dataesr/scientific-paragraphs-categorization huggingface dataset:
Phylome reconstruction The phylome, a complete collection of phylogenetic trees for each gene in A. adeninivorans, was reconstructed. Seventeen additional species were included in the phylome: three Pezizomycotina species and fourteen Saccharomycotina species. The phylome was reconstructed using a previously described pipeline  [35]. Briefly, for each gene encoded in A. adeninivorans, a BLAST search was performed against the proteome database containing the 18 proteomes. Results were filtered according to e-values < 1e-05 and minimal overlaps with hit sequences at 50% of the query length. A maximum of 150 matches were accepted for each A. adeninivorans protein. Multiple-sequence alignments were performed in forward and reverse orders  [61] , using three programs: Muscle  [39]  v3. 8. 31, MAFFT v6.
Detection of horizontally acquired genes Gene transfers from prokaryotes to A. adeninivorans were detected using a previously published pipeline  [36]. Briefly, a BLAST search was performed for each protein encoded in A. adeninivorans against a database that contained 102 completely-sequenced fungi (downloaded from their respective databases), 95 other eukaryotes and 1,395 prokaryotes (downloaded from KEGG as of June 2011). Only genes present in more than 30 prokaryotes, less than 10 fungi and no other eukaryotes were considered to be putative transfers.
Species phylogeny The species tree was reconstructed by concatenating 253 genes that were found in all the genomes included in the phylome database and that were exclusively one-to-one orthologs. The genes were concatenated and the tree was reconstructed using RaxML  [70]. A second tree was reconstructed using a super-tree approach as implemented in Duptree  [71] , this algorithm tries to find the species tree that minimizes the number of duplication events that occurred in a set of gene trees. In this case the 4,992 trees reconstructed in the phylome were used.
Microarray design and hybridization for gene expression analyses Based on 6,025 annotated chromosomal sequences and 36 putative mitochondrial genes oligos were designed using Agilent Technologies eArray software (design number 035454). Depending on the sequence length of the genes up to ten 60-mers per gene were created resulting in a total of 56,312 A. adeninivorans specific oligos. The microarray was produced by Agilent Technologies (Böblingen, Germany) in 8×60k format. Overnight cultures of A. adeninivorans LS3 in YMM with nitrate were shifted to YMM containing 4 mM adenine as the sole nitrogen source and YMM with nitrate as a control, respectively. After 2 h of shaking at 30°C and 180 rpm cells were harvested and total RNA was isolated. Probe labeling and microarray hybridization (duplicates) were executed according to the manufacturer's instructions (Agilent Technologies "One-Color Microarray-Based Gene Expression Analysis"; v6.
Acknowledgements The authors would like to thank  S. König  for 454 sequencing,  D. Stengel  for 454 data submission to EMBL/ENA,  S. Flemming  for technical assistance in bioinformatics analysis and software installation, and  T. Schmutzer  and  B. Steuernagel  for fruitful discussions about the analysis of the 454 data. This work was supported in part by funding from the  Consortium National de Recherche en Génomique (CNRG)  to Génoscope, from  CNRS  ( GDR 2354 ,  Génolevures ),  ANR  ( ANR-05-BLAN-0331 , GENARISE). The computing framework was supported by the funding of the  University of Bordeaux 1 , the  Aquitaine Région  in the program " Génotypage et Génomique Comparée ", the  ACI IMPBIO  " Génolevures En Ligne " and  INRIA. We thank the  System and Network Administration team in LaBRI  for excellent help and advice.
Fluorescence Activated Cell Sorting (FACS) on blood and SVF cells. Cells were pre-incubated (20 minutes on ice) with purified 2. 4G2 monoclonal antibody in order to block Fc receptors (1:50, BD Bioscience, San Diego, CA, USA). Cells were then incubated (45 minutes on ice) with primary antibodies (listed in Table  S1 ) before being resuspended in PBS containing 0. 5% BSA. Acquisition was made on 5610 5 cells using a FACS LSR Fortessa (BD Biosciences). Data were analyzed using the FlowJo 765 (Tree Star Inc. ; Ashland, OR, USA). Measurement of cytokine levels in adipose tissue explants and blood. For quantification of cytokines secreted by the visceral adipose tissue, tissue explants were cultured for 24 hours in DMEM without serum and supplemented with 1% of penicillin and streptomycin (50 U/ml, GIBCO, Life Technologies).
Beadchips were washed and stained according to manufacturer's protocol. Arrays were scanned by chip scanner Bead Array (Illumina), and images analyzed by Genome Studio (Illumina). Data were exported and processed using Genespring GX 11. 5. 1 (Agilent, Santa Clara, CA, USA). Data from HFD-Ve and HFD-Rapa mice were compared to data obtained from regular chowfed mice. Genes that were differentially regulated in the experimental groups were identified using the p-value cut-off of 0. 05. These genes were further analyzed using the Ingenuity Pathway software (Ingenuity, Redwood City, CA, USA). The microarray dataset has been submitted to Gene Expression Omnibus with accession number GSE53980. Quantitative PCR. RNAs (400 ng) were reverse transcribed using the High Capacity cDNA Reverse Transcript Kit from Applied Biosystems (Foster City, CA, USA).
Adipose Tissue and Liver Histological Analysis Histology and Morphometric Analysis. Liver, visceral white (VWAT) and BAT samples were overnight fixed in 4% paraformaldehyde before embedding in paraffin. Multiple sections were obtained and stained with hematoxylin and eosin. For the morphometric analysis, at least 10 fields (representing approximately 100 adipocytes) per slide were analyzed. Images were acquired using an optical microscope (Axioplan 2 Imaging, Zeiss, Go ¨ttingen, Germany) and analyzed using the Image J software. Immunohistochemical staining. VWAT tissue sections (5 mice per group) were stained with mAb anti-F4/80 (1:500, eBioscience, San Diego, CA, USA). Staining was visualized using the Image J software. The specificity of the staining was verified by replacing each primary antibody by nonspecific IgG (Rat IgG1k isotype Control (eBRG1) eBioscience).
After washing, Ab binding was revealed by incubation with horseradish peroxidase (HRP)-conjugated secondary antibodies (2 hours incubation at room temperature, anti-Rabbit IgG HRP-linked antibody, 1:5000, #7074, Cell Signaling) and ECL (ECL Plus Western Blotting Detection System, Amersham, Buckinghamshire, UK). Signals were quantified using the ImageJ software.
In contrast, pathways related to lipid or carbohydrate metabolism were predicted to be under-expressed (Figure  3C ). Then, we assessed the expression levels of pro-inflammatory cytokines (e. g. Il-1a, Il-1b, Il-6 and Tnfa) and anti-inflammatory cytokines (e. g. Il-4 and Il-10) transcripts in the VWAT. Figure  3D  shows that rapamycin had no discernible effect on the expression of Tnfa, Il-4 and Il-10, yet it markedly enhanced the expression of Il-6 (3-fold increase), Il-1aand Il-1b (2-fold increase). The expression data were further supported by protein secretion analysis from VWAT explants which showed that adipose tissue samples from rapamycin-treated mice secreted more IL-6 and MCP-1 than control explants whereas the amount of TNFa and IL-10 was comparable (Figure  3E ). Adipose tissue inflammation was associated with systemic inflammation, as revealed by higher blood levels of IL-6 and TNFa and decreased level of IL-10 in Rapa mice, compared to controls (Figure  3F ).
Acknowledgments The authors acknowledge the staff of the animal facility of the  Pasteur Institute in Lille  for animal husbandry and care. We thank  Dr. Morgane Baron  ( CNRS UMR8199 ) for manuscript reviewing and  Dr. Francois Trottein  ( CNRS UMR8204 , Inserm  U1019 ,  Lille Pasteur Institute ) for fruitful discussions. We also thank  Emeric Deruy  and  Antonino Bongiovanni  ( CNRS UMR8204 , Inserm  U1019 ,  Lille Pasteur Institute ) for flow cytometry and microscopy (Axioplan 2) facility and analysis.
05). #Indicates significant differences between Evimu + (i) (evolved ex planta-in planta) and Ev-imu + (i9) (evolved ex planta) populations (t-test, p,0. 05). `Indicates significant differences between Evimu + and Ev-Dimu populations for each series of competition experiments (either Ev-imu + (i) versus Ev-Dimu(i) or Ev-imu + (i9) versus Ev-Dimu(i9), t-test, p,0. 001). See Figure  S5B  and S5C and Data S3 for details. (C) Relative ex planta fitness of imuA2B2C2 + versus DimuA2B2C2 populations following coinoculations of final populations derived from ex planta-in planta lineages. Bacteria recovered from the Jensen medium were counted 7 days after inoculation in Gibson tubes containing M. pudica plants. imuA2B2C2 + ancestors better survived in Jensen-Mimosa than DimuA2B2C2, in accordance with results presented in Figure  S2A.
`Indicates significant differences between imu + and Dimu populations for each series of competition experiments (either An-imu + (i) versus An-Dimu(i) or Ev-imu + (i) versus Ev-Dimu(i), t-test, p,0. 01). No significant difference was observed between ancestral imu + clones and evolved imu + populations. Raw data are provided in Data S3. doi:10. 1371/journal. pbio. 1001942. g003 (i) 82% of all plasmid imuBC cassettes fall in the six genera that contain pSym-rhizobia, and (ii) 45% of the symbiotic plasmids carry a imuBC cassette (Figure  5 ; Table  S3 ). Noteworthy, vestigial imuBC genes were found in some rhizobia (e. g. , Rhizobium sp. IRBG74 GenBank, http://www. ncbi. nlm. nih. gov/Genbank, accession number CDI11787. 1/CDI11788. 1) suggesting that mutagenesis cassettes have been lost, possibly as a result of counterselection of hypermutagenesis in well-adapted symbiotic populations.
Genome Re-sequencing Individual clones and pools of clones were re-sequenced using the Illumina/Solexa technology, either the GA2X or HiSeq technology (Table  S1 ). Sequence data production was performed by the C. E. A/IG/Genoscope (clones A16, B16, C16, G16, H16, I16, M16, N16, S16, and pools N1-3, J1, JM1-2), DNA Vision (pool JM6), or the PlaGe platform (other pools of clones and RCM252-RCM271 clones). Average sequence coverage of pools and clones from pools is indicated in Table  S1. High throughput sequencing (HTS) data were analyzed using bioinformatic pipeline implemented in the Microscope platform  [53]. The current pipeline is a ''Master'' shell script that launches the various modules of the analysis (i. e. , a collection of C homemade software) and controls for all tasks having been completed without errors.
In a first step, the HTS data were preprocessed to assess its quality. This step includes options such as read trimming, merging, or splitting paired-end reads. In a second step, reads were mapped onto the reference replicons (RefSeq accession number NC_003295. fna and NC_003296. fna for the R. solanacearum str. GMI1000 chromosome and megaplasmid, respectively, RefSeq accession number NC_010528. fna, NC_010530. fna, and NC_010529. fna for the C. taiwanensis str. LMG19424 Chromosome 1, Chromosome 2, and pRalta, respectively) using the SSAHA2 package  [54]. Only unique matches having an alignment score equal to at least half of their length were retained as seeds for full Smith-Waterman realignment  [55]  with a both sides five nucleotides extended region of the reference genome. All computed alignments were then screened for discrepancies between read and reference sequences and in fine, a score based on coverage, allele frequency, quality of bases, and strand bias was computed for each detected event to assess its relevance.
Phylogeny and Distribution of Plasmid Cassettes Genomes of aand b-proteobacteria larger than 1 Mb were downloaded from GenBank RefSeq as available in February 2013. ImuABC cassettes were identified in protein coding sequences as genomically contiguous matches of PFAM profiles for Y-and Cpolymerases (respectively, PF00817. 15 and PF07733. 7). Rhizobial genomes were identified by the presence of the common nodABC genes, respectively, PFAM domains PF02474, PF01522, PF00535. Profiles were searched using hmmer with eval ,10 25 and only hits whose alignments covered more than half of the profile were selected. nodABC and imuBC genes were classified according to the replicon where they were encoded as chromosomal or plasmid-encoded. Amino acid sequences of imuBC genes extracted from GenBank RefSeq complete genomes as available in February 2013 were aligned with Muscle  [60]  or MAFFT  [61]  and informative positions were extracted using BMGE  [62].
Sequence Data Sequence data for clones (SYMPA) or pools of clones (MUTA) are available on https://www. genoscope. cns. fr/agc/microscope/ expdata/evoProject. php M. pudica plants and alive population sizes were estimated at different times. Twelve independent experiments were performed for each strain. GMI1000pRalta was labeled with the same spectinomycin-resistance cassette as GMI1000pRaltaDi-muA2B2C2 to avoid cassette-dependent growth modification (see Methods). The loss of the cassette significantly reduced the survival of the bacterium in the medium with Mimosa (p,0. 001, ttest; p,0. 001, Signed-rank test). (C,D, and E) Bacteria containing the replicative but unstable plasmid pLAFR6 were grown in log phase for several days in rich BG medium (C), in minimal MM 2% glycerol medium (D), or inoculated into Jensen-filled Gibson tubes containing or not M.
pudica plantlets (E). The presence of pLAFR6 was determined by plating bacteria on appropriate medium. Dots represent independent replicates from three independent experiments, diamonds represent the mean. The rate of plasmid loss per generation was similar (R 2 = 0. 9601) in (C) (y = 20. 0297x+0. 9748) and (D) (y = 20. 0276x+1. 0869) and thus independent from the culture medium. On the basis of this rate, we estimated a maximum of five and three generations, respectively after 21 days in Jensen or Jensen Mimosa, suggesting that cells expressing the growth advantage in stationary phase phenotype  [65]  were not significantly selected during this period. Raw data are provided in Data S5. (EPS) Percentage of imuA2B2C2 + strains in nodule populations following co-inoculation with pairs of An-imu + (i) and An-Dimu(i) ancestors or with each pair of Ev-imu + (i) and Ev-Dimu(i) populations evolved through ex planta-in planta cycles (see Figure  3A ).
Bacteria recovered from the Jensen medium were counted 7 days after inoculation of Gibson tubes containing Mimosa plants. Values   chromosomal cassettes. Abbreviations: Ac. , Acidovorax; Ag. , Agrobacterium; Bo. , Bordetella; Br. , Brucella; Bu. , Burkholderia; Ca. , Caulobacter; Cu. , Cupriavidus; Fr. , Frankia; Me. , Mesorhizobium; Mt. , Methylobacterium; P. , Pseudomonas; Ra. , Ralstonia; Ro. , Rhodobacter; Rh. , Rhizobium; S. , Sinorhizobium; V. , Vibrio; X. , Xanthomonas. Alignments are provided in Data S8. (EPS) Table  S1  Number of point mutations detected in pools of clones. The clones were randomly isolated 21 days after inoculation of a founder strain in a Gibson tube filled with Jensen medium and containing or not M. pudica plantlets. Each pool contains equimolar concentration of DNA from 19 (J4) or 20 (others) clones from a same compartment.
001). See FigureS5Band S5C and Data S3 for details. (C) Relative ex planta fitness of imuA2B2C2 + versus DimuA2B2C2 populations following coinoculations of final populations derived from ex planta-in planta lineages. Bacteria recovered from the Jensen medium were counted 7 days after inoculation in Gibson tubes containing M. pudica plants. imuA2B2C2 + ancestors better survived in Jensen-Mimosa than DimuA2B2C2, in accordance with results presented in FigureS2A. `Indicates significant differences between imu + and Dimu populations for each series of competition experiments (either An-imu + (i) versus An-Dimu(i) or Ev-imu + (i) versus Ev-Dimu(i), t-test, p,0. 01). No significant difference was observed between ancestral imu + clones and evolved imu + populations. Raw data are provided in Data S3.
Bacteria recovered from the Jensen medium were counted 7 days after inoculation of Gibson tubes containing Mimosa plants. Values  are from three independent competition experiments. *Indicates significant differences between imu + and Dimu ancestors/populations for each competition experiment. Horizontal bars represent means. Raw data are provided in Data S3. (EPS) Figure S6 Phylogenetic tree of the ImuBC cassette. Maximum-likelihood phylogenetic tree of the concatenated ImuBC amino-acid sequences. Sequences were chosen among completely sequenced strains, with a focus on aand b-rhizobia. Numbers at the nodes indicate bootstraps (1,000 experiments). Frankia sp. Eu1c was used to root the tree. When appropriate, names of the plasmids carrying an ImuBC copy are indicated in brackets. Plasmid cassettes are in green and rhizobia are underscored.
Funding: PR and CC were supported by the  French National Research Agency  ( ANR-08-BLAN-0295-01 ) and by the  French Laboratory of Excellence project ''TULIP'' (innovative project ), respectively. This work was supported by funds from the  French National Institute for Agricultural Research (Plant Health  and the  Environment Division) , the  French National Research Agency  ( ANR-12-ADAP-0014-01 ), and the  French Laboratory of Excellence project ''TULIP''  ( ANR-10-LABX-41 ;  ANR-11-IDEX-0002-02 ), and by a  European Research Council  starting grant [EVOMOBILOME nu281605] to EPCR. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Acknowledgements. F. Domine thanks  CEN Grenoble  for hosting him to carry out the experimental work. The assistance of  François Touvier  to operate the snow heater and of  Jean-Michel Panel  and  Jacques Roulle  to operate the cold room are gratefully acknowledged. J. -C. Gallet was supported through the projects " Long Range transport of Black Carbon and the effect on snow albedo in North East China and in the Arctic " funded by the  Norwegian Research Council (Norklima program , project  193717 ) and " Satellite Remote Sensing of Atmosphere-Surface Systems and Ground Truth Measurements " funded by the  Norwegian Research Council (Norklima program , project  209681/E10 ). Edited by:  M. Schneebeli.
So, to test piRNA association with the chimeras, HA-tagged proteins were immunoprecipitated and bound small RNAs examined by 5 ′ -end labeling (Fig. 3D ). Repeatedly, only the Siwi-Ago3 chimera showed the presence of small RNAs. We prepared several additional mutants with single domain swaps (Fig. 3A ) but did not manage to get Ago3-Siwi chimeric constructs that bound RNAs. We believe that structural incompatibilities of the fused domains might have resulted in proteins that are misfolded and nonfunctional. To examine the small RNAs associated with the HA-Siwi-Ago3 chimera, we prepared three independent deep-se- quencing libraries (data from only two libraries are presented in Fig. 4 ). Sequences present in the HA-Siwi-Ago3 chimera libraries had a peak size of 27 nt, very similar to Ago3 piRNAs and different from those bound by Siwi (28 nt) (Fig.
Furthermore, the N termini of Piwi proteins are decorated with a variable number of arginine residues that are targets for symmetrical dimethylation by PRMT5  (Heo and Kim 2009; Kirino et al. 2009 ). These marks are recognized by the Tudor domain in Tudor domain-containing proteins, many of which are confirmed piRNA biogenesis factors. Thus, the N termini of Piwi proteins were considered to be key features in distinguishing them during piRNA biogenesis. Our data described above now implicate the MID-PIWI module of Ago3 as a landmark to distinguish it from Siwi in the BmN4 cellular environment. It remains to be seen whether this is also true for Siwi in BmN4 cells and for other Piwi proteins in other systems. Biogenesis of piRNAs begins in the nucleus with precursor transcription from piRNA clusters, but most biogenesis factors are localized to the cytoplasm, in peri-nuclear granules called nuages.
Expression, purification, crystallization, and data collection The His 6 -tagged MIWI MID domain was expressed in Escherichia coli BL21 Rosetta cells. Soluble protein was purified by a Ni 2+ -affinity chromatography using chelating sepharose beads (GE Healthcare). Tag removal was performed by proteolytic digestion using Tobacco Etch Virus (TEV) protease and a subsequent Ni 2+ -affinity step. The protein was further purified by size-exclusion chromatography in 25 mM Tris-HCl, pH 8. 0, 500 mM NaCl, 1 mM dithiothreitol (DTT), performed on a Superdex 75 10/300 GL column (GE Healthcare). The selenomethionine derivative (SeMet) of the MIWI MID domain (S480-E616) was expressed in E. coli B834 (DE3) cells grown in minimal M9 medium supplemented with 50 mg/mL L-SeMet (Sigma) and induced with 1 mM IPTG (EMBL Protein Expression and Purification Core facility).
ACKNOWLEDGMENTS We thank the  High-throughput Crystallization facility in EMBL-Grenoble , and the  EMBL Core facilities (Gene Core, Protein Expression and Purification Core Facility) at EMBL Heidelberg , for their support. We also thank the  ESRF  and  EMBL-Grenoble beamline  staff for help, especially  Silvia Russi  for assistance with data collection and analysis. E. C. is supported by a fellowship from  Region Rhône Alps  ( CIBLE 2009 ) and R. R. P. by a fellowship from the  EU (EIPOD). This work was supported by grants from the  EU  ( ERC Starting Grant  "pisilence") and  National Institutes of Health  ( 1R01HD069592-01A1 ) to R. S. P. and ( 1R21HG003794-01 ) to  R. S. Work in the Pillai lab  is supported by the  EMBL. February 5, 2014; accepted February 27, 2014.
Overview of PDG model The physiological process-based module This module corresponds to the CASTANEA library hosted on the CAPSIS platform. Initially developed at the stand scale, CASTANEA  (Dufrêne et al. 2005)  simulates canopy photosynthesis (i. e. , gross primary production, GPP) and transpiration, maintenance and growth respiration, seasonal development and assimilate partitioning to leaves, carbohydrate storage (hereafter reserves), stems, branches, and coarse and fine roots. The meteorological driving variables are global radiation, rainfall, wind speed, air humidity, and temperature. A complete description of the model is given in  Dufrêne et al. (2005) , and the submodel of carbon allocation is described by  Davi et al. (2009). In its initial version, CASTANEA simulated CO 2 and H 2 O fluxes, considering one average tree as representative of the whole stand.
Acknowledgements We thank  K Csill  ery,  M. Cailleret ,  E Klein ,  F Lef  evre,  O. Savolainen , and two anonymous reviewers for useful comments on a previous version of this manuscript. We are indebted to  F de Coligny ,  P. Dreyfus ,  C. Pichot  for the informatics development on CAPSIS. We thank  A Amm ,  A Bontemps  and  M Cailleret ,  J Gauz€  ere for their PhD studies that allowed the calibration of PDG. This calibration benefitted from the support of  UEFM  ( F Jean ,  O Gilg ,  M Pringarbe ,  F Rei ,  N Turion ). The development of the PDG model was funded by  FRB  (project  VARIADAPT ),  ERA-Net BiodivERsA   LINKTREE  project ( ANR-08-Biodiversa-006-06 ), and  ERA-Net BiodivERsA   TipTree  project ( ANR-12-EBID-003 ). Simulations were performed on the computation cluster of  INRA BioSp, Avignon.
Binding of Bye1 to class II genes promoters requires Set1C-mediated tri-methylation of H3K4 Bye1 has been shown to interact with H3K4me3 via its PHD finger in vitro and, globally, to co-localize with the H3K4me3 modified +1 nucleosome downstream the TSS  [17, 20]. To assess a role of H3K4 methylation in Bye1 recruitment to promoter regions in vivo, we performed ChIP of Bye1-Myc in strains lacking either Set1 or Spp1 subunits of the Set1C complex. Set1 is the catalytic subunit of the complex responsible for all types of H3K4 methylation (mono-, di-or tri-) while Spp1 is required only for trimethylation of H3K4  [21]. We found that specific depletion of H3K4me3 is sufficient to abolish Bye1 binding to gene promoters tested within the dataset, but doesn't affect it in the body of class II and class III genes (Figure  4 ).