bluuebunny/crossref_metadata_2025_split huggingface dataset:
Load‐sensitive coupling of proton translocation and torque generation in the bacterial flagellar motor
Authors: Che Yong‐Suk , Nakamura Shuichi , Morimoto Yusuke V. , Kami‐ike Nobunori , Namba Keiichi , Minamino Tohru 
Published: November 2013

SummaryThe Salmonella flagellar motor consists of a rotor and about a dozen stator elements. Each stator element, consisting of MotA and MotB, acts as a proton channel to couple proton flow with torque generation. A highly conserved Asp33 residue of MotB is directly involved in the energy coupling mechanism, but it remains unknown how it carries out this function. Here, we show that the MotB(D33E) mutation dramatically alters motor performance in response to changes in external load. Rotation speeds of the MotA/B(D33E) and MotA(V35F)/B(D33E) motors were markedly slower than the wild‐type motor and fluctuated considerably at low load but not at high load, whereas the rotation rate of the wild‐type motor was stable at any load. At low load, pausing events were frequently observed in both mutant motors. The proton conductivities of these mutant stator channels in their ‘unplugged’ forms were only half of the conductivity of the wild‐type channel. These results suggest that the D33E mutation induces a load‐dependent inactivation of the MotA/B complex. We propose that the stator element is a load‐sensitive proton channel that efficiently couples proton translocation with torque generation and that Asp33 of MotB is critical for this co‐ordinated proton translocation.
Knowledge‐How and Epistemic Luck
Authors: Carter J. Adam , Pritchard Duncan 
Published: November 2013

AbstractReductive intellectualists (e.g., Stanley & Williamson 2001; Stanley 2011a; 2011b; Brogaard 2008b; 2009; 2011) hold that knowledge‐how is a kind of knowledge‐that. For this thesis to hold water, it is obviously important that knowledge‐how and knowledge‐that have the same epistemic properties. In particular, knowledge‐how ought to be compatible with epistemic luck to the same extent as knowledge‐that. It is argued,contrareductive intellectualism, that knowledge‐how is compatible with a species of epistemic luck which is not compatible with knowledge‐that, and thus it is claimed that knowledge‐how and knowledge‐that come apart.
De novo assembly of maritime pine transcriptome: implications for forest breeding and biotechnology
Authors: Canales Javier , Bautista Rocio , Label Philippe , Gómez‐Maldonado Josefa , Lesur Isabelle , Fernández‐Pozo Noe , Rueda‐López Marina , Guerrero‐Fernández Dario , Castro‐Rodríguez Vanessa , Benzekri Hicham , Cañas Rafael A. , Guevara María‐Angeles , Rodrigues Andreia , Seoane Pedro , Teyssier Caroline , Morel Alexandre , Ehrenmann François , Le Provost Grégoire , Lalanne Céline , Noirot Céline , Klopp Christophe , Reymond Isabelle , García‐Gutiérrez Angel , Trontin Jean‐François , Lelu‐Walter Marie‐Anne , Miguel Celia , Cervera María Teresa , Cantón Francisco R. , Plomion Christophe , Harvengt Luc , Avila Concepción , Gonzalo Claros M. , Cánovas Francisco M. 
Published: November 2013

SummaryMaritime pine (Pinus pinasterAit.) is a widely distributed conifer species in Southwestern Europe and one of the most advanced models for conifer research. In the current work, comprehensive characterization of the maritime pine transcriptome was performed using a combination of two different next‐generation sequencing platforms, 454 and Illumina. De novo assembly of the transcriptome provided a catalogue of 26 020 unique transcripts in maritime pine trees and a collection of 9641 full‐length cDNAs. Quality of the transcriptome assembly was validated by RT‐PCR amplification of selected transcripts for structural and regulatory genes. Transcription factors and enzyme‐encoding transcripts were annotated. Furthermore, the available sequencing data permitted the identification of polymorphisms and the establishment of robust single nucleotide polymorphism (SNP) and simple‐sequence repeat (SSR) databases for genotyping applications and integration of translational genomics in maritime pine breeding programmes. All our data are freely available at SustainpineDB, the P. pinaster expressional database. Results reported here on the maritime pine transcriptome represent a valuable resource for future basic and applied studies on this ecological and economically important pine species.
Partner preferences across sexual orientations and biological sex
Authors: WILLIS JARRYD T. 
Published: November 2013

AbstractThis study examined how partner preferences differ across interpersonal contexts (romantic attachment and relationship expectations) based on sexuality and biological sex. Participants completed measures of attachment and behavioral expectations for their romantic partners, cross‐sex friends, and same‐sex friends. The attachment anxiety results revealed an effect of sexuality: Single heterosexuals scored higher for their cross‐sex friends than same‐sex friends, single lesbian/gay individuals scored higher for same‐sex friends than cross‐sex friends, and bisexuals' attachment anxiety was equal regardless of friends' biological sex. The behavioral expectation results revealed an effect of biological sex indicating that, regardless of sexuality, women are preferred over men for emotional/social needs. Finally, an interaction revealed that lesbians have higher expectations for their girlfriends/wives than straight men have for theirs.
Puccinia psidii in Queensland, Australia: disease symptoms, distribution and impact
Authors: Pegg G. S. , Giblin F. R. , McTaggart A. R. , Guymer G. P. , Taylor H. , Ireland K. B. , Shivas R. G. , Perry S. 
Published: November 2013

Puccinia psidii has long been considered a significant threat to Australian plant industries and ecosystems. In April 2010, P. psidii was detected for the first time in Australia on the central coast of New South Wales (NSW). The fungus spread rapidly along the east coast and in December 2010 was found in Queensland (Qld) followed by Victoria a year later. Puccinia psidii was initially restricted to the southeastern part of Qld but spread as far north as Mossman. In Qld, 48 species of Myrtaceae are considered highly or extremely susceptible to the disease. The impact of P. psidii on individual trees and shrubs has ranged from minor leaf spots, foliage, stem and branch dieback to reduced fecundity. Tree death, as a result of repeated infection, has been recorded for Rhodomyrtus psidioides. Rust infection has also been recorded on flower buds, flowers and fruits of 28 host species. Morphological and molecular characteristics were used to confirm the identification of P. psidii from a range of Myrtaceae in Qld and compared with isolates from NSW and overseas. A reconstructed phylogeny based on the LSU and SSU regions of rDNA did not resolve the familial placement of P. psidii, but indicated that it does not belong to the Pucciniaceae. Uredo rangelii was found to be con‐specific with all isolates of P. psidii in morphology, ITS and LSU sequence data, and host range.
Matrix‐rich and associated matrix‐poor sandstones: Avulsion splays in slope and basin‐floor strata
Authors: Terlaky Viktor , Arnott Robert William Charles 
Published: November 2013

AbstractA common facies observed in deep‐water slope and especially basin‐floor rocks of the Neoproterozoic Windermere Supergroup (British Columbia, Canada) is structureless, coarse‐tail graded, medium‐grained to coarse‐grained sandstone with from 30% to >50% mud matrix content (i.e. matrix‐rich). Bed contacts are commonly sharp, flat and loaded. Matrix‐rich sandstone beds typically form laterally continuous units that are up to several metres thick and several tens to hundreds of metres wide, and commonly adjacent to units of comparatively matrix‐poor, scour‐based sandstone beds with large tabular mudstone and sandstone clasts. Matrix‐rich units are common in proximal basin‐floor (Upper Kaza Group) deposits, but occur also in more distal basin‐floor (Middle Kaza Group) and slope (Isaac Formation) deposits. Regardless of stratigraphic setting, matrix‐rich units typically are directly and abruptly overlain by architectural elements comprising matrix‐poor coarse sandstone (i.e. channels and splays). Despite a number of similarities with previously described matrix‐rich beds in the literature, for example slurry beds, linked debrites and co‐genetic turbidites, a number of important differences exist, including the stratal make‐up of individual beds (for example, the lack of a clean sandstone turbidite base) and their stratigraphic occurrence (present throughout base of slope and basin‐floor strata, but most common in proximal lobe deposits) and accordingly suggest a different mode of emplacement. The matrix‐rich, poorly sorted nature of the beds and the abundance and size of tabular clasts in laterally equivalent sandstones imply intense upstream scouring, most probably related to significant erosion by an energetic plane‐wall jet or within a submerged hydraulic jump. Rapid energy loss coupled with rapid charging of the flow with fine‐grained sediment probably changed the rheology of the flow and promoted deposition along the margins of the jet. Moreover, these distinctive matrix‐rich strata are interpreted to represent the energetic initiation of the local sedimentary system, most probably caused by a local upflow avulsion.
An Efficient Technique for Surface Strain Recovery from Photogrammetric Data using Meshless Interpolation
Authors: Godinho L. , Dias‐da‐Costa D. , Valença J. , Areias P. 
Published: November 2013

ABSTRACTIn recent years, techniques for monitoring displacements and surface strains in laboratorial tests have been introduced. Some of those methods are based on photogrammetry and image post‐processing, allowing both displacement and strain fields to be monitored at a significant number of target points at any stage.This manuscript aims at contributing by proposing a simple and comprehensive approach for monitoring experimental tests using photogrammetry. An innovative strategy is introduced to efficiently recover the strain fields at the surface of a loaded specimen. This technique is based on a meshless approach and does not require any triangulation of data points. In this approach, shape functions are constructed from radial basis function interpolation in local subdomains, for which different numbers of data points may be included. To allow accounting for the presence of generic geometries, which may include concavities or convexities, the selection of interpolating points is performed considering a line‐of‐sight algorithm, avoiding inappropriate selection of neighbouring points.A number of practical examples are here presented for different concrete specimens tested in the laboratory. The presented results indicate that the proposed method can provide smooth strain fields, which allow an easy identification of microcracking development at early stages of loading.
Quantum Walks in Brain Microtubules—A Biomolecular Basis for Quantum Cognition?
Authors: Hameroff Stuart 
Published: November 2013

AbstractCognitive decisions are best described by quantum mathematics. Do quantum information devices operate in the brain? What would they look like? Fuss and Navarro (2013) describe quantum lattice registers in which quantum superpositioned pathways interact (compute/integrate) as ‘quantum walks’ akin to Feynman's path integral in a lattice (e.g. the ‘Feynman quantum chessboard’). Simultaneous alternate pathways eventually reduce (collapse), selecting one particular pathway in a cognitive decision, or choice. This paper describes how quantum walks in a Feynman chessboard are conceptually identical to ‘topological qubits’ in brain neuronal microtubules, as described in the Penrose‐Hameroff 'Orch OR' theory of consciousness.
β‐Catenin transcriptional activity is minimal in canine osteosarcoma and its targeted inhibition results in minimal changes to cell line behaviour
Authors: Piskun Caroline M. , Stein Timothy J. 
Published: November 2013

AbstractCanine osteosarcoma (OS) is an aggressive malignancy associated with poor outcomes. Therapeutic improvements are likely to develop from an improved understanding of signalling pathways contributing to OS development and progression. The Wnt signalling pathway is of interest for its role in osteoblast differentiation, its dysregulation in numerous cancer types, and the relative frequency of cytoplasmic accumulation of β‐catenin in canine OS. This study aimed to determine the biological impact of inhibiting canonical Wnt signalling in canine OS, by utilizing either β‐catenin siRNA or a dominant‐negative T‐cell factor (TCF) construct. There were no consistent, significant changes in cell line behaviour with either method compared to parental cell lines. Interestingly, β‐catenin transcriptional activity was three‐fold higher in normal canine primary osteoblasts compared to canine OS cell lines. These results suggest canonical Wnt signalling is minimally active in canine OS and its targeted inhibition is not a relevant therapeutic strategy.
Genetic screening for PRA‐associated mutations in multiple dog breeds shows that PRA is heterogeneous within and between breeds
Authors: Downs Louise M. , Hitti Rebekkah , Pregnolato Silvia , Mellersh Cathryn S. 
Published: November 2013

AbstractObjectiveTo assess the extent of progressive retinal atrophy (PRA) genetic heterogeneity within and between domestic dog breeds.MethodsDNA from 231 dogs with PRA, representing 36 breeds, was screened for 17 mutations previously associated with PRA in at least one breed of dog. Screening methods included amplified fragment size discrimination using gel electrophoresis or detection of fluorescence, (TaqMan®; Life Technologies, Carlsbad, CA, USA) allelic discrimination, and Sanger sequencing.ResultsOf the 231 dogs screened, 129 were homozygous for a PRA‐associated mutation, 29 dogs were carriers, and 73 were homozygous for the wild‐type allele at all loci tested. In two of the 129 dogs, homozygous mutations were identified that had not previously been observed in the respective breeds: one Chinese Crested dog was homozygous for the RCD3‐associated mutation usually found in the Cardigan Welsh Corgi, and one Standard Poodle was homozygous for the RCD4‐associated mutation previously reported to segregate in Gordon and Irish Setters. In the majority of the breeds (15/21) in which a PRA‐associated mutation is known to segregate, cases were identified that did not carry any of the known PRA‐associated mutations.ConclusionProgressive retinal atrophy in the dog displays significant genetic heterogeneity within as well as between breeds. There are also several instances where PRA‐associated mutations segregate among breeds with no known close ancestry.
Defining Stem Cell Dynamics in Models of Intestinal Tumor Initiation
Authors: Vermeulen Louis , Morrissey Edward , van der Heijden Maartje , Nicholson Anna M. , Sottoriva Andrea , Buczacki Simon , Kemp Richard , Tavaré Simon , Winton Douglas J. 
Published: November 2013

Limiting Tumor InitiationWhat is the competitive advantage of cells with frequently occurring mutations during tumor development?Vermeulenet al.(p.995; see the Perspective byBozic and Nowak) quantified the advantages ofApc-loss,Krasactivation, andP53mutation during tumor initiation in the mouse intestine. The mutations conferred only a limited clonal advantage. Indeed, many mutated stem cells were stochastically replaced by wild-type stem cells, helping to limit tumor initiation.
Prevalence and Molecular Characterization of Pertactin-Deficient Bordetella pertussis in the United States
Authors: Pawloski L. C. , Queenan A. M. , Cassiday P. K. , Lynch A. S. , Harrison M. J. , Shang W. , Williams M. M. , Bowden K. E. , Burgos-Rivera B. , Qin X. , Messonnier N. , Tondella M. L. 
Published: November 2013

ABSTRACTPertussis has shown a striking resurgence in the United States, with a return to record numbers of reported cases as last observed in the 1950s.Bordetella pertussisisolates lacking pertactin, a key antigen component of the acellular pertussis vaccine, have been observed, suggesting thatB. pertussisis losing pertactin in response to vaccine immunity. Screening of 1,300 isolates from outbreak and surveillance studies (historical isolates collected from 1935 up to 2009, isolates from the 2010 California pertussis outbreak, U.S. isolates from routine surveillance between 2010-2012, and isolates from the 2012 Washington pertussis outbreak) by conventional PCR and later by Western blotting andprnsequencing analyses ultimately identified 306 pertactin-deficient isolates. Of these pertactin-deficient strains, 276 were identified as having an IS481in theprngene (prnIS481positive). The firstprnIS481-positive isolate was found in 1994, and the nextprnIS481-positive isolates were not detected until 2010. The prevalence of pertactin-deficient isolates increased substantially to more than 50% of collected isolates in 2012. Sequence analysis of pertactin-deficient isolates revealed various types of mutations in theprngene, including two deletions, single nucleotide substitutions resulting in a stop codon, an inversion in the promoter, and a single nucleotide insertion resulting in a frameshift mutation. All but one mutation type were found inprn2 alleles. CDC 013 was a predominant pulsed-field gel electrophoresis (PFGE) profile in the pertactin-positive isolates (203/994) but was found in only 5% (16/306) of the pertactin-deficient isolates. Interestingly, PFGE profiles CDC 002 and CDC 237 represented 55% (167/306) of the identified pertactin-deficient isolates. These results indicate that there has been a recent dramatic increase in pertactin-deficientB. pertussisisolates throughout the United States.
Cryo-Electron Microscopy Reconstruction Shows Poliovirus 135S Particles Poised for Membrane Interaction and RNA Release
Authors: Butan Carmen , Filman David J. , Hogle James M. 
Published: November 2013

ABSTRACT
During infection, binding of mature poliovirus to cell surface receptors induces an irreversible expansion of the capsid, to form an infectious cell-entry intermediate particle that sediments at 135S. In these expanded virions, the major capsid proteins (VP1 to VP3) adopt an altered icosahedral arrangement to open holes in the capsid at 2-fold and quasi-3-fold axes, and internal polypeptides VP4 and the N terminus of VP1, which can bind membranes, become externalized. Cryo-electron microscopy images for 117,330 particles were collected using Leginon and reconstructed using FREALIGN. Improved rigid-body positioning of major capsid proteins established reliably which polypeptide segments become disordered or rearranged. The virus-to-135S transition includes expansion of 4%, rearrangements of the GH loops of VP3 and VP1, and disordering of C-terminal extensions of VP1 and VP2. The N terminus of VP1 rearranges to become externalized near its quasi-3-fold exit, binds to rearranged GH loops of VP3 and VP1, and attaches to the top surface of VP2. These details improve our understanding of subsequent stages of infection, including endocytosis and RNA transfer into the cytoplasm.
Hypervariable Region 1 Deletion and Required Adaptive Envelope Mutations Confer Decreased Dependency on Scavenger Receptor Class B Type I and Low-Density Lipoprotein Receptor for Hepatitis C Virus
Authors: Prentoe Jannick , Serre Stéphanie B. N. , Ramirez Santseharay , Nicosia Alfredo , Gottwein Judith M. , Bukh Jens 
Published: November 2013

ABSTRACT

Hypervariable region 1 (HVR1) of envelope protein 2 (E2) of hepatitis C virus (HCV) serves important yet undefined roles in the viral life cycle. We previously showed that the viability of HVR1-deleted JFH1-based recombinants with Core-NS2 of H77 (H77
ΔHVR1
, genotype 1a) and S52 (S52
ΔHVR1
, genotype 3a) in Huh7.5 cells was rescued by E2 substitutions N476D/S733F and an E1 substitution, A369V, respectively; HVR1-deleted J6 (J6
ΔHVR1
, genotype 2a) was fully viable. In single-cycle production assays, where HCV RNA was transfected into entry-deficient Huh7-derived S29 cells with low CD81 expression, we found no effect of HVR1 deletion on replication or particle release for H77 and S52. HCV pseudoparticle assays in Huh7.5 cells showed that HVR1 deletion decreased entry by 20- to 100-fold for H77, J6, and S52; N476D/S733F restored entry for H77
ΔHVR1
, while A369V further impaired S52
ΔHVR1
entry. We investigated receptor usage by antibody blocking and receptor silencing in Huh7.5 cells, followed by inoculation of parental and HVR1-deleted HCV recombinants. Compared to parental viruses, scavenger receptor class B type I (SR-BI) dependency was decreased for H77
ΔHVR1/N476D/S733F
, H77
N476D/S733F
, S52
ΔHVR1/A369V
, and S52
A369V
, but not for J6
ΔHVR1
. Low-density lipoprotein receptor (LDLr) dependency was decreased for HVR1-deleted viruses, but not for H77
N476D/S733F
and S52
A369V
. Soluble LDLr neutralization revealed strong inhibition of parental HCV but limited effect against HVR1-deleted viruses. Apolipoprotein E (ApoE)-specific HCV neutralization was similar for H77, J6, and S52 viruses with and without HVR1. In conclusion, HVR1 and HVR1-related adaptive envelope mutations appeared to be involved in LDLr and SR-BI dependency, respectively. Also, LDLr served ApoE-independent but HVR1-dependent functions in HCV entry.
Newly Identified Phosphorylation Site in the Vesicular Stomatitis Virus P Protein Is Required for Viral RNA Synthesis
Authors: Mondal Arindam , Victor Ken G. , Pudupakam R. S. , Lyons Charles E. , Wertz Gail W. 
Published: November 2013

ABSTRACT
The vesicular stomatitis virus (VSV) RNA-dependent RNA polymerase consists of two viral proteins; the large (L) protein is the main catalytic subunit, and the phosphoprotein (P) is an essential cofactor for polymerase function. The P protein interacts with the L protein and the N-RNA template, thus connecting the polymerase to the template. P protein also binds to free N protein to maintain it in a soluble, encapsidation-competent form. Previously, five sites of phosphorylation were identified on the P protein and these sites were reported to be differentially important for mRNA synthesis or genomic replication. The previous studies were carried out by biochemical analysis of portions of the authentic viral P protein or by analysis of bacterium-expressed, exogenously phosphorylated P protein by mutagenesis. However, there has been no systematic biochemical search for phosphorylation sites on authentic, virus-expressed P protein. In this study, we analyzed the P protein isolated from VSV-infected cells for sites of phosphorylation by mass spectrometry. We report the identification of Tyr14 as a previously unidentified phosphorylation site of VSV P and show that it is essential for viral transcription and replication. However, our mass spectral analysis failed to observe the phosphorylation of previously reported C-terminal residues Ser226 and Ser227 and mutagenic analyses did not demonstrate a role for these sites in RNA synthesis.