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Flat-Field Effects As described in Section 3. 2, the calibration process does not yet correct the data for variations associated with pointing fluctuations. An analysis of PROBA2 attitude over several orbits reveals that pointing is stable up to 90 arcseconds. Spacecraft jitter introduces fluctuations in the LYRA signa...
10.1007/s11207-013-0252-5
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Physics and Astronomy
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Radiometric Accuracy From Equation (4), the maximal uncertainty on the calibrated LYRA data is described by ∆E cal E cal = ∆i i + ∆ λ Edλ λ Edλ + ∆A A + ∆ λ EF Ddλ λ EF Ddλ (5) where i = i uncal + i d + corr. We will discuss the terms of this equation one by one.
10.1007/s11207-013-0252-5
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Physics and Astronomy
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Conclusion All in all, we consider the uncertainty on LYRA calibrated data to be of the order of 30 -40 % for all channels except Lyman-α, where it is about 120 %. In an attempt to validate those uncertainties, we have used alternative spectra in Equation ( 4 ) and have seen how LYRA data were affected. Unfortunately,...
10.1007/s11207-013-0252-5
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Physics and Astronomy
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Conclusion After more than two years of operations, LYRA demonstrated its ability to produce time series of solar irradiance in the XUV-EUV-MUV range with a very favorable sampling rate. Uncalibrated and calibrated data products, as well as various quicklooks and a list of flares, are distributed via the instrument web...
10.1007/s11207-013-0252-5
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Acknowledgements The authors acknowledge the support from the Belgian Federal Science Policy Office through the ESA-PRODEX programme. LYRA is a project of the Centre Spatial de Liège , the Physikalisch-Meteorologisches Observatorium Davos , and the Royal Observatory of Belgium , funded by the Belgian Federal Sci...
10.1007/s11207-013-0252-5
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Affimetrix exon array One microgram of total RNA was processed with the GeneChip WT Sense Target Labeling kit and hybridized to GeneChip Human Exon 1. 0 ST arrays. Affymetrix exon-array data were normalized with quantile normalization. Antigenomic probes were used to perform the background correction. Only probes targe...
10.1093/nar/gkt1216
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Biochemistry, Genetics and Molecular Biology
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Sampling Taxonomic sampling was carried out at 80 localities throughout Grande Terre, Ile des Pins and Loyalty Islands. We gathered 153 specimens, representing 4 species (including 3 new species), at 17 localities from the centre-east (Houailou) to the south-east (Foret Nord) (Table 1 ). Most of the sampled sites were...
10.1371/journal.pone.0080811
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Environmental Science
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g. , [45, 46, 47] ). Molecular sampling included sequences from 3 fragments of coding mitochondrial genes (Cytochrome b (Cytb, 346 bp), Cytochrome c Oxidase 1 (CO1, 670 bp) and Cytochrome c Oxidase 2 (CO2, 381 bp)) and 4 fragments of nuclear genes ((Elongation factor-1 alpha (EF1a, 367 bp), Histone Class 3 (H3, 331 bp...
10.1371/journal.pone.0080811
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15 mL of Taq polymerase and 1 mL of DNA. The PCR consisted of an initial denaturing step at 94uC for 4 min, 40 amplification cycles (denaturation at 94uC for 30 s, annealing at between 48 and 55uC (Table 3 ) for 40 s, and extension at 72uC for 40 s), and a final step at 72uC for 7 min. PCR products were checked on aga...
10.1371/journal.pone.0080811
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Analyses were performed with MrBayes 3. 1. 2 [61]. Four Markov chains were run simultaneously for 20 million generations, sampling every 100 generations to ensure independence of samples. The first 20,000 trees generated were determined empirically from the log-likelihood values using TRACER V1. 4 and discarded as burn...
10.1371/journal.pone.0080811
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Geographical distribution, soil diversity and niche modelling We aimed to test whether certain environmental parameters (soil, climate) could have influenced the distribution of the genus. Ecological niche models (ENM) were constructed using the maximum entropy niche modelling approach implemented in MAXENT [73, 74]. ...
10.1371/journal.pone.0080811
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2,013
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Environmental Science
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Geographical distribution and soil diversity Caledonula fuscovittata has a large distribution with twelve distant localities, always on non-metalliferous soils (Figure 2 ). Specimens of this species collected on Mont Mou and Mont Koghis (ultramafic massifs) were collected on non-metalliferous soils at the base of thes...
10.1371/journal.pone.0080811
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Molecular sampling, voucher references and GenBank accession numbers of specimens included in the molecular study.
10.1371/journal.pone.0080811
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2,013
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Environmental Science
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Acknowledgments We are grateful to Shepherd Myers and Keith Arakaki ( Bishop Museum, Honolulu ), George Beccaloni (The Natural History Museum, London ), for loans of specimens, to Gae ¨l Kergoat (CBGP) for specimen collection in Mont Kouakoue, and to Gilbert Hodebert for the habitus drawings. We sincerely th...
10.1371/journal.pone.0080811
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Global analysis of gene expression during embryonic development Using the newly developed "INRA-BF2I_A. pisum_Nim blegen-ACYPI_4x72k_v1" microarray (ArrayExpress design ID: A-MEXP-1999), built on the pea aphid genome v1. 0 assembly [23] , we obtained gene expression profiles of aphid embryos belonging to three distinc...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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Microarray data validation by quantitative RT-PCR To validate the data obtained from the microarray analysis in our first experiment, we repeated the experiment for the same four stages and quantified the expression of eight A. pisum genes, belonging to four functional classes (3 developmental genes, 3 amino acid pathw...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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Numbers in red identify the genes increasing in expression during development; in dark blue, the genes decreasing in expression during development; and, in black, the genes found to be significant in two or more groups where the expression changes are not varying in the same direction in the different comparisons. coef...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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Developmental genes expression analysis Among the 387 pea aphid developmental genes annotated by Shigenobu et al. [55] , using homology with Drosophila melanogaster, 368 were present in our microarrays and were analysed. In our dataset, 118 genes (32%) showed significant differential expression in at least one of the t...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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Metabolism gene expression: the amino acid pathways To explore the general metabolic changes that take place during the parthenogenetic development of the pea aphid, we analyzed the relevant genes (Additional file 1: Table S1 ) using the annotations available in the AcypiCyc database, which contains the global reconst...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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For example, 16. 8% of the total number of differentially expressed enzyme-coding genes in our dataset forms part of the amino acid metabolism group and, in the pea aphid genome, the percentage of genes coding for this class is 16. 4%. So, the number of detected genes is not significantly different from the number that...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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Embryo development specific regulation of the gene ACYPI004243 The matching profiles of the enzyme-coding gene expression for tyrosine synthesis and the accumulation of this amino acid in the LE and L1 embryo groups prompted us to perform a more detailed analysis of the genes involved in this pathway (Figure 3B and 3...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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6. 1. 5) and the enzymatic activity aromatic amino acid transaminase (EC 2. 6. 1. 57) (Additional file 2: Table S9 ). This additional in silico analysis confirmed the hypothetical role of these four genes in coding the enzymes catalyzing the aspartate, tyrosine and aromatic amino acids transamination reactions. The tw...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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It is worth noting that the genes ACYPI004243 and ACYPI003009 mapped to the same contig in the pea aphid genome. An analysis of the protein sequences was performed and the alignment of the four proteins revealed the expected conservation, with the exception of the ACYPI000044-PA protein sequence that has a unique N-ter...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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Discussion In this study, the transcriptome analysis of parthenogenetic development in embryonic pea aphids enabled us to characterize the gene expression profiles at key stages in the development of this insect. A comprehensive transcriptome dataset, such as this, is important for the ongoing genome annotation effort ...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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A comprehensive analysis of the genes involved in metabolism, performed using the AcypiCyc database annotations [56] , did not reveal any significant global change in gene expression in the specific pathways. Nevertheless, the known central role of amino acid metabolism pathways in this symbiotic relationship [29] a...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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Microarray experiments and data collection The "INRA-BF2I_A. pisum_Nimblegen-ACYPI_4x72k_v1" microarray for the pea aphid was developed in collaboration with NimbleGen using the pea aphid genome v1. 0 assembly [23]. This NimbleGen 385 K 4-plex (4 × 72,000 probes) high-density array can accommodate four samples that ar...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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Labelling (using the NimbleGen One-Color DNA Labelling Kits and Cy3 Random Nonamers), hybridization on the arrays (at 42°C for 16-20 hours) and scanning (using MS 200 Microarray Scanner and the MS 200 Data Collection Software) were carried out by Roche NimbleGen, as described in the NimbleGen arrays user's guide for ge...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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Microarray data analysis Microarray data were normalized, using the RMA method [68] , and then transformed into log2. A one-way between groups ANOVA analysis was performed using the Limma package in the R software [69] : two by two comparisons were performed to identify any differentially expressed genes between the ...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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All HCL (Hierarchical Clustering) analyses were carried out using the TMeV software [71] , applying the average linkage method with euclidean distance and no leaf order optimization. Gene Ontology analysis was carried out using the Blast2GO software [72] to perform the GOSSIP test ( [73] ; http://gossip. gene-group...
10.1186/1471-2164-14-235
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Validation of microarray data by qRT-PCR Total RNA was reverse-transcribed in cDNA using the SuperScript ™ III First-Strand Synthesis System for RT-PCR (Invitrogen, Paisley, UK), with random primers, according to the manufacturer's instructions. This protocol involved three principal steps: (1) an incubation for 5 min ...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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For the data normalization, two genes were tested in the different developmental stage groups analysed here: actin (ACYPI000064) and rpl32 (ACYPI000074). Real-time RT-PCR data were analysed using the BestKeeper © software tool [76] and the actin gene was retained as the best candidate for data normalization. An analy...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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Sequence analyses The four protein sequences (ACYPI006213-PA, ACYPI 003009-PA, ACYPI004243-PA and ACYPI000044-PA) for the aspartate transaminase enzymatic activity (E. C. 2. 6. 1. 1) were obtained from PhylomeDB [59] , together with their corresponding arthropod orthologs and paralogs. The data set was completed with ...
10.1186/1471-2164-14-235
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Acknowledgements Funding: This work was supported by the Agence National de la Recherche (ANR, France) , the Biotechnology and Biological Sciences Research Council (BBSRC, UK) « MetNet4SysBio » project grant ( 2008-2010 ), and an INSA-Lyon BQR program grant ( 2008-2009 ) to SC. AR was the recipient of a PhD fell...
10.1186/1471-2164-14-235
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Agricultural and Biological Sciences
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General DNA techniques Oligonucleotides were designed, and in silico analysis was carried out with the afa-8 sequence of E. coli 239KH89 (accession number AF072900). The sequences of the oligonucleotides (Eurogentec) used in this study are listed in Supplementary Table S1. All polymerase chain reaction (PCR) products ...
10.1093/nar/gkt208
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Biochemistry, Genetics and Molecular Biology
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Quantitative RT-PCR For quantitative reverse transcription PCR (qRT-PCR) analyses of gene expression, we used Primer3 software to design specific primer pairs. Real-time PCR was performed with the Bio-Rad iQ system and iQ SYBR Green supermix (Bio-Rad), according to the manufacturer's instructions. The thermocycling pro...
10.1093/nar/gkt208
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Biochemistry, Genetics and Molecular Biology
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The identification of a Rho-independent terminator beginning 240 bp downstream from the stop codon of the afaD gene suggests that the afaD mRNA has a long 3 0 UTR. Another Rho-independent terminator was found 25 bp downstream from the afaE stop codon. In a previous study, the $230-nt SQ109 sRNA gene was identified betw...
10.1093/nar/gkt208
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Biochemistry, Genetics and Molecular Biology
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AfaR interacts with the afaD mRNA via an antisense mechanism Our working hypothesis is that AfaR is an antisense RNA that regulates AfaD production. We therefore used intaRNA software (45) to analyse in silico the likelihood of AfaR forming double-stranded antisense pairs with other afa-8 gene mRNAs. One significant ...
10.1093/nar/gkt208
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Biochemistry, Genetics and Molecular Biology
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The pairing of the afaR and afaD mRNAs is dependent on Hfq In E. coli, most antisense sRNAs make use of the Hfq protein to capture their mRNA targets (46). We assessed the contribution of Hfq to the AfaR-mediated regulation of afaD mRNA in vivo by comparing the levels of afaD transcripts in the hfq-depleted strain JW4...
10.1093/nar/gkt208
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Biochemistry, Genetics and Molecular Biology
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ACKNOWLEDGMENTS We thank Patrick Trieu-Cuot for his critical comments on the manuscript and Carol Gross , who kindly provided us with E. coli strains.
10.1093/nar/gkt208
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Biochemistry, Genetics and Molecular Biology
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FUNDING Institut Pasteur [ PTR165 ]; Agence National de la Recherche funding for the ERA-NET Pathogenomics project [ ANR-06-PATHO-002-03 ]. Funding for open access charge: Institut Pasteur.
10.1093/nar/gkt208
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Biochemistry, Genetics and Molecular Biology
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Crystal data Hydrogen-bond geometry (A ˚, ). Symmetry code: (i) Àx þ 1; Ày þ 2; Àz. Data collection: APEX2 (Bruker, 2009) ; cell refinement: SAINT-Plus (Bruker, 2009) ; data reduction: SAINT-Plus; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL97 (Sheldri...
10.1107/s1600536813013780
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Chemistry
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Computing details Data collection: APEX2 (Bruker, 2009) ; cell refinement: SAINT-Plus (Bruker, 2009) ; data reduction: SAINT-Plus (Bruker, 2009) ; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) ; molecular graphics: ORTEP-3 for Windo...
10.1107/s1600536813013780
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Chemistry
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Related literature (i) Àx þ 2; Ày þ 1; Àz. Data collection: APEX2 (Bruker, 2009) ; cell refinement: SAINT (Bruker, 2009) ; data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) ; molecular graphics: ORTEP-3 for Windows...
10.1107/s1600536813011811
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Chemistry
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Computing details Data collection: APEX2 (Bruker, 2009) ; cell refinement: SAINT (Bruker, 2009) ; data reduction: SAINT (Bruker, 2009) ; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008) ; program(s) used to refine structure: SHELXL97 (Sheldrick, 2008) ; molecular graphics: ORTEP-3 for Windows (Farru...
10.1107/s1600536813011811
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A new landscape format has easy to use tables comparing related targets. It is a condensed version of material contemporary to late 2013, which is presented in greater detail and constantly updated on the website www. guidetopharmacology. org, superseding data presented in previous Guides to Receptors and Channels. It ...
10.1111/bph.12445
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Biochemistry, Genetics and Molecular Biology
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A new landscape format has easy to use tables comparing related targets. It is a condensed version of material contemporary to late 2013, which is presented in greater detail and constantly updated on the website www. guidetopharmacology. org, superseding data presented in previous Guides to Receptors and Channels. It ...
10.1111/bph.12445
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3x10 -10 M -Rat) [176], [ 3 H ]ketanserin (Antagonist) (2x10 -10 -2. 9x10 -9 M) [166, 198] [ 3 H]LSD (Agonist, Full agonist) (2. 1x10 -9 M) [198] , [ 3 H]mesulergine (5x10 -9 -1x10 -8 M), [ 3 [ 125 I]LSD, [ 3 H]5-CT [ 3 H]5-CT (Agonist), [ 125 I]SB258585 (Antagonist) (1x10 -9 M) [156], [ 3 H]LSD (Agonist, Full agoni...
10.1111/bph.12445
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Biochemistry, Genetics and Molecular Biology
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in altered striatal signalling [63]. S. P. H. Alexander et al. The Concise Guide to PHARMACOLOGY 2013/14: G Protein-Coupled Receptors. British Journal of Pharmacology (2013) 170, 1459-1581 Searchable database: http://www. guidetopharmacology. org/index. jsp Orphan GPCRs 1464 Full Contents of Concise Guide: http://onlin...
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H. Alexander et al. The Concise Guide to PHARMACOLOGY 2013/14: G Protein-Coupled Receptors. British Journal of Pharmacology (2013) 170, 1459-1581 Searchable database: http://www. guidetopharmacology. org/index. jsp Orphan GPCRs 1465 Full Contents of Concise Guide: http://onlinelibrary. wiley. com/doi/10. 1111/bph. 1244...
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Biochemistry, Genetics and Molecular Biology
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-S. P. H. Alexander et al. The Concise Guide to PHARMACOLOGY 2013/14: G Protein-Coupled Receptors. British Journal of Pharmacology (2013) 170, 1459-1581 Searchable database: http://www. guidetopharmacology. org/index. jsp Leukotriene, lipoxin and oxoeicosanoid receptors 1523 Full Contents of Concise Guide: http://onlin...
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Biochemistry, Genetics and Molecular Biology
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Acknowledgements We are extremely grateful to the long list of collaborators who assisted in the construction of the Concise Guide to PHARMACOLOGY 2013/14 and to the website www. guidetopharmacology. org,, as well as to the Guides to Receptors and Channels. We are also extremely grateful for the financial contributions...
10.1111/bph.12445
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Biochemistry, Genetics and Molecular Biology
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-S. P. H. Alexander et al. The Concise Guide to PHARMACOLOGY 2013/14: G Protein-Coupled Receptors. British Journal of Pharmacology (2013) 170, 1459-1581 Searchable database: http://www. guidetopharmacology. org/index. jsp Leukotriene, lipoxin and oxoeicosanoid receptors 1523 Full Contents of Concise Guide: http://onlin...
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Biochemistry, Genetics and Molecular Biology
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jsp Orphan GPCRs 1466 Full Contents of Concise Guide: http://onlinelibrary. wiley. com/doi/10. 1111/bph. 12444/full Comment GPR45 GPR45, Q9Y5Y3 - - Gi/Go -S. P. H. Alexander et al. The Concise Guide to PHARMACOLOGY 2013/14: G Protein-Coupled Receptors. British Journal of Pharmacology (2013) 170, 1459-1581 Searchable da...
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jsp Orphan GPCRs 1467 Full Contents of Concise Guide: http://onlinelibrary. wiley. com/doi/10. 1111/bph. 12444/full Nomenclature HGNC, UniProt Principal Comment transduction MRGPRG MRGPRG, Q86SM5 - - S. P. H. Alexander et al. The Concise Guide to PHARMACOLOGY 2013/14: G Protein-Coupled Receptors. British Journal of Pha...
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Biochemistry, Genetics and Molecular Biology
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Searchable database: http://www. guidetopharmacology. org/index. jsp 5-Hydroxytryptamine receptors 1471 Full Contents of Concise Guide: http://onlinelibrary. wiley. com/doi/10. 1111/bph. 12444/full H. Alexander et al. The Concise Guide to PHARMACOLOGY 2013/14: G Protein-Coupled Receptors. British Journal of Pharmacolog...
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jsp Adhesion Class GPCRs 1478 Full Contents of Concise Guide: http://onlinelibrary. wiley. com/doi/10. 1111/bph. 12444/full Comment LPHN1 LPHN1, O94910 - LPHN2 LPHN2, O95490 - LPHN3 LPHN3, Q9HAR2 - , Q7Z7M1 -S. P. H. Alexander et al. The Concise Guide to PHARMACOLOGY 2013/14: G Protein-Coupled Receptors. British Journa...
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