundamental requirement for nucleation but is a specific requirement for WASP-mediated activation. During activation, WASP limits nucleation rates by releasing slowly from nascent branches. The cross-linked complex is inhibited by WASP’s CA region, even though CA potently stimulates cross-linking, suggesting that slow WASP detachment masks the activating potential of the short-pitch conformational switch. We use structure-based mutations and WASP–Arp fusion chimeras to determine how WASP stimulates movement toward the short-pitch conformation. Our data indicate that WASP displaces the autoinhibitory Arp3 C-terminal tail from a hydrophobic groove at Arp3′s barbed end to destabilize the inactive state, providing a mechanism by which WASP stimulates the short-pitch conformation and activates Arp2/3 complex.
- Published
- 2016
46. The effect of the Wenchuan earthquake and government aid on rural households
- Author
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Lei Wang, Jingliang Lu, Shuaizhang Feng, and Patrick J. Nolen
- Subjects
Consumption (economics) ,Government ,Geography ,Economic inequality ,Development economics ,Household income ,East Asia ,Subsidy ,Natural disaster ,Socioeconomics ,China - Abstract
This chapter discusses the impact of the 2008 Sichuan earthquake on household income, consumption, and income inequality using a unique dataset collected in rural Sichuan. We find that household income fell by 14 percent because of the earthquake and that income inequality did not increase. With regard to government support, living subsidies were more than enough to offset losses in annual income, but reconstruction aid, such as grants and bank loans for housing, accounted for less than 60 percent of total house-rebuilding costs.
- Published
- 2016
- Full Text
- View/download PDF
47. Salience, risky choices and gender
- Author
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Alison L. Booth and Patrick J. Nolen
- Subjects
Economics and Econometrics ,ComputingMilieux_THECOMPUTINGPROFESSION ,Salience (language) ,Salient ,Cognition ,Risk aversion (psychology) ,Psychology ,Finance ,Cognitive psychology - Abstract
Risk theories typically assume individuals make risky choices using probability weights that differ from objective probabilities. Recent theories suggest that probability weights vary depending on which portion of a risky environment is made salient. Using experimental data we show that salience affects young men and women differently, even after controlling for cognitive and non-cognitive skills. Men are significantly more likely than women to switch from a certain to a risky choice once the upside of winning is made salient, even though the expected value of the choice remains the same.
- Published
- 2012
- Full Text
- View/download PDF
48. Structural Characterization and Computer-Aided Optimization of a Small-Molecule Inhibitor of the Arp2/3 Complex, a Key Regulator of the Actin Cytoskeleton
- Author
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Adam C. Glass, Shih-Yuan Liu, Zoe Cournia, Min Suk Han, Brad J. Nolen, George Patargias, and Andrew W. Baggett
- Subjects
Models, Molecular ,Regulator ,Arp2/3 complex ,macromolecular substances ,Biochemistry ,Actin-Related Protein 2-3 Complex ,Article ,Small Molecule Libraries ,Structure-Activity Relationship ,Drug Discovery ,Animals ,Structure–activity relationship ,General Pharmacology, Toxicology and Pharmaceutics ,Actin ,Pharmacology ,Dose-Response Relationship, Drug ,Molecular Structure ,biology ,Organic Chemistry ,Stereoisomerism ,Actin cytoskeleton ,Small molecule ,Cell biology ,Actin Cytoskeleton ,Docking (molecular) ,biology.protein ,Computer-Aided Design ,Molecular Medicine ,Cattle - Abstract
CK-666 (1) is a recently discovered small-molecule inhibitor of the actin-related protein 2/3 (Arp2/3) complex, a key actin cytoskeleton regulator with roles in bacterial pathogenesis and cancer cell motility. Although 1 is commercially available, the crystal structure of Arp2/3 complex with 1 bound has not been reported, making its mechanism of action uncertain. Furthermore, its relatively low potency increases its potential for off-target effects in vivo, complicating interpretation of its influence in cell biological studies and precluding its clinical use. Herein we report the crystal structure of 1 bound to Arp2/3 complex, which reveals that 1 binds between the Arp2 and Arp3 subunits to stabilize the inactive conformation of the complex. Based on the crystal structure, we used computational docking and free-energy perturbation calculations of monosubstituted derivatives of 1 to guide optimization efforts. Biochemical assays of ten newly synthesized compounds led to the identification of compound 2, which exhibits a threefold increase in inhibitory activity in vitro relative to 1. In addition, our computational analyses unveiled a surface groove at the interface of the Arp2 and Arp3 subunits that can be exploited for additional structure-based optimization.
- Published
- 2012
- Full Text
- View/download PDF
49. Choosing to compete: How different are girls and boys?
- Author
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Patrick J. Nolen and Alison L. Booth
- Subjects
Competition (economics) ,Organizational Behavior and Human Resource Management ,Economics and Econometrics ,Stylized fact ,education ,Tournament ,Controlled experiment ,Psychology ,Piece work ,Social learning ,Social psychology ,Nature versus nurture ,Test (assessment) - Abstract
Using a controlled experiment, we examine the role of nurture in explaining the stylized fact that women shy away from competition. Our subjects (students just under 15 years of age) attend publicly-funded single-sex and coeducational schools. We find robust differences between the competitive choices of girls from single-sex and coed schools. Moreover, girls from single-sex schools behave more like boys even when randomly assigned to mixed-sex experimental groups. Thus it is untrue that the average female avoids competitive behaviour more than the average male. This suggests that observed gender differences might reflect social learning rather than inherent gender traits.
- Published
- 2012
- Full Text
- View/download PDF
50. Characterization of two classes of small molecule inhibitors of Arp2/3 complex
- Author
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Brad J. Nolen, J. Hartman, Alan J. Russell, Z. Jia, D.W. Pierce, Chad D. McCormick, Thomas D. Pollard, R. Sakowicz, and N. Tomasevic
- Subjects
Models, Molecular ,Indoles ,Podosome ,Listeria ,Protein Conformation ,Arp2/3 complex ,macromolecular substances ,Thiophenes ,Crystallography, X-Ray ,Article ,Actin-Related Protein 2-3 Complex ,Monocytes ,Cell Line ,03 medical and health sciences ,0302 clinical medicine ,Biopolymers ,Schizosaccharomyces ,Animals ,Humans ,Actin-binding protein ,Actin ,030304 developmental biology ,0303 health sciences ,Multidisciplinary ,biology ,Actin remodeling ,Actin cytoskeleton ,Actins ,Cell biology ,Actin Cytoskeleton ,Thiazoles ,Actin-Related Protein 3 ,Actin-Related Protein 2 ,biology.protein ,Cattle ,biological phenomena, cell phenomena, and immunity ,Hydrophobic and Hydrophilic Interactions ,030217 neurology & neurosurgery - Abstract
Polymerization of actin filaments directed by the actin-related protein (Arp)2/3 complex supports many types of cellular movements. However, questions remain regarding the relative contributions of Arp2/3 complex versus other mechanisms of actin filament nucleation to processes such as path finding by neuronal growth cones; this is because of the lack of simple methods to inhibit Arp2/3 complex reversibly in living cells. Here we describe two classes of small molecules that bind to different sites on the Arp2/3 complex and inhibit its ability to nucleate actin filaments. CK-0944636 binds between Arp2 and Arp3, where it appears to block movement of Arp2 and Arp3 into their active conformation. CK-0993548 inserts into the hydrophobic core of Arp3 and alters its conformation. Both classes of compounds inhibit formation of actin filament comet tails by Listeria and podosomes by monocytes. Two inhibitors with different mechanisms of action provide a powerful approach for studying the Arp2/3 complex in living cells.
- Published
- 2009
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