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cc-by | " (F) Graph showing centrosome reorientation with the wound edge cells expressing the indicated constructs. Data are given as means ± SD of three independent experiments, with a total of ≥100 cells. (G) HeLa cells were transfected with the indicated constructs. (left) After 16 h, cells were fixed and stained with the i... | 10.1083/jcb.201206010 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Colocalization of IFs, APC, and microtubules was quantified using the ImageJ software (National Institutes of Health). Statistical analysis was performed using a Student's t test. IF organization in astrocytes. The astrocyte monolayer was scratched, and front cells were immediately microinjected. Cells were fixed after... | 10.1083/jcb.201206010 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Fig. S3 shows that the role of APC in IF organization does not involve -catenin-mediated transcription or APC function at microtubule plus ends and is not correlated with APC-mediated regulation of microtubule stability. Table S1 shows the sequences of the various siRNA used in this study. Online supplemental mater... | 10.1083/jcb.201206010 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Machu and P. Roux from the Plate-Forme d'Imagerie Dynamique/Imagopole of Institut Pasteur, D. Vignjevic and S. Robine for technical support, and S. Carbonetto and J. -B. Manneville for critical reading of the manuscript. Y. Sakamoto is funded by the Uehara Memorial Foundation, and B. Boëda is supported by Institut Nati... | 10.1083/jcb.201206010 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Machu and P. Roux from the Plate-Forme d'Imagerie Dynamique/Imagopole of Institut Pasteur, D. Vignjevic and S. Robine for technical support, and S. Carbonetto and J. -B. Manneville for critical reading of the manuscript. Y. Sakamoto is funded by the Uehara Memorial Foundation, and B. Boëda is supported by Institut Nati... | 10.1083/jcb.201206010 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 02. 003 Bershadsky, A. D. , E. A. Vaisberg, and J. M. Vasiliev. 1991. Pseudopodial activity at the active edge of migrating fibroblast is decreased after druginduced microtubule depolymerization. Cell Motil. Cytoskeleton. 19:152-158. http://dx. doi. org/10. 1002/cm. 970190303 Bugyi, B. , and M. F. Carlier. 2010. Contro... | 10.1083/jcb.201206010 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | IFNa/v-DC and IFNb-DC show differential gene expression profile Monocytes were differentiated into DC using GM-CSF and different type I IFN subtypes. In order to investigate effects not caused by different specific activities in inducing early transcriptional response, IFN concentrations were adjusted as described in t... | 10.1371/journal.pone.0058465 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Monocytes from three independent donors were differentiated into DC with IFNa1, a2, a8, a21 or v, and expression of VSIG4, CXCL11, CLEC5A and IDO1 was measured. The results obtained confirmed that all IFNa subtypes are equipotent in regulating the expression of these genes and showed that the IFNv-DC is closely related... | 10.1371/journal.pone.0058465 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Measurement of cell surface markers characteristic of DC differentiation state Expression of cell surface markers characteristic of DC differentiation state was measured by flow cytometry on a FACS CANTO instrument using the following antibodies: CD14-FITC, CD83-FITC, CD80-PE, CD86-APC, HLA-DR-FITC, HLA-ABC-PE, CD40-AP... | 10.1371/journal.pone.0058465 | article | en | 2,013 | false | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | RNA isolation and Affymetrix GeneChip processing Total RNA was isolated from IFN-DC using the High pure RNA isolation kit according to manufacturer's instructions (Roche Diagnostics, France). RNA quality was assessed on an Agilent 2100 bioanalyzer. 200 ng of total RNA from each sample was prepared for hybridization wit... | 10.1371/journal.pone.0058465 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Hierarchical clustering was applied to one axis (array) using the weighted pair-group method with centroid average as implemented in the program Cluster [45]. The results were analysed with Tree View [45]. Microarray data were analyzed according to a previously described procedure [20] , which allows on the one hand... | 10.1371/journal.pone.0058465 | article | en | 2,013 | false | true | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Multiplex analysis of chemokines Chemokines in the cell culture supernatant were simultaneously measured using Luminex xMAP technology (Austin, TX, USA) and commercially available antibody beads, according to manufacturer's recommendations (Human Chemokine 10-Plex pane-l+IL8 from Invitrogen; Milliplex MAP kit Human I-T... | 10.1371/journal.pone.0058465 | article | en | 2,013 | true | false | false | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Acknowledgments We thank Sandra Pellegrini , Mark Livingstone and Frederique Michel for critical reading of the manuscript, Maria Ferrantini , Stefano Santini , Caterina Lapenta , Sylvie van der Werf and Guillaume Cartron for helpful discussions, Christophe Duperray for his assistance in FACS sorting, Ma... | 10.1371/journal.pone.0058465 | article | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Funding was from the European Community 's Seventh Framework Programme under grant agreement nu 223608 (GU and JP). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. | 10.1371/journal.pone.0058465 | article | en | 2,013 | false | false | true | false | Immunology and Microbiology | https://openalex.org/fields/24 |
cc-by | Replication of the in-cis miRNAs in an independent breast cancer cohort In order to validate the 70 identified in-cis miRNAs, miRNA expression and copy number data from an independent breast cancer cohort consisting of 123 breast cancer patients were analyzed. In addition, 26 in-cis miR-NAs were selected for methylatio... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The number in parentheses under aberration type represents the number of in-cis miRNAs in the given aberration category. Inter-chromosomal and intra-chromosomal lines (the latter is seen as independent lines on chromosomes 8 and 13) link in-cis miRNAs to other members of the same miRNA family (see legend). miRNA family... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Materials and methods All computational analyses were performed in R v. 2. 13. 0 [71] unless otherwise specified. The miRNA copy number, methylation and expression data analyzed in this work are available in Additional file 10 for the discovery cohort and Additional file 11 for the replication cohort. All experimenta... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | miRNA expression profiling The miRNA expression profiling for the discovery and replication cohort was performed using the 8x15k 'Human miRNA Microarray Kit (V2)' with design id 019118 from Agilent (Agilent Technologies, Santa Clara, CA, USA). In brief, 100 ng total RNA was dephosphorylated, labeled and hybridized for ... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | miRNAs that were detected in less than 10% of the samples were excluded. In the discovery cohort this resulted in 461 unique mature miRNAs. When a mature miRNA is encoded several places in the genome, the genomic origin of a transcript cannot be directly inferred from miRNA expression microarrays (unless the pre-miRNAs... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | DNA copy number analysis The DNA copy number data for the discovery cohort were generated using Illumina Human-1 109 k BeadChip SNP arrays (Illumina) and are described in [82]. For the replication cohort, the Comparative Genomic Hybridization 244 k Agilent Microarrays (Agilent Technologies) were used [83]. Copy numbe... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | mRNA expression profiling The mRNA expression data for the discovery dataset were measured using Agilent 4x44K one-color oligonucleotide arrays (Agilent Technologies) and have previously been published [4] and submitted to GEO with accession number GSE19783. For the replication dataset the mRNA was measured using the... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | , Danvers, MA, USA), respectively, followed by exposure to Alexa Fluor 680-tagged secondary antibodies (Invitrogen Inc. ). For total protein measurement, the arrays were stained with Sypro Ruby Blot solution (Invitrogen Inc. ). The slides were scanned with Tecan LS400 (Tecan Inc. , Durham, NC, USA) microarray scanner a... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Network analysis using IPA Networks containing mRNAs correlated to candidate miRNAs were generated with IPA (Ingenuity Systems) [93]. For each candidate miRNA, a dataset containing the list of all the positively correlated (Spearman's rho >0. 3) and negatively correlated (Spearman's rho < -0. 3) mRNAs (overlapping bot... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | It takes a set of gene identifiers as input and finds genes that are co-expressed in the compendium with the input genes. We first utilized SEEK to determine the extent to which the mRNAs that we identified as positively or negatively correlated to each candidate miRNA were supported by other datasets. We input the lis... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements MRA had a PhD fellowship from the Norwegian Research Council (grant number 193387/V50 ). This work was supported by grants from the Norwegian Research Council (grant numbers 183621/S10 and 175240/S10 ), the Norwegian Cancer Society (grant numbers 419616 and 419628 ) and the KG Jebsen Cent... | 10.1186/gb-2013-14-11-r126 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | However, with the increasing number of whole cp genome available, many structural rearrangements, large IR expansion and gene loss have been reported [2, 5, 6]. These events can be used for the reconstruction of plant phylogeny [7]. Besides, the availability of whole chloroplast genomes or complete sets of cp genes h... | 10.1371/journal.pone.0067350 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Sequence Data A reference nuclear genome sequence of the doubled-haploid Pahang accession (DH-Pahang) was produced based on DNA extraction enriched in nuclear content. A total of 27,495,411 reads were generated using Roche/454 GSFLX pyrosequencing platform. An addition of 1,069,954 paired-Sanger 10 kb insert-size reads... | 10.1371/journal.pone.0067350 | article | en | 2,013 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Genome Annotation The genome was annotated by using DOGMA [20] , followed with manual corrections for start codons. Intron positions were determined based on those of P. dactylifera [21] and Elaeis guineensis [22]. The transfer RNA genes were annotated using DOGMA and tRNAscan-SE (version1. 23) [23]. Some intron-co... | 10.1371/journal.pone.0067350 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Codon Usage Codon usage frequencies and the relative synonymous codon usage (RSCU) was calculated from coding sequences (CDS) of all different protein coding genes in the M. acuminata chloroplast genome using seqinr R-cran package [24]. | 10.1371/journal.pone.0067350 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Phylogenetic Analysis The phylogeny was performed using 79 plastid protein-coding genes derived from 48 plant species (Table S1 ) with complete chloroplast sequence, most belonging to monocotyledons. A codon based alignment was performed for each gene using homemade scripts that grouped together homologous genes and t... | 10.1371/journal.pone.0067350 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Musa Chloroplast Structure Comparison with others Whole cp Genomes Gene positions of the different cp genomes were collected from the Genbank file and ordered based on their positions within the genome. Gene order and composition were then compared between the different species. Large events, e. g. gene loss, IR gene g... | 10.1371/journal.pone.0067350 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgments We thank the SouthGreen Bioinformatics Platform -UMR AGAP -CIRAD (http://southgreen. cirad. fr)for providing us with computational resources. We thank Dr Jim Leebens-Mack for critical reading of the manuscript. | 10.1371/journal.pone.0067350 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | This is why, in this manuscript, data from the surface and data along the water column are addressed separately (e. g. for principal component analysis). From station 5, the sampling depths were de- cided based on the chlorophyll a profile measured with an in situ fluorometer during the downward cast. Due to the maxima... | 10.5194/bg-10-5947-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Altimetry and large scale climatic condition The altimeter data (sea level anomaly) were produced by Ssalto/Duacs and distributed by Aviso, with support from CNES (http://www. aviso. oceanobs. com/duacs/). The sea level anomaly map centred on the 18/01/2011 (the process generates maps compiling data collected six weeks... | 10.5194/bg-10-5947-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The flow cytometer is equipped with a blue (488 nm) air-cooled argon laser and a red (634 nm) diode laser. For each particle (cell), five optical parameters were recorded: two light scatter signals, namely forward and right angle light scatter, and three fluorescences corresponding to emissions in green (515- 545 nm), ... | 10.5194/bg-10-5947-2013 | article | en | 2,013 | true | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Statistical analyses Statistical analyses were performed using the R software (vegan package) and Biplot macro for Excel ® (Lipkovich and Smith, 2002). Kruskal-Wallis tests were performed in order to compare the abundances of ultraphytoplankton at the various sampling stations. To analyse the multivariate dataset, pri... | 10.5194/bg-10-5947-2013 | article | en | 2,013 | true | true | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Choice of two different PCAs was motivated by the lack of sampling point below the seawater surface from stations 1 to 4. Station 12 was not included in the PCA performed on the vertical profiles because several variables were missing. In addition to the PCA, the relationships between phytoplankton communities and envi... | 10.5194/bg-10-5947-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | The first axe is negatively correlated with temperature and salinity representing the mesoscale circulation. The second axe is negatively correlated with nutrient concentrations which represent the different conditions between the samples collected at surface or deeper in the water column. Partial redundancy analysis (... | 10.5194/bg-10-5947-2013 | article | en | 2,013 | true | false | false | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | Acknowledgements. We thank Captain Akira Noda , crew members, and scientists of the RT/V Shinyo Maru of Tokyo University of Marine Science and Technology, (TUMSAT) for their cooperation at sea. We are grateful to Yuta Nakagawa for his help during the cruise. We are also grateful to the Mediterranean Institute of ... | 10.5194/bg-10-5947-2013 | article | en | 2,013 | false | false | true | false | Earth and Planetary Sciences | https://openalex.org/fields/19 |
cc-by | There are many ways to build effective networks based on observed spiking activity. A commonly used network inference algorithm is Granger causality analysis [11, 12]. The strength of a causal link between two network nodes is measured by how well the knowledge of past activity of one node helps to predict the activit... | 10.1371/journal.pcbi.1003138 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Steel electrodes were placed into these wells with reference electrodes in the bath to record electrical signals. These signals were recorded with an AM Systems Model 1700 AC Amplifier and digitized with an Axon Instruments Digidata 1440A (Axon Instruments, Sunnyvale, CA). pClamp software (Molecular Devices, Sunnyvale,... | 10.1371/journal.pcbi.1003138 | article | en | 2,013 | true | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Spike trains were analyzed off-line using Spike2 software (CED, Cambridge, UK) and then exported to MATLAB for further processing. Recordings were obtained from four preparations for recording periods ranging between 140 and 300 seconds. Results reported in the text and figures refer to a single data set (#1), unless o... | 10.1371/journal.pcbi.1003138 | article | en | 2,013 | true | true | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | For the application of picrotoxin (PTX), the control condition consists of 360 s of recordings before the application and 120 s of stationary activity 6 minutes after application of PTX (Sigma Aldrich, St. Louis, MO) at 10 {5 M added to the saline. Spike trains were acquired as described previously. The model selection... | 10.1371/journal.pcbi.1003138 | article | en | 2,013 | true | false | false | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Acknowledgments The authors thank Anatoly Rinberg for supplying the CsCl data and Kyle Lepage for useful comments on the manuscript. | 10.1371/journal.pcbi.1003138 | article | en | 2,013 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Funding: FG is supported by the Swiss National Science Foundation (SNSF) under the grant number 200020-132871 and by EU - FP7 program ( BrainScaleS project 269921 ). EM and GJG are supported by NIH grant MH 46742 , and TK is supported by NIH grant F32 NS099590. UE is supported by NSF grant IIS 0643993 ... | 10.1371/journal.pcbi.1003138 | article | en | 2,013 | false | false | true | false | Neuroscience | https://openalex.org/fields/28 |
cc-by | Acknowledgements We would like to thank Jenny Boughman and two anonymous reviewers for helpful comments on the manuscript. This work was funded by the Agence National de la Recherche ( Hi-Flo project ANR-08-BLAN-0334-01 ). This is article 2012-XXX of Institut des Sciences de l'Evolution de Montpellier. | 10.1093/czoolo/59.1.72 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 91%) and 73 (1. 13%) contigs identified as significantly differentially expressed by EdgeR and DESeq, respectively). The differences in relative expression between the endo-and ecodormancy libraries and relative read numbers for each contig are displayed as MA plots (smear-plot) in Figure 3. A Venn diagram displaying ... | 10.1186/1471-2164-14-236 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Genes upregulated during ecodormancy Ecodormancy is a short-term phenomenon induced by a prolonged period of cold and long-day conditions, which provide an initial signal triggering a shift from endodormancy [46]. In this section we discuss the genes up-regulated during ecodormancy according to the pathway highlighted... | 10.1186/1471-2164-14-236 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Cleaning, assembly and annotation of the dormant bud transcriptome Reads were extracted with the sfffile program of Roche 454 Life Science software (Branford, CT, USA). Each 454-read was screened by cross_match [86] for primers and adaptors and was then masked. The longest non masked region was extracted and further ... | 10.1186/1471-2164-14-236 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | We also used two R Bioconductor packages: edgeR [30] and DESeq [31]. We applied a false discovery rate (FDR) of 0. 2 as a type I error for significant differential expression. The genes identified as differentially expressed with the three methods were combined, to define a minimum (MN) and a maximum (MX) set of dif... | 10.1186/1471-2164-14-236 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | The FDR was set at 0. 05. We used both the MN and MX sets for goseq analysis. Homology searches were carried out with BlastX [93] against the SWISS-PROT [94] and TAIR9 protein databases. The e-value cutoff for the Blast searches was set at 1 × 10 -5. Gene ontology (GO) [95] annotations were based on the top Blast h... | 10.1186/1471-2164-14-236 | article | en | 2,013 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Enrichment analyses Enrichment Analysis for Pathways and groups (EAPG) and Sub-networks (FNSE) for selected genes were performed using Ariadne Pathway Studio 9 Desktop edition Software and the Resnet Plant Version 4 database (Ariadne Genomics Inc. , Rockville, MD, USA). As described on Ariadne web site (http://www. ari... | 10.1186/1471-2164-14-236 | article | en | 2,013 | true | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Reverse transcription and quantitative real-time PCR (qPCR) The following criteria was applied to select candidate genes: (1) first, genes displaying the strongest differential expression in previous statistical analyses were selected, and (2) the molecular function of the genes selected in bud development in other spe... | 10.1186/1471-2164-14-236 | article | en | 2,013 | true | false | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Primer pairs are listed in Additional file 6: Table S7. We performed qPCR and data analysis as previously described [99]. Briefly, data were analyzed with the Excel (Microsoft) macro GENEX v1. 10 (Gene Expression Analysis for iCycle iQ W Real-Time PCR Detection System, v1. 10, 2004, Bio-Rad Laboratories), using the m... | 10.1186/1471-2164-14-236 | article | en | 2,013 | false | true | false | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Acknowledgments The study was carried out with financial support from the European Commission ( FP6-2004-GLOBAL-3 , Network of Excellence EVOLTREE "Evolution of Trees as Drivers of Terrestrial Biodiversity ", N°016322 ) and INRA (AIP Bioressource) to A. Kremer. SU received postdoctoral support from INRA. VL and... | 10.1186/1471-2164-14-236 | article | en | 2,013 | false | false | true | false | Agricultural and Biological Sciences | https://openalex.org/fields/11 |
cc-by | Seventeen clones were PCR amplified using the primers M13d (CGCCAGGGTTTTCCCAGTCACGAC) and M13r (TCACACAGGAAACAGCTATGAC) and the obtained products were sequenced. The obtained sequences were compared with sequences deposited in the GenBank database by using the BLAST program through the NCBI server. This strain exhibite... | 10.4056/sigs.4267953 | article | en | 2,013 | true | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 5% trifluoroacetic acid) per spot was applied. MALDI-TOF MS was conducted using the Microflex LT spectrometer (Bruker Daltonics). All spectra were recorded in linear, positive ion mode. The acceleration voltage was 20 kV. Spectra were collected as a sum of 240 shots across a spot. Preprocessing and identification steps... | 10.4056/sigs.4267953 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Genome project history The organism was selected for sequencing on the basis of its phylogenetic position and 16S rRNA similarity to other members of the genus Oceanobacillus, and is part of a "culturomics" study of the human digestive flora aiming at isolating all bacterial species within human feces. It was the secon... | 10.4056/sigs.4267953 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Genome annotation Open Reading Frames (ORFs) were predicted using Prodigal [50] with default parameters but the predicted ORFs were excluded if they were spanning a sequencing GAP region. The predicted bacterial protein sequences were searched against the GenBank database [51] and the Clusters of Orthologous Groups (CO... | 10.4056/sigs.4267953 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | To estimate the mean level of nucleotide sequence similarity at the genome level between O. massiliensis and O. iheyensis (GenBank accession number PRJNA57867), the only available Oceanobacillus genome to date, we compared the ORFs only using comparison sequence based in the server RAST [57] at a query coverage of ≥7... | 10.4056/sigs.4267953 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Genome properties The genome is 3,532,675 bp long with 40. 35% GC content (Table 4 and Figure 5 ). It is composed of 95 Contigs (9 Scaffolds). Of the 3,589 predicted genes, 3,519 were protein-coding genes, and 72 were RNAs (1 gene is 16S rRNA, 1 gene is 23S rRNA, 9 genes are 5S rRNA, and 61 are tRNA genes). A total ... | 10.4056/sigs.4267953 | article | en | 2,013 | false | true | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Figure1. Phylog enetic tree hig hlig hting the position of Oceanobacillus massiliensis st rain N'Diop T relative to other type strains within the Oceanobacillus, Ornithinibacillus, and Virgibac illus g enera. GenBank accession numbers are indicated in parentheses. Sequences were alig ned using CLUSTALX, and phylog enet... | 10.4056/sigs.4267953 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | The N'Diop T spectra were imported into the MALDI BioTyper software (version 3. 0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 4,108 bacteria including the spectra from Oceanobacillus profundus CIP 109535 T , Oceanobacillus picturae CIP 108264 T , Ocea... | 10.4056/sigs.4267953 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgements The authors thank Julien Paganini at Xegen Company (www. xegen. fr)for automati ng the genomic annotation process. | 10.4056/sigs.4267953 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | However, the weak overlap of the public datasets suggests that they are far from being complete. The impact of cellular proteins on the influenza virus replication has been extensively studied using RNAi screens [19] [20] [21] [22] [23] [24]. Although poorly overlapping at the gene level, these screens better converge... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | In the present study we conducted stringent yeast two-hybrid screens to identify human proteins interacting with NS1 and NS2 from 9 influenza A virus strains representative of the variability in nature. The functional impact of all NS1 and NS2 interactors on viral replication was systematically addressed by RNA interfe... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | From a total of 1422 possible interactions tested (79 cellular proteins tested against 9 NS1 and 9 NS2 proteins), 562 tested positive. In this way, we identified 33 cellular proteins interacting exclusively with NS1, 28 exclusively with NS2, and 18 with both NS1 and NS2. The vast majority (97. 5%) of the NS1 and NS2 in... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Together with previously published data available in the VirHostNet database [39] , we now provide a list of 111 nonredundant cellular proteins interacting exclusively with NS1, 32 exclusively with NS2 and 18 with both proteins (a complete list of influenza virus interactors is given in Table S3 ). Consistent with ob... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 2610 216 ) (Figure 1D ). This suggests that influenza NS1 and NS2 proteins preferentially target pleiotropic cellular proteins [44]. Finally, an assessment of Gene Ontology categories revealed a significant enrichment (p-value = 3. 3610 214 ) for DRBD-containing proteins (DRBPs) in the interaction dataset. Strikingly... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | ADAR1 was co-expressed in HEK293T cells with NS1 or its RBD and with the editing reporter construct. The NS1 effector domain or DLG4, which does not bind to ADAR1 (data not shown), was used as negative control in analogous cotransfection experiments. NS1 RBD and full-length NS1 increased the Firefly luciferase signal b... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For NS1, there is a strong overlap with hits published by others (11 of the 51 interactors identified in the present study, which is well above the average overlap) [41, 53] , suggesting that the NS1 interactome dataset is now close to completion. In case of NS2, only 4 cellular interactors have been published and one... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | 7%, exact Fisher test, p-value,2. 2610 216 ) indicating that these cellular proteins are likely to be involved in a generic process of viral infection [39]. Our interaction dataset indicates that NS1 and NS2 proteins are likely to be involved in multiple steps of the viral replication cycle, paving the way for challen... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | For instance, the CPSF4 interaction with NS1 has been described as a potential therapeutic target [55] and is confirmed in our study. Three NS1 proteins also interacted with CPSF3L, a protein participating in the endonuclease activity of CPSF, suggesting that the corresponding viruses evolved alternative strategies t... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Functional analysis DAVID database was used for functional annotation [72]. DAVID functional annotation chart tool was used to perform Gene Ontology categories analysis. Gene Ontology terms with a Benjamini-Hochberg corrected p-value smaller than 5. 10 2 were considered as significantly overrepresented. siRNA screenin... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | true | false | false | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Acknowledgments The authors want to thank Pauline Radreau-Pierini and Patrick Le ´cine for critical reading of the manuscript, Bruno Lina and Vincent Moules for NS1 and NS2 cDNAs, Adolfo Garcia-Sastre and Juan Ortin for NS1 mutants and Amelie Cessieux for technical assistance. | 10.1371/journal.ppat.1003440 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | This work was funded by ANR , ANRS , Inserm and the FUI from the French Ministry of Industry. RB was supported by the Deutsche Forschungsgemeinschaft ( FOR1202 , TP1 ). RB and VL are also supported by the European Union 's 7th program ( FP7/2007-2013) under grant agreement no 267429 (SysPatho). The fund... | 10.1371/journal.ppat.1003440 | article | en | 2,013 | false | false | true | false | Biochemistry, Genetics and Molecular Biology | https://openalex.org/fields/13 |
cc-by | Burkholderia pseudomallei (Bp), the causative agent of the often-deadly infectious disease melioidosis, contains one of the largest prokaryotic genomes sequenced to date, at 7. 2 Mb with two large circular chromosomes (1 and 2). To comprehensively delineate the Bp transcriptome, we integrated whole-genome tiling array ... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | This versatility suggests that Bp could prove useful as a model to study how pathogens adapt to extreme environments and different hosts. Indeed, it has been proposed that Bp is an example of ''accidental virulence'', where genetic pathways used by the bacterium to survive in environmental niches may have indirectly co... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Genomic Landscape of the Bp Condition-Dependent Transcriptome Whole-genome tiling microarrays containing strand-specific probes overlapping at 35-base resolution were used to profile Bp transcriptional responses under 82 different conditions (Figure S1A-C ). Conditions were selected to mimic natural exposures Bp might... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Abundance of Condition-Dependent Non-coding RNAs in Bp Non-coding RNAs (ncRNAs) are emerging as an important class of regulatory molecules in several prokaryotes [18]. Using stringent filtering criteria and manual curation (see Materials and Methods), we identified a ''high-confidence'' set of 766 ncRNA transcripts ra... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Transcript boundaries correspond to predicted start and stop coordinates of Sanger annotated genes and FGENESB novel genes. (C) Differential expression of a Bp operon. Expression of a predicted flagella operon (BPSL0026 -BPSL0032) in a specific condition (taurine exposure). (D) Antisense transcription. BPSL0095, a gene... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Among the upregulated genes, we identified five that might function as potential effector proteins -BPSS1498 (tssD-5), BPSL3319 (fliC), BPSS1525 (bopE), BPSS1529 (bipD) and BPSS1532 (bipB). These effectors were identified using the program PSORTb 3. 0 [43] -a subcellular localization prediction tool. Notably, several... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Discussion In this study, we integrated strand-specific whole-genome transcriptional data over 80 environmental, chemical and genetic perturbations to generate a transcriptional condition compendium of Bp. Previous molecular studies on Bp have largely focused on protein-coding genes defined by the original genome annot... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | pylori and L. monocytogenes, antisense RNAs are involved in regulating metabolic enzymes and virulence factors [5, 55]. Taken collectively, these results strongly suggest that several features of Bp biology are likely to be modulated by other molecular entities beyond protein-coding genes, specifically ncRNAs and anti... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Interestingly, when compared against other prokaryotic transcriptome studies, the transcriptional landscape of Bp Chr 1 bears high resemblance to other single chromosomal microbes E. coli, L. monocytogenes and B. subtilis [4, 5, 56] , while the consistently lower expression levels of Bp Chr 2 and its condition respons... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | In the Bp network, examples of co-expressed genes included clusters related to motility, aerobic respiration, detoxification, and ribosomal function (Figure 4A ). Besides known genes, such ''guilt-by-association'' approaches can also often shed light on genes with poorly-understood or unknown functions. Despite ongoin... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | BpK96243 Tiling Microarrays and Expression Profiling High-density tiling arrays were fabricated by Roche NimbleGen (Roche NimbleGen, USA) based on the BpK96243 reference genome [8]. Bacterial RNAs were extracted and processed for microarray hybridization as described in [13]. In total, 166 samples were profiled; howe... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Microarray data has been deposited into the Gene Expression Omnibus (GEO) under accession number GSE43205. | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Identification and Annotation of Transcriptionally Active Regions (TARs) A moving window binomial approach was performed for de novo TAR identification [14] (Text S1). TARs were visualized using Artemis (Sanger, UK) or SignalMap (Roche NimbleGen, USA), and annotated against Sanger coding genes [8], ncRNAs (Rfam, [18... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | g. Sanger genes). Expression levels were visualized using GeneSpring GX 11. 0 software (Agilent, USA), using a. 2-fold change cutoff (Text S1). | 10.1371/journal.pgen.1003795 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Gene Co-expression Networks and Co-expression Clusters Co-expression associations between genes were defined by the ARACNe algorithm [21]. Each gene pair was assigned to a mutual information score (MIS) greater than zero, and we retained the top 2% of gene pairs (MIS §0:3168). The MISs were also used to form a weighte... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | To identify the optimal level of cluster granularity, the clustering analysis was performed using different inflation parameters (1. 0 -3. 5) and at each value the clustering results were evaluated for structural efficiency and functional coherence, measured by the fraction of gene pairs within the cluster sharing iden... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Clusters connected by Z §17were deemed significant. The condition-dependent co-expression network was visualized using Cytoscape 2. 8. 1. heat stress. 158 genes were commonly down-regulated by at least 2-fold in the presence of chloramphenicol (K9Chlamp), ceftazidime (K9Ceft), 2M of sorbitol (K9Sorb) or under 42uC for ... | 10.1371/journal.pgen.1003795 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Acknowledgments Thanks to PATRIC (www. patricbrc. org)members Alice R. Wattam , Maulik Shukla and Yang Zhang for significant efforts in support of this work's dissemination. | 10.1371/journal.pgen.1003795 | article | en | 2,013 | false | false | true | false | Medicine | https://openalex.org/fields/27 |
cc-by | Transcriptomic analysis In order to compare gene expression patterns between ASCmo and ASCn, a comprehensive transcriptomic analysis was performed using Affymetrix whole-transcript expression array. To visualize gene expression data we performed Principal Component Analysis (PCA) that demonstrated the independence of t... | 10.1186/1471-2164-14-625 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Finally, we have observed a significantly reduced expression of DAPK1 in ASCmo. The death-associated protein kinase-1 (DAPK1) is the prototypic member of a family of death-related kinases. However, DAPKs can also act as a survival factors and block apoptosis in response to certain cytokine signals modulating the balanc... | 10.1186/1471-2164-14-625 | article | en | 2,013 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Flow cytometry characterization For further characterization, cell surface antigen phenotype was performed on ASCmo and ASCn at passage 0 and passage 3. The following cell-surface epitopes were marked with anti-human antibodies: CD105-fluorescein isothiocyanate (GeneTex), CD90-fluorescein isothiocyanate (FITC), CD29-ph... | 10.1186/1471-2164-14-625 | article | en | 2,013 | false | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Single strand DNA was obtained from 10 ug of cRNA. Then 5. 5 ug of single strand DNA were fragmented and labelled with biotin using the WT Terminal Labeling Kit (Affymetrix). Hybridization controls from the Hybridization, Wash and Stain Kit (Affymetrix) were added to the sample. Every sample was hybridized to GeneChip ... | 10.1186/1471-2164-14-625 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Bioinformatics was used to analyze the extracted log2 expression data. The raw data from the array experiments has been deposited in NCBI's Gene Expression Omnibus [54] and is accessible through GEO Series accession number (GSE48964; http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE48964). Microarray quality... | 10.1186/1471-2164-14-625 | article | en | 2,013 | true | true | false | false | Medicine | https://openalex.org/fields/27 |
cc-by | Adjusted p-value, FDR <0. 6 and fold change ≥ ±1. 5 were used to obtain differential expressed genes. Some of the modified genes were validated using real-time PCR in ASC from additional non-obese individuals (n = 8) and morbidly obese patients (n = 16). Differential expressed genes were associated with biological func... | 10.1186/1471-2164-14-625 | article | en | 2,013 | true | false | false | false | Medicine | https://openalex.org/fields/27 |
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