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cc-by | Materials and Methods Sampling, library preparation and sequencing. A total of 18 samples of C. melanopterus were included from 8 different locations (Fig. 1 ): Northern Territory and Queensland, Australia (N = 11), Oman (N = 1), Philippines (N = 1), Thailand (N = 1), Malaysia (N = 1), South Kalimantan, Indonesia (N = ... | 10.1038/srep33753 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Read mapping, variant calling and filtering. A Burrows-Wheeler Aligner (BWA 50 ) was used to map reads to the reference sequence generated by de novo assembly 51. Duplicate read marking was performed with Picard v. 1. 129 (http://broadinstitute. github. io/picard/), local realignment with the Genome Analysis ToolKit... | 10.1038/srep33753 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Demographic Inference. We developed an ABC 24 framework to estimate parameters and compare demographic models. The folded site frequency spectrum (SFS) and total number of SNPs were used as summary statistics, to avoid phasing issues. Mutation and recombination rates were allowed to vary across loci using hyperprior ... | 10.1038/srep33753 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | We generated 100,000 simulations for each demographic model using fastsimcoal2 v2. 5. 1 57. Each simulation includes 995 and 998 gene genealogies for SCD and SID respectively, to be consistent with our real data. Prior distributions are displayed in Table 3 , Supplementary Tables S3 and S9. The posterior probabilit... | 10.1038/srep33753 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Analyses were performed in the R environment 54 with the library abc 59. We performed cross-validation for both model selection and parameter estimation by randomly generating pods from the prior distributions under each model. For each cross-validation experiment we generated 1000 pods and we applied the same infer... | 10.1038/srep33753 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | S4 , panel a). In this case, pods were simulated with demographic parameters estimated in our real SCD data under model CHG1, to which we added a recent bottleneck characterised by I bott and T bott. Note that here I bott represents the ratio between the ancestral effective population size Ne and the new one (while in ... | 10.1038/srep33753 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Figure1. Sampling locations with sample size. Samples in blue were included in the scatter dataset (SCD, 9 samples). Samples in orange were considered for the single deme dataset (SID, 11 samples). Map of sampling locations was generated with the library "rworldmap" with R software (v3. 0. 2, https://cran. r-project. o... | 10.1038/srep33753 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ). N anc : effective population size of the ancestral deme; T i : time of the onset of the island (in generations); Nm: product of the effective population size N and the migration rate m for each deme; SCD: scatter dataset (9 individuals); SID: single deme dataset (11 individuals); pooled dataset: SCD + SID without sh... | 10.1038/srep33753 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements The authors thank Giorgio Bertorelle and Oscar Lao for helpful comments and suggestions and Laurent Excoffier for sharing fastsimcoal v2. 5. 2 before publication. Data analysis was performed on the computer cluster Genotoul bioinformatics platform (www. bioinfo. genotoul. fr). This work was suppo... | 10.1038/srep33753 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data accessibility. A vcf file containing all variants used in this study is being submitted to the Dryad database (http://datadryad. org/). | 10.1038/srep33753 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 04 38. 61 28. 51 117. 80 U: 0. 05-250 Pooled dataset N anc 52,541 58,148 8176 84,492 U: 100-100,000 T i 65,004 18,329 4255 176,692 U: 100-200,000 Nm 58. 7 51. 4 38. 3 150. 9 U: 0. 05-250. | 10.1038/srep33753 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Peptides were separated on a BEH300 C18 (75 × 250 mm, 1. 7 mm) nanoAcquity UPLC column (Waters) using a stepwise 60-min gradient between 3% and 85% (v/v) ACN in 0. 1% (v/v) FA. Data acquisition was performed using a top-20 strategy where survey MS scans (m/z range 375-1,600) were acquired in the Orbitrap (R = 30,000) a... | 10.15252/embr.201643353 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The sample was analyzed in technical duplicates (for DSG crosslinker) or triplicates (for DSS crosslinker). To assign the fragment ion spectra, raw files were converted to centroid mzXML using the Mass Matrix file converter tool and then searched using xQuest [51] against a fasta database containing the sequences of ... | 10.15252/embr.201643353 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ITC measurements Isothermal titration calorimetry was performed with a VP-ITC Microcal calorimeter (Microcal, Northampton, MA, USA). To measure the Elp1 Elp4 interactions, Elp1 samples were dialyzed extensively against ITC buffer (20 mM Tris-HCl, pH 7. 5, 150 mM NaCl, 2 mM b-mercaptoethanol). Lyophilized synthesized pe... | 10.15252/embr.201643353 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Structural modeling As initial structures for the modeling, we used the available crystal structures of Elongator subunits or homology models if crystal structures were not available. For WD40 domains of Elp1, we built homology models based on coatomer b'-subunit (PDB code: 3MKQ, chain A) based on the alignment generat... | 10.15252/embr.201643353 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This model is predicted to be of high confidence owing to the high sequence conservation between yeast and D. mccartyi Elp3. For Elp4, Elp5, and Elp6, we used the crystal structure of Elp456 hexamer (PDB code: 4A8J). Short loops and regions missing in the structures were added to the models as flexible loops and helice... | 10.15252/embr.201643353 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Briefly, each domain was fitted using global search with an arbitrarily large number of 10,000 random initial placements and a normalized cross-correlation score as a fitting metric. The fits were then clustered, in the case of Elp123 sub-complex taking the twofold symmetry axis into account. The P-values for the cross... | 10.15252/embr.201643353 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Mapping of the sequence conservation onto protein structures was performed using ConSurf server [67] based on the multiple sequence alignments of Elp families retrieved from eggNOG database [68]. The electrostatic potential was mapped to protein structures using Pymol and APBS [69]. | 10.15252/embr.201643353 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Crystallization and structure determination of Elp2 Native and selenomethionine substituted crystals were grown at 18°C using the hanging drop vapor diffusion method. Purified Elp2 protein in gel filtration buffer was concentrated to 10 mg/ml and combined with equal volume of 100 mM Tris pH 7. 5, 10% PEG 6K, 1,750 mM N... | 10.15252/embr.201643353 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Accession numbers The atomic coordinates and structure factors for Elp2 (PDB ID 5M2N) have been deposited with the European Protein Data Bank (PDBe). The EM density maps of Elp123 (EMDB EMD-4151), holoElongator (EMD-4152), and partial Elp123 (EMD-4153) have been deposited with the EMData Bank (EMDB). Expanded View for ... | 10.15252/embr.201643353 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements We acknowledge support by the EMBL Heidelberg Crystallization Platform , the Protein Expression and Purification Core facility , and the Proteomics. | 10.15252/embr.201643353 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Even if the care episode does not concern the rare disease. Writing a systematic review about a rare diseases, or doing a short review in order to write a research article, requires querying one or more bibliographic databases with as much relevant keywords as possible [6]. It seems of public health importance to prov... | 10.1186/s12911-016-0333-0 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | PubMed overview PubMed is the most frequently used bibliographic database used by biomedical scientist throughout the world. It therefore constitute a standard in terms of information retrieval. MEDLINE is the major component of PubMed, gathering almost 90 % of the 26 millions of PubMed citations. MEDLINE curators affe... | 10.1186/s12911-016-0333-0 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Terminological queries In addition to the MeSH thesaurus, several other terminologies and ontologies are available on rare diseases: (a) a formal ontology named HRDO (Human Rare Disease Ontology) [14] was developed based on the Orphanet classification. This ontology is available in five European languages: English, F... | 10.1186/s12911-016-0333-0 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgement The authors are grateful to the DCR -Rouen University Hospital Research Center that provided funds to edit the final manuscript. The authors thank Richard Medeiros , Medical Editor -Medical Editing International for his valuable editing of the manuscript. | 10.1186/s12911-016-0333-0 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | These genera could potentially correspond to either bacteria-enriched post-mortem that may participate in decomposition or, alternatively, particular residents of the ancient oral microbiomes analyzed in this study (Supplementary Tables 2 and 3 ). All together, our results indicate that although ancient dental pulps ... | 10.1038/s41522-016-0008-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Genera found in blanks of polymerase chain reaction (PCR) and extraction were excluded from the analysis. The Jaccard distance was used to sort samples and genera. Richness was estimated using an even rarefaction of the reference-based OTU table at 1000 sequences per sample and counting the number of known genera obser... | 10.1038/s41522-016-0008-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | As an additional filter, these sequences were then compared against the full NCBI database and only sequences that showed 100 % similarity against non-ambiguous species (i. e. , only showed perfect hit against the same species that in PATRIC DB) were conserved. Bacteria that are commonly associated with oral pathologie... | 10.1038/s41522-016-0008-8 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGEMENTS This work was done under a "management of talents" fellowship from the A*MIDEX foundation awarded to CD. All authors read and approved the final version of the manuscript. | 10.1038/s41522-016-0008-8 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Localization microscopy using confocal fluorescence imaging of nuclear pore complexes is a super-resolution microscopic technique 'Localization microscopy' relies on detection of the centroid of point-like structures, and is classically not limited by diffraction, but by the signal-to-noise ratio of individual detectio... | 10.1242/jcs.188250 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | , 1997). Importantly, detection of 22 spots per nucleus provided sufficient connecting points to evaluate the nuclear envelope position in 3D. Refractive index mismatch between optical setup and biological object is known to generate spherical aberration along the z-axis (Fig. 1A, B ). We measured and corrected this de... | 10.1242/jcs.188250 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In a sphere, distances between detected cNPCs and the nuclear center are the same in each dimension (x, y and z) (Fig. S1A, C ). Simulating the elongation along the z-axis (Fig. S1A, B ) modified the distribution of normalized distances between detected cNPCs and nuclear center along the x, y and z axes (compare Fig. S... | 10.1242/jcs.188250 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | However, data collection of serial sections analyzed by TEM is a time-consuming technical performance and has been reported for sampling of less than 100 nuclei (Winey et al. , 1997). Innovative imaging techniques, relying on cryo-fixation but with less tedious exploration of 3D space, as highvoltage scanning transmi... | 10.1242/jcs.188250 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | NucQuant: post-acquisition correction of z aberration Confocal images were processed and analyzed with MATLAB (MathWorks) script NucQuant, a modified version of nucloc (http://www. nucloc. org/). We calculated the distances between the nuclear center and the cNPCs. For each nucleus these distances were normalized by nu... | 10.1242/jcs.188250 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | NPC clustering by k-means To reconstruct the nuclear envelope, we measured the distribution of NPCs in the clusters. After extracting the NPC positions and correcting the z aberration (x i , y i , z i ), we used the k-means clustering method with Euclidian squared distance (MATLAB) to group the NPCs in different cluste... | 10.1242/jcs.188250 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements We are grateful to Michael Pilsl and Jorge Perez-Fernandez for strain construction and initial characterization of the nuclear shape. We thank Aureĺien Bancaud for helpful advice. This work benefited from the assistance of the imaging platform of Toulouse TRI. | 10.1242/jcs.188250 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data availability The NucQuant software implementing the methods described in this paper is available to download at GitHub (https://github. com/ogadal/nucquant). | 10.1242/jcs.188250 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Data were obtained as OD and given as % of control, with control = cell in complete medium and, % of control = (OD sample/OD mean of control) ×100. [ 3 H]-Thymidine incorporation. Cells were inoculated into round-bottom 96-well plates at 2. 5 × 10 4 cells per well in of 200 μ L, stimulated under various conditions and ... | 10.1038/srep26162 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Mouse antibodies for MARCO (Clone ED31) and CD204 (Clone 2F8) were from AbD Serotec. Mouse antibody for CD36 (Clone HM36) was from Biolegend. Human antibodies for CD90 (Clone DG3), CD105 (Clone 43A4E1), CD73 (Clone AD2), CD34 (Clone 581), CD45 (Clone 5B1) and CD14 (Clone M5E2) were from Becton Dickinson. Detection of p... | 10.1038/srep26162 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ELISA data are given as picogram (intracellular cytokine) per milligram (pg/mg) total protein. ELISA. Samples for ELISA were supernatants or cell lysates of cells stimulated under conditions with cells plated at 10 6 cells in 1 mL final volume per well, in 24-well plates. Cell culture supernatants or cell lysates or bi... | 10.1038/srep26162 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical analysis. Data are given as mean ± SEM, unpaired t test or one-way ANOVA with a multiple comparison test were performed using GraphPad Prism 5. 0 (GraphPad Software, Inc). P < 0. 05 was considered statistically significant. | 10.1038/srep26162 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements This study was supported by the Program to Disseminate Tenure Tracking System of the Ministry of Education, Culture, Sports, Science and Technology (MEXT), Japan. This work was supported by intramural funding to A. N. from Kochi Medical School (KMS) , Kochi University, Japan. | 10.1038/srep26162 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | e. , <1 mm interaction range) before hard-wall contact were used for further analysis. Force curves on the COC were acquired at desired positions, with a lateral resolution of a few micrometers (determined by the accuracy of the microscope's manual xy translation stage) and an accuracy in the distance from the glass su... | 10.1016/j.bpj.2016.03.023 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For in vivo expanded matrix, it adds another 200 mm to the total thickness. For in vitro expansion, the cell-free coat remains appreciable but its thickness reduces by 50%, indicating that factors in the follicle that are not present in vitro might play an important role in the formation of this part of the matrix. To ... | 10.1016/j.bpj.2016.03.023 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS We thank Luis Yate ( CIC biomaGUNE ) for the preparation of gold-coated glass coverslips, and Lionel Bureau ( Laboratory of Interdisciplinary Physics ) and Jessica Kwok ( University of Leeds ) for fruitful discussions. This work was supported by the European Research Council Starting Grant JELL... | 10.1016/j.bpj.2016.03.023 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS We thank Luis Yate ( CIC biomaGUNE ) for the preparation of gold-coated glass coverslips, and Lionel Bureau ( Laboratory of Interdisciplinary Physics ) and Jessica Kwok ( University of Leeds ) for fruitful discussions. This work was supported by the European Research Council Starting Grant JELL... | 10.1016/j.bpj.2016.03.023 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In Situ Apoptosis RPE flat mounts were fixed in 4% paraformaldehyde (PFA) and permeabilized with 0. 1% Triton X-100 and 0. 1% sodium citrate for 7 min followed by incubation in sodium citrate buffer (10 mM sodium citrate, 0. 5% Tween 20, pH 6. 0) for 1 min at 86 °C. Apoptosis was detected by the terminal deoxynucleotid... | 10.1016/j.ebiom.2016.03.048 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Detection of Intracellular ROS The in situ production of ROS in the RPE was assessed using dihydroethidium (DHE, structure is provided in Supplemental Fig. 1a ) staining. RPE flat mounts were fixed in 4% PFA and mounted on gelatin-coated slides. In a dark chamber, RPE was loaded with 5 μM DHE for 30 min at room tempera... | 10.1016/j.ebiom.2016.03.048 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Conventional PCR For the PCR reaction, specific sense and antisense primers were selected (Table 1 ), based on GenBank TRP sequences, using GeneJockey II (Biosoft, Cambridge, UK). Each sample was amplified using Maxima SYBR Green/ROX qPCR Master Mix (Thermo Scientific, Auburn, AL) in an automated thermal cycler (Bio-R... | 10.1016/j.ebiom.2016.03.048 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Ca 2+ Imaging For Ca 2+ imaging studies, ARPE-19 cells at confluence were plated onto round coverslips covered with poly-L-lysine (10 μg/ml, Sigma Chemical) and incubated in the dark with 10 μM fluo 8-AM (Invitrogen) dissolved in the extracellular buffer containing: 150 mM NaCl, 20 mM HEPES, 0. 1 mg/ml bovine serum alb... | 10.1016/j.ebiom.2016.03.048 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Statistical Analysis In general, all results were replicated in three or more independent experiments. The number of replicates (n) in each experiment and how often it was independently repeated (N) is indicated in each figure legend. Serum PRL levels are reported as mean ± S. D. and all others as mean ± S. E. M. ; all... | 10.1016/j.ebiom.2016.03.048 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements We would like to thank M. Diaz Muñoz and M. Flourakis for insights. R. Meléndez García , D. Arredondo Zamarripa , E. Arnold , X. Ruiz-Herrera , G. Baeza Cruz , and N. Adán are Master's and Doctoral students from Programa de Posgrado en Ciencias , Universidad Nacional Autónoma de México (UNA... | 10.1016/j.ebiom.2016.03.048 | article | en | 2,016 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Guinea-Pig Isolated Urinary Bladder Guinea-pigs were sacrificed by cervical dislocation, to avoid the possible effect of anesthetics on bladder smooth muscle response and/or drugs tested in experiments. The whole urinary bladder was excised and the detrusor muscle was dissected free from connective tissue and urotheliu... | 10.3389/fphar.2016.00234 | article | en | 2,016 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Cystometric Studies Guinea-pigs were anesthetized with urethane 1. 5 g/kg (i. p. ), a tracheotomy was performed and a PE cannula was inserted into the trachea. A polyethylene catheter (0. 3 and 0. 7 mm of internal and outer diameters, respectively) was implanted into the bladder through the dome. A catheter (0. 58 and ... | 10.3389/fphar.2016.00234 | article | en | 2,016 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Data were analyzed with Chart and Microsoft Excel softwares. At the end of the cystometric experiments, animals were killed by a lethal dose (100 mg/kg, i. p. ) of pentobarbital followed by cervical dislocation. | 10.3389/fphar.2016.00234 | article | en | 2,016 | false | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Acknowledgments V. A. acknowledges the French Referral Center for FAP and Other Rare Peripheral Neuropathies (NNERF) , the Labex LERMIT , and the French Federation of Cardiology as institutional funding sources. | 10.1111/ajt.13755 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | net). Alignment around indels was then improved using GATK ver. 3. 2 (refs 45,46). The average coverage per genome was about  17 and  30 for the parental light and dark lines, respectively,  44 and  80 for BC7 and NN introgression lines, respectively, and  21 for D. orena. Genome mapping. The PoPoolation2 ver. 1. ... | 10.1038/ncomms10400 | article | en | 2,016 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Dark strain ancestry proportion was averaged across SNPs within 100 kb windows. As a quality filter, windows with fewer than 1 fixed difference per 1,000 sites between the parental strains were excluded as potentially identical-by-descent between these strains. Genetic distances (D xy ) were then compared between the t... | 10.1038/ncomms10400 | article | en | 2,016 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | This tree was used to define the light and dark haplogroups. For each locus, DNA polymorphism was analysed using DnaSP ver. 5. 10. 1 (ref. 49). We estimated genetic differentiation (F ST ) within and between the two populations and the two haplogroups, as well as genetic divergence (D xy ) between the two haplogroups a... | 10.1038/ncomms10400 | article | en | 2,016 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The BEAST v. 1. 8 software package 53 was used to infer the phylogenetic relationships between the sequences. A run of 10,000,000 generations under the coalescence model was conducted and sampled every 1,000 generations. A burn-in period of 2,500 generations was used. Divergence times were estimated by assuming the m... | 10.1038/ncomms10400 | article | en | 2,016 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgements We thank four anonymous reviewers for constructive comments, S. B. Carroll for discussion, the late D. Lachaise for collections of initial D. erecta lines, the late N. Bangart and M. J. Monette for laboratory assistance and J. B. Lack for bioinformatic assistance. Funding was provided by the ... | 10.1038/ncomms10400 | article | en | 2,016 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | In summary, we present preclinical evidence demonstrating that CLU-KD significantly augments the anti-tumor activity of cabazitaxel in a mCRPC model. These preclinical data support the current phase III study of OGX-011 in combination with cabazitaxel as a second-line treatment of mCRPC (NCT01578655; clinicaltrials. go... | 10.15252/emmm.201506059 | article | en | 2,016 | false | false | false | true | Medicine | https://openalex.org/fields/27 |
cc-by | Cell impedance assay (xCELLigence RTCA) PC3 cells were seeded overnight 24 h after CLU silencing at 10,000 cells/well in 96-well E-plates (Roche). Measurements were taken continuously for ~60 h at 37°C. The RTCA software was used for data analysis, with statistical analysis using GraphPad Prism 5. 0c (GraphPad Software... | 10.15252/emmm.201506059 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Flow cytometry analysis Fixed synchronized cells were treated with 20 lg DNase-free RNase for 30 min and stained with propidium iodide (10 lg/ml) for 1 h. The percentage of cells in G1, S, G2, M, and sub-G1 phases was quantified using FACSCanto (Becton Dickinson) and analyzed with Cyflogic software. For phosphohistone ... | 10.15252/emmm.201506059 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Oligo microarray technology Total RNA quality was assessed with the Agilent 2100 bioanalyzer prior to microarray analysis. Samples with a RIN value of ≥ 8. 0 were deemed acceptable for microarray analysis. Samples were prepared following Agilent's One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp ... | 10.15252/emmm.201506059 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | The images produced by each array were captured with a Perkin-Elmer ScanArray Reader laser array scanner (Waltham, MA). Signal quantification was performed with ImaGene 9. 0 from BioDiscovery (El Segundo, CA). The background-corrected raw intensity data were logarithmically transformed with base 2. Since Z normalizatio... | 10.15252/emmm.201506059 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Statistical analysis The in vitro data were assessed using Student's t-test, ANCOVA, ANOVA and the Mann-Whitney test. The t-test was followed by Welch's correction when equal variance was not assumed. ANOVA was followed by a post hoc Bonferroni analysis. ANOVA followed by Dunnett's post hoc analysis was used to compare... | 10.15252/emmm.201506059 | article | en | 2,016 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | and a 40% mean increase in population of G2/M cells (Fig 1B). To further investigate the role of CLU in cell cycle regulation, microarray transcriptome analysis was performed on PC3 cells transiently transfected with siRNA targeting clusterin mRNA (siCLU) or scramble RNA (siSCR). As shown in Fig EV1A, differential expr... | 10.15252/emmm.201506059 | article | en | 2,016 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgements This project was supported by a Terry Fox New Frontiers Program Project Grant TFF116129 , a Prostate Cancer Foundation of British Columbia (PCFBC) Grant 2013 , and a Prostate Cancer Canada Team Grant T2013-01. We would like to thank Mr. Dulguun Battsogt for his technical support and Mr. Rob... | 10.15252/emmm.201506059 | article | en | 2,016 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | 5 nm). This implies a partial membrane protein coverage. To calculate the mass of protein deposited per unit surface, we calculate L, the number of moles per volume with the following equation: = × L 1/(N V ), A p rot where N A is the Avogrado number and Vprot is the volume of the protein (approximated to a cylinder of... | 10.1038/srep36181 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Then if all molecules added bind to the surface of the prism, the TIR will return to its initial position while p-and s-polarizations resonances will evolve according to the change of mass density and anisotropy induced by the binding. Upon saturation of the system with the molecular partner, the TIR starts to increase... | 10.1038/srep36181 | article | en | 2,016 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In terms of data analysis, quantitative information on the affinity (anywhere from pM to mM) or kinetics (msec) can be obtained (this is further described in sections 2. 4 and 2. 5). Another type of analysis is possible that consists in spectral simulation to obtain all optical parameters that characterize a PWR spectr... | 10.1038/srep36181 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Cleared lysate samples were incubated at 4 °C for 3 hours with 300 nM 3 H-Cpd1 (an antagonist for the CCR5 receptor 57 ) in the presence of unlabelled competitors indicated (maraviroc and Cpd1) or a DMSO vehicle control. Unbound radioligand was then separated by size exclusion chromatography prior to reading bound ra... | 10.1038/srep36181 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For polarized ATR-FTIR experiments, the reconstitution process was performed in the same manner, the only difference being that the chamber is of about 200 μ L rather than 280 μ L. After incubating the protein with the lipid membrane during 1 h, the excess of detergent and non-inserted receptor is washed out with buffe... | 10.1038/srep36181 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The first concentration point was chosen to be approximately 1 order of magnitude lower than the published dissociation constant (K D ) value for that ligand. Incremental amounts of ligand were then added in a cumulative fashion, and the PWR spectra were acquired for each point when equilibrium was reached (i. e. , whe... | 10.1038/srep36181 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements M. De Maria and N. Tschammer thank to Graduate Training School GRK1962 of German Research Foundation (DFG) for the financial support. N. T. participates in the European COST Action CM1207 (GLISTEN: GPCR-Ligand Interactions, Structures, and Transmembrane Signalling : a European Research Network).... | 10.1038/srep36181 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | METHODS The European Group for Blood and Marrow Transplantation (EBMT) (www. ebmt. org) is a nonprofit organization established in 1974 to allow scientists and physicians involved in clinical SCT to share their experience and develop cooperative studies. The EBMT is divided into working parties, whose mission is the im... | 10.1016/j.bbmt.2015.12.011 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | EBMT centers, which are homogenously distributed through European countries, are required to send patient data to the central EBMT database on a yearly basis. There are 2 levels of data: minimal essential data type A, which are compulsory and considered major items, such as demographic data, disease classification, typ... | 10.1016/j.bbmt.2015.12.011 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | DFS and OS rates were measured from the date of surgery to the date of last follow-up or death and the date of relapse, respectively. TRM was defined as mortality from any cause other than disease progression within 365 days of transplantation. NRM was defined as mortality from any cause other than disease progression ... | 10.1016/j.bbmt.2015.12.011 | article | en | 2,015 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | RESULTS Among adjuvant patients with BC reported in the EBMT registry, 583 patients with 4 or more involved nodes at surgery were available for OS analysis and represent the body of this article. Informed consent to collect and register data to the EBMT record was obtained from participants. The baseline patient and tr... | 10.1016/j.bbmt.2015.12.011 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | DISCUSSION The present study, reporting a retrospective data analysis on HDC and AHSCT for high-risk BC in Europe, includes 1 of the largest series in this field. Because it comes from a registry and derives from patients transplanted in many cases when only limited information on tumor biology was available, many para... | 10.1016/j.bbmt.2015.12.011 | article | en | 2,015 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | HeLa cells were treated with BI2536 or with DMSO vehicle for 2 h before CLM treatment for 1 hour and were then incubated for different time periods in presence or absence of BI2536. As shown in Figure 2A , large BRCA1 foci were efficiently formed in control cells 2 h following CLM treatment. However, when cells were p... | 10.18632/oncotarget.6825 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Plk1-BRCA1 complex formation is dependent on CDK1 activity Since our data showed that Plk1 is necessary for efficient BRCA1 foci formation upon DNA damage, we next investigate whether BRCA1 can form a complex with Plk1. We assessed the co-immunoprecipitation of BRCA1 and Plk1 using antibodies against either protein in ... | 10.18632/oncotarget.6825 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | As expected, a much higher level of 32 P incorporation was obtained onto recombinant BRCA1 using Plk1 immunoprecipitated from cells that were synchronized in mitosis using paclitaxel (PTX) (Figure 4D ) since the maximal activity and expression of Plk1 coincide with the G2/M cell cycle phases [39]. Phosphorylation of ... | 10.18632/oncotarget.6825 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 40 oil immersion lens or a Plan-Apochromat 40X 0. 95 lens and 405-, 488-and 559nm lasers excitation. Images were taken with the same exposure time when comparing experimental conditions and were analyzed using Image J software (NIH). | 10.18632/oncotarget.6825 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Statistical analysis Results are presented as the mean ± SEM with significance calculated by two-tailed Student's t or Chisquare tests with standard software (GraphPad Prism, GraphPad Software, La Jolla, CA, USA). Significance was assigned for a P-value < 0. 05. *, P < 0. 05; **, P < 0. 01; ***, P < 0. 001. | 10.18632/oncotarget.6825 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ACKNOWLEDGMENTS We wish to thank Dr. N. Foray ( CRCL, Lyon, France ) for providing the GST-tagged BRCA1 constructs, Dr. J. H. Chung ( NHLBI, NIH, Bethesda, USA ) for the HA-tagged wtBRCA1 vector, Dr J. M. Stark ( Beckman Research Institute, Duarte, CA, USA ) for the HEK/DR-GFP cell line and Dr N. Puget ( LBCMCP... | 10.18632/oncotarget.6825 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Femtosecond transient absorption measurements Transient absorption measurements on the femtosecond time scale were performed at RT essentially as described earlier (Gibasiewicz et al. 2009) using the 1 kHz femtosecond laser system (Ti:sapphire, Spectra Physics) and a grating polychromator (Spectra Pro 150, Acton Rese... | 10.1007/s11120-016-0239-9 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This way, the experiments took less time that was essential for maintaining RCs in fully closed state all the time during the measurements. The temporal evolution of the transient absorption spectra was subjected to global and target analysis (Holzwarth 1996; van Stokkum et al. 2004 ) using the software package Asufit... | 10.1007/s11120-016-0239-9 | article | en | 2,016 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Femtosecond transient absorption measurements from 400 to 700 nm In order to verify the above considerations on the different sizes of the initial free energy gap between P ? B A -and the unrelaxed (P ? H A -) 1 state, RT femtosecond transient absorption measurements were performed over 2 ns and in a wide 400-700 nm sp... | 10.1007/s11120-016-0239-9 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In brief, assuming that the 20 ns SADS is contributed to exclusively by relaxed state (P ? H A -) 2 (with the band at *545 nm assigned to H A -and the band at *600 nm assigned to P ? ), the ''excess'' of the photobleaching signal of the *600 nm band in the fast charge recombination SADS (0. 49-1. 6 ns) relative to the ... | 10.1007/s11120-016-0239-9 | article | en | 2,016 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements K. G. acknowledges financial support from the National Science Center, Poland (project entitled '' Bio-semiconductor hybrids for photovoltaic cells '' No. 2012/07/B/NZ1/02639. MRJ acknowledges funding from the Biotechnology and Biological Sciences Research Council of the UK (Project BB/I022570/1 )... | 10.1007/s11120-016-0239-9 | article | en | 2,016 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 30) reports: r. m. s. d. between C␣ atoms of MotA and similar PBP structures are Ͼ2. 2 Å with sequence identity around 17-29%. The closest structure (r. m. s. d. of 1. 8 Å Ͼ301 C␣ atoms and 32% sequence identity) is that of A. tumefaciens Atu4243 in complex with GABA (PDB code 4EUO) (28). The two x-ray structures of t... | 10.1074/jbc.m116.745562 | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 46 Å). SocA belongs to cluster F (29) and resembles several PBPs from the same cluster, which mainly bind amino acids or derivatives of amino acids such as ArtI from Caldanaerobacter subterraneus and STM4351 from Salmonella enterica, both in complex with arginine (PDB codes 4YMX and 2Y7I with r. m. s. d. of 1. 14 Å and... | 10.1074/jbc.m116.745562 | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | SocA Is Present in Numerous Bacteria-SocA relatives search in the bacterial kingdom (protein database at NCBI), and subsequent phylogenetic analysis reveals Ͼ240 PBPs with conserved DFG binding signature. To refine this analysis, we reconstructed a phylogeny with the SocA relatives extracted from the complete genome NC... | 10.1074/jbc.m116.745562 | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Crystals were transferred to a cryo-protectant solution (paraffin oil or 22% (w/v) PEG 400) and flash-frozen in liquid nitrogen. Diffraction data were collected at 100 K on the PROX-IMA I and II beamlines at SOLEIL synchrotron (Saint-Aubin, France). Data collection and processing statistics are given in Table 1. All s... | 10.1074/jbc.m116.745562 | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Each ligand had no emission signal at 335 nm. The data were analyzed using Origin 7 software (ORIGIN) and fitted to the equation f ϭ ⌬Fluorescence max ϫ abs(x)/(KD ϩ abs(x)), where KD indicates the dissociation constant, abs indicates absolute value, and x indicates ligand concentration. Isothermal titration microcalor... | 10.1074/jbc.m116.745562 | article | en | 2,016 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | This software uses the relationship between the heat generated by each injection and ⌬H (enthalpy change in Kcal⅐mol Ϫ1 ), K a (the association binding constant in M Ϫ1 ), n (the number of binding sites), total protein concentration, and free and total ligand concentrations. Phylogenetic Analysis-Sequences were analyze... | 10.1074/jbc.m116.745562 | article | en | 2,016 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgments-This work has benefited from the I2BC crystallization platform and @TOME-2, both supported by FRISBI ANR-10-INSB-05-01. We acknowledge SOLEIL for provision of synchrotron radiation facilities (proposals ID 20130869 and 20140774) in using Proxima beamlines. We are grateful to Gavin Fox for critical rea... | 10.1074/jbc.m116.745562 | article | en | 2,016 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | 9 31. 5 50. 6 Protein Crystallization conditions PDB code Space group Cell parameters (Å,°) R sym (%) Completeness (%) I/ CC 1/2 R cryst (%) R free (%) ) Average B (Å 2 Protein Ligand Solvent Values for the highest resolution shell are in parentheses. CC 1/2 , percentage of correlation between intensities from random h... | 10.1074/jbc.m116.745562 | article | en | 2,016 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
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