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Search Results: 1 - 10 of 65053 matches for " John van Noort "
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Multiple Aspects of ATP-Dependent Nucleosome Translocation by RSC and Mi-2 Are Directed by the Underlying DNA Sequence
Joke J. F. A. van Vugt, Martijn de Jager, Magdalena Murawska, Alexander Brehm, John van Noort, Colin Logie
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0006345
Abstract: Background Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted. Methodology/Principal Findings We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type) and native RSC from yeast (SWI/SNF-type) repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps. Conclusions/Significance Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase-catalyzed repositioning. Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA. This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo.
T. Witte, Tussen Coolsingel en Binnenhof. Stadsregionale capriolen in Rotterdam Rijnmond
J. van den Noort
BMGN : Low Countries Historical Review , 2003,
C. Wagenaar, Welvaartsstad in wording. De wederopbouw van Rotterdam, 1940-1952
J. van den Noort
BMGN : Low Countries Historical Review , 1994,
Spatially coupled inversion of spectro-polarimetric image data I: Method and first results
M. van Noort
Physics , 2012, DOI: 10.1051/0004-6361/201220220
Abstract: When inverting solar spectra, image degradation effects that are present in the data are usually approximated or not considered. We develop a data reduction method that takes these issues into account and minimizes the resulting errors. By accounting for the diffraction PSF of the telescope during the inversions, we can produce a self-consistent solution that best fits the observed data, while simultaneously requiring fewer free parameters than conventional approaches. Simulations using realistic MHD data indicate that the method is stable for all resolutions, including those with pixel scales well beyond those that can be resolved with a 0.5m telescope, such as the Hinode SOT. Application of the presented method to reduce full Stokes data from the Hinode spectro-polarimeter results in dramatically increased image contrast and an increase in the resolution of the data to the diffraction limit of the telescope in almost all Stokes and fit parameters. The resulting data allow for detecting and interpreting solar features that have so far only been observed with 1m class ground-based telescopes. The new inversion method allows for accurate fitting of solar spectro-polarimetric imaging data over a large field of view, while simultaneously improving the noise statistics and spatial resolution of the results significantly.
Internet-based monitoring of influenza-like illness (ILI) in the general population of the Netherlands during the 2003–2004 influenza season
Richard L Marquet, Aad IM Bartelds, Sander P van Noort, Carl E Koppeschaar, John Paget, Fran?ois G Schellevis, Jouke van der Zee
BMC Public Health , 2006, DOI: 10.1186/1471-2458-6-242
Abstract: Direct mailings to schools and universities, and repeated interviews on television and radio, and in newspapers were used to kindle the enthusiasm of a broad section of the public for GIS. Strict symptomatic criteria for ILI were formulated with the assistance of expert institutes and only participants who responded at least five times to weekly e-mails asking them about possible ILI symptoms were included in the survey. Validation of GIS was done at different levels: 1) some key demographic (age distribution) and public health statistics (prevalence of asthma and diabetes, and influenza vaccination rates) for the Dutch population were compared with corresponding figures calculated from GIS; 2) the ILI rates in GIS were compared with the ILI consultation rates reported by GPs participating in the Dutch Sentinel Practice Network.13,300 persons (53% of total responders), replied at least five times to weekly e-mails and were included in the survey. As expected, there was a marked under-representation of the age groups 0–10 years and 81->90 years in the GIS population, although the similarities were remarkable for most other age groups, albeit that the age groups between 21 and 70 years were slightly overrepresented. There were striking similarities between GIS and the Dutch population with regard to the prevalence of asthma (6.4% vs. 6.9%) and the influenza vaccination rates, and to a lesser degree for diabetes (2.4% vs. 3.5%). The vaccination rates in patients with asthma or diabetes, and persons older than 65 years were 68%, 85%, and 85% respectively in GIS, while the corresponding percentages in the Dutch population were 73%, 85% and 87%. There was also a marked similarity between the seasonal course of ILI measured by GIS and the GPs. Although the ILI rate in GIS was about 10 times higher, the curves followed an almost similar pattern, with peak incidences occurring in the same week.The current study demonstrates that recruitment of a high number of persons willin
New species of the plesiomorphic genus Nixonia Masner (Hymenoptera, Platygastroidea, Platygastridae) from South Africa
Simon van Noort,Norman Johnson
ZooKeys , 2009, DOI: 10.3897/zookeys.20.112
Abstract: Two new species of Nixonia Masner (Hymenoptera, Platygastridae, Scelioninae), Nixonia masneri sp. n. and Nixonia mcgregori sp. n. are described from South Africa and further records of Nixonia corrugata Johnson & Masner, Nixonia lamorali Johnson & Masner, Nixonia stygica Johnson & Masner are documented. Johnson and Masner’s 2006 identification key is modified to include the newly described species. Online interactive Lucid matrix and Lucid Phoenix dichotomous keys are available on WaspWeb at http://www.waspweb.org/Platygastroidea/Keys/index.htm. Lucid data files in lif and sdd format are available at: doi:10.3897/zookeys.20.112.app.1.ik and doi:10.3897/zookeys.20.112.app.2.ik.
A revision of Anacharoides Cameron, 1904 (Hymenoptera, Figitidae) with a description of a new species
Matthew Buffington,Simon van Noort
ZooKeys , 2009, DOI: 10.3897/zookeys.20.124
Abstract: Anacharoides Cameron is revised and six species are recognized: A. nicknacki Buffington & van Noort, sp. n., A. pallida Quinlan, A. paragi Benoit, A. quadrus Quinlan, A. striaticeps Cameron and A. stygius Benoit. A key to species is provided. Anacharoides striaticeps was determined to be a variable species, and consequently a number of names have been proposed for this species. Here we clarify the identity of A. striaticeps and provide evidence for the following new synonymies of A. striaticeps: Anacharoides elongaticornis Benoit, syn. n., Anacharoides eurytergis Benoit, syn. n., Anacharoides decellius Quinlan, syn. n., Anacharoides sanitas Quinlan, syn. n., Anacharoides nigra Quinlan, syn. n., Anacharoides arcus Quinlan, syn. n., Anacharoides suspensus Quinlan, syn. n.. The holotype of Anacharoides rufa (Kieffer) is lost; examination of a specimen possibly determined by Kieffer from 1913 housed in the Museum is conspecific with A. pallida, but no nomenclature action is pursued at this time. The syn. n. of A. astrida Quinlan with A. quadrus is also hypothesized. Definitive host records for the genus, based on isolated puparia, are reported to be the syrphids Ischiodon Sack and Paragus Latreille. Species of this genus of figitid wasp are endemic to sub-Saharan Africa, Madagascar, the southern Arabian Peninsula and the Canary Islands. Images of all species contained within this paper are available from http://morphbank.net. An online Lucid interactive key to species of Anacharoides and images are available at http://www.waspweb.org/Cynipoidea/Figitidae/ Aspicerinae/Anacharoides/index.htm.
Revision of the Afrotropical Oberthuerellinae (Cynipoidea, Liopteridae)
Matthew Buffington,Simon van Noort
ZooKeys , 2012, DOI: 10.3897/zookeys.202.2136
Abstract: The Afrotropical Oberthuerellinae are revised, and new dichotomous and multi-entry keys to the species of Oberthuerella, Tessmannella, and Xenocynips are provided. All previously described species in these genera are redescribed; descriptions are augmented by color images of the holotype for each species. The following 11 species are described as new: Oberthuerella cyclopia Buffington & van Noort; O. eschara Buffington & van Noort; O. kibalensis van Noort & Buffington; O. pardolatus Buffington & van Noort; O. sharkeyi Buffington & van Noort; O. simba Buffington & van Noort; Tessmannella copelandi Buffington & van Noort; T. kiplingi Buffington & van Noort; T. roberti Buffington & van Noort; Xenocynips rhothion Buffington & van Noort; and X. ronquisti Buffington & van Noort. We provide identification keys to the genera and species occurring in the Afrotropical region. Online dichotomous and interactive Lucid keys to genera and species are available at http://www.waspweb.org/Cynipoidea/Keys/index.htm
Codivergence and multiple host species use by fig wasp populations of the Ficus pollination mutualism
Michael J McLeish, Simon van Noort
BMC Evolutionary Biology , 2012, DOI: 10.1186/1471-2148-12-1
Abstract: Statistical parsimony and AMOVA revealed deep divergences at the COI locus within several pollinating fig wasp species that persist on the same host Ficus species. Changes in branching patterns estimated using the generalized mixed Yule coalescent test indicated lineage duplication on the same Ficus species. Conversely, Elisabethiella and Alfonsiella fig wasp species are able to reproduce on multiple, but closely related host fig species. Tree reconciliation tests indicate significant codiversification as well as significant incongruence between fig wasp and Ficus phylogenies.The findings demonstrate more relaxed pollinating fig wasp host specificity than previously appreciated. Evolutionarily conservative host associations have been tempered by horizontal transfer and lineage duplication among closely related Ficus species. Independent and asynchronistic diversification of pollinating fig wasps is best explained by a combination of both sympatric and allopatric models of speciation. Pollinator host preference constraints permit reproduction on closely related Ficus species, but uncertainty of the frequency and duration of these associations requires better resolution.Several lines of theory have been proposed to account for the enormous diversity of phytophagous insects. Diversification conceivably ensues by ecological opportunity and adaptation to the exploitation of previously unattainable resources [1,2]; by restricted gene flow through allopatric means [3,4]; and disruptive selection and sympatric speciation [5,6]. In order to discern among potential mechanisms driving speciation, both historical pattern and ecological scale processes are important to consider [7-10]. Comparative phylogenetic approaches that test congruence between host and associate populations can contribute to greater resolution in unravelling ecological scale processes [11-14]. Here we interpret the codiversification between Ficus host species and populations of a group of African fig wasp
Revision of Khoikhoiinae (Hymenoptera, Braconidae)
Michael Sharkey,Simon van Noort,James Whitfield
ZooKeys , 2009, DOI: 10.3897/zookeys.20.108
Abstract: The species of the two genera of Khoikhoiinae (Hymenoptera, Braconidae) are revised. Thirteen species are recognized, of which five are new and eight were previously described: Khoikhoia anthelion Sharkey, sp. n., K. lission Mason, 1984, K. oligospilos Sharkey, sp. n., K. semiadusta Mason, 1983, K. solata Mason, 1983, K. townesi Mason, 1983, K. turneri Mason, 1984, Sania browni Sharkey, sp. n., S. capensis Mason, 1983, S. henryi Mason, 1983, S. marjoriae Mason, 1983, S. masneri Sharkey, sp. n., and S. masoni Sharkey, sp. n.. All are from the Cape Region of South Africa, and all but one species are confined to the western Cape. A dichotomous key to species is presented; links to electronic interactive keys and to distribution maps are also included. Based on phylogenetic position and morphological characters, speculations on life history are made, and it is suggested that some species may be parasitoids of wood- or stem-boring Lepidoptera. The DELTA data matrix and images for the key are available at 10.3897/zookeys.20.108.app.1.ik; Intkey files are available at 10.3897/zookeys.20.108.app.2.ik; Lucid files in LIF and SDD format are available at doi:10.3897/zookeys.20.108.app.3.ik and doi:10.3897/zookeys.20.108.app.4.ik. Publishing of DELTA raw data will facilitate future workers to edit keys and to add newly discovered taxa.
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