dataesr/scientific-paragraphs-categorization huggingface dataset:
After the thermal cycling, the plate was then analyzed on droplet reader. Wells containing all reagents and RNA/DNA-free water were used as negative control. The software package provided with the ddPCR system (QuantaSoft v1. 7, Bio-Rad) was used for data acquisition. For mycotoxin analysis, each of twelve remaining spikelets by conditions was grinded with liquid nitrogen and 5 mL of acetonitrile/water/acetic acid (79:20:1, v/v/v) was added. Samples were homogenized by mechanical agitation for 20 min. Samples were preliminarily diluted 1:50 in water/acetic acid (99. 5:0. 5; mobile phase of analyzer) and filtered with a CA filter (0. 45 µm, Carl Roth GmbH, Karlsruhe, Germany) before injection. Mycotoxin detection and quantification were achieved using an Ultra High-Performance Liquid Chromatography (UHPLC, Shimadzu, Tokyo, Japan) coupled with a mass spectrometer (8040, Shimadzu, Tokyo, Japan) as described in  [17].
Data Treatment and Statistical Analysis With the aim of considering complete growth and mycotoxin production kinetics, and not only a final point, three parameters have been extracted from the curves: the area under the curve, the maximum speed and the plateau reached. The area under disease progression and mycotoxin production curve was finally chosen because it is the most discriminant parameter to differentiate several conditions. Statistical data analysis was performed with R Software (3. 4. 4, R Foundation for Statistical Computing, Vienna, Austria, 2017). Normality and homogeneity of variances were verified and the effect of BCA treatments or difference between conditions was tested with a one-way ANOVA and multiple comparisons of means were done with Tukey's test (α = 0. 05). Graphics program used for the artwork was Adobe Illustrator (Adobe, San Jose, CA, USA).
Acknowledgments: Thanks to IAGE companies for their support in realization of ddPCR for detection and quantification of F. graminearum and Xeda. Special thanks go to  Maureen PELLAN , graphic designer, for her support in the artwork of F. graminearum and wheat life cycle. Thanks also to  Jean-Benoit Morel  and his BGPI research group for their advice and support regarding the choice of variety and growth of wheat spikelets. We thank the  DeSangosse ® , LallemandPlantCare ® , Xeda International ® and Florimond Desprez ® companies  for their donations of different commercial biocontrol agents (respectively Polyversum ® , Mycostop ® , and Xedavir ® ) and Miradoux ® wheat seed.
Phylogenetic analysis A Maximum likelihood phylogenetic tree covering the different strains of our study was obtained by analysis of the pan-genome single-nucleotide polymorphism (SNP) using ksnp3 program  (22) , itself calling FastTree2  (23). Results from this initial analysis were analyzed to identify groups of clonal strains whose genome sequences were different by less than 10 snps among the snp positions identified in all 499 strains. Only one strain per group were kept which led to a set of 269 E. coli strains. A new pan-genome single-nucleotide polymorphism (SNP) analysis was performed using ksnp3 program to produce a Maximum-Likelihood (ML) phylogenetic tree for these non-clonal strains. The strain of E. albertii was included as an outgroup. Graphical representation of the ML-tree was performed using the iTOL web server  (24).
In silico LPS core type determination, ECOR and serogroup typing The type of core LPS was analyzed based on the presence of different alleles of the waaL gene as described previously  (25). In silico ECOR typing was performed using the ClermonTyping script  (26). Serogroup analysis was performed using serotype specific sequences from ECTyper (https://github. com/phac-nml/ecoli_serotyping). The phylogroup determined by the ClermonTyping was, for a few strains, not consistent with the phylogenetic clustering performed by ksnp. In such situations, the ksnp clustering was retained. ST and STc analyses were performed using the MLSTar package (v 0. 1. 3) using Achtman scheme and STc were allocated based on pubmlst. org database. Virulence genes repertoire analysis   (27)  and a presence/absence matrix was generated as described in Kempf et al.
Association analyses For each type of core, a 2x2 contingency table was generated with the number of strains possessing or not the analyzed specific core and the number of strains positive for each virulence gene group. A strain was considered positive for a virulence gene group when its enrichment score was higher than 0. 7. The p-value for the probability that each contingency table was a random distribution was calculated by a fisher exact test using stats (v4. 0. Heatmaps of p-values were generated using the pheatmap package (v1. 0. 12).
Distribution of LPS core types in the different phylogroups The aim of this study was to investigate the relationship between the different types of LPS core, the phylogenetic group and the carriage of virulence genes in the E. coli species. To this end, we first randomly selected 500 Escherichia genomes in Genbank including 499 E. coli genomes and 1 E. albertii genome. Despite being randomly selected, an initial snp analysis suggested that some strains might be clonal. Because of this potential clonality, before undertaking more in-depth studies, we removed from our dataset strains that could be considered as representative of the same clones and only one strain per such group was kept (see methods). This filtering resulted in a set of 269 strains to which was added the E. albertii genome as outgroup.
Distribution of strains among the main E. coli phylogroups in this dataset of 269 strains was as follows: 83 phylogroup A strains (30. 7 %), 87 B1 strains (32. 2 %), 49 B2 strains (18. 1%), 10 C strains (3. 7 %), 22 D strains (8. 1 %), 14 E strains (5. 2 %), 4 F strains (1. 5 %) (Figure  1 ). Prevalence of the different LPS core types in this set of E. coli strains were 14 (5. 2%) for K-12, 105 (38. 9%) for R1, 27 (10. 0%) for R2, 84 (31. 1%) for R3, 35 (13. 0%) for R4 (Figure  1 ). LPS core type could not be attributed for 5 strains (1. 9%) The prevalence of each core type in each of the different E. coli phylogroups was then analyzed which showed that the proportion of the different LPS core types was highly variable depending on the phylogroup of strains (Figure  2 ). This distribution is non-random as indicated by a Fisher exact test (p<0.
Relationships between phylogeny, LPS core types and virulence gene repertoire We analyzed the distribution of LPS core types in a genome-wide, SNP-based phylogenetic analysis of the 269 E. coli strains. The genome sequence GCA_001286085, annotated as an E. albertii sequence in the GenBank database and identified as such by Clermontyper, was used as an outgroup. Again, this analysis clearly differentiated the seven major phylogenetic groups described in the E. coli species. The ST complex (STc) to which each strain belongs was determined in silico. We further investigated the link between phylogeny, specific LPS core types and the carriage of specific virulence genes by defining the repertoire of virulence genes carried by each strain based on the virulence gene dataset published by Leimbach and colleagues  [26].
Interestingly, B2 strains with a K-12 LPS core all belonged to the STc131 complex. When the 500 strains from our initial dataset were considered, this finding was confirmed (Figure  7 ). This cluster of B2 strains with a K-12 LPS core types, all belonging to STc131, are enriched in VGG #9, 13 and 35 containing the fec operon, the lateral flagellar genes and the aerobactin operon respectively (  Fig 7). A group of B2 strains related to the STc28 with a R3 LPS core type are the only ones carrying the VGG#1-2 genes corresponding to the T3SS and some of its effectors. These strains also possess an O-antigen capsule cluster (etk, etp and gfcBCDE genes -found in VGG #43) and are devoid of any of the five T6SS analyzed. Other B2 strains, belonging to the STc73, STc95, STc12 and STc14, almost all carried an R1 core type and were enriched in VGG #18-19, 24-26, 28, 33, and 36 corresponding, among others, to the colibacin operon and several frimbriae gene clusters (Figure  7 ).
Distribution of T6SS and iron acquisition genes Among the virulence genes analyzed, the distribution of Type 6 secretion systems and iron acquisition systems highlighted features of particular interest. First, our virulence dataset covered five different T6SS operons which were not distributed evenly between strains of the different phylogroups (Figure  8 ). The T6SS from strain 536, belonging to VGG #20, was mostly present in B2 strains, while the one from strain Ecc-1470 (VGG #37) was mostly present in E and B1 strains and absent from B2 strains. The T6SS from strain APEC-O1 (VGG #26) was largely present in B2 strains, with the notable exception of strains from STc131 and STc73 complexes. Interestingly, B2 strains from STc28 did not possess any of the five T6SS. Among D strains, strains possessed either T6SS from APEC-O1 or from ECC-1470 but never both.
DISCUSSION The initial purpose of this study was to investigate the distribution of the different LPS core types in the E. coli species. LPS core types are encoded by the waa locus genes located approximately 100kb from the origin of replication in the E. coli species. The five distinct regions share highly similar 5' and 3' regions, encompassing waaDFC and waaA-waaQGP genes, while showing variable regions in between with lower GC% values which may correlate to requirement for higher level of transcription for this essential biosynthetic locus (Supplementary figure  1 )  (28). After selecting a random set of 500 E. coli genomes from Genbank and restricting our dataset to 269 E. coli genomes with more than 10 snp differences, we thus set out to examine the prevalence of the difference core types, each core type being characterized by the presence of the O-antigen waaL specific ligase as previously described  (25).
[results] Results CrTRXz folds as a canonical thioredoxin Recombinant TRXz from Chlamydomonas reinhardtii (CrTRXz) was heterologously expressed in E. coli as a 149 amino acids polypeptide (predicted mature protein including residues 56-183 plus the Nterminal affinity tag) and purified to homogeneity by metal-affinity chromatography. Purified CrTRXz was crystallized, the crystals were cryoprotected and submitted to X-ray diffraction for the collection of a complete dataset indexed in space group P3 2 21 and solved by molecular replacement with CrTRXf2 (PDB ID code: 6I1C) as a search model. Model correction and completion up to 116 amino acid residues and one water molecule was refined to R=0. 2296 and R free =0. 2335 at a resolution of 2. 4 Å (Table  1 ). CrTRXz folds according to the canonical TRX topology (SCOPe entry c.
Residues 58-60 and 170-183 were not built because of a lack of interpretable electron density. Pairwise alignments of equivalent C α of CrTRXf2 and CrTRXm onto CrTRXz yielded a root mean square deviation (RMSD) of 0. 838 Å and 1. 356 Å respectively, confirming the close structural similarity between the experimentally solved Chlamydomonas TRX structures (Figure  S2 ). Further alignments with experimentally determined structures from the protein data bank (PDB) revealed also high similarities with Plasmodium falciparum TRX2 (PDB identifier 3UL3, RMSD=1. 16 Å), resurrected ancestral TRX from inferred last bacterial common ancestor (4BA7, RMSD=1. 18 Å), Bacteroides fragilis TRXP (3HXS, RMSD=1. 19 Å), and with 20 other TRXs with RMSD ≤ 1. 30 Å. CrTRXz topology is classical among TRXs.
Notably, CrTRXz presents the z-type conserved apolar L94 immediately after the redox site WCGPC, while all other plastidial TRX possess in this position either a positively charged residue (R/K for m-, x-and ftype) or an hydrogen bond donor residue (Q for y-type). Differential electrostatic repartition is particularly marked in the vicinity of the redox site and represents a significant qualitative difference with CrTRXf2 and CrTRXm equivalent surfaces (Figure  4B, 4D  and 4F ). The principal determinants of CrTRXf2 selectivity were proposed to be K78, K114, N130, K131, N133, K134, K143 and K164 (PDB entry 6I1C numbering  (Lemaire et al. , 2018) ). Equivalent positions on structurally aligned CrTRXz are occupied by E63, Q102, D119, E120, N121, P122, Q131 and E151. Seven out of these eight residues are conserved in TRXz homologs (Figure  S1 ) and the electronegative surface is predicted conserved in a land plant ortholog (Figure  S4 ), supporting an important function for type-z physiological functions in plants.
TRXz is electro-complementary to known protein interactants Four candidate proteins are described as TRXz interactants in Arabidopsis thaliana: FLN1, FLN2, PRIN2 and MRL7  (Yua et al. , 2014 , Arsova et al. , 2010 , Diaz et al. , 2018). The molecular structure of these proteins is not experimentally determined but their structures were predicted by homology using the PHYRE software  (Kelley et al. , 2015)  (Figure  5 ). AtFLN1 possesses five cysteines and based on the protein model, adjacent C105 and C106 are buried within the structure and seems to be affected by TRX only in a solvent exposed unfolded state. C204, C398 and C418 are predicted to be solventexposed and available for TRX redox interaction (Figure  5A ) even though they probably do not form intramolecular disulfide bridges as they appear too distant.
Discussion Here, we report the experimental structure of a TRXz from the model eukaryotic alga Chlamydomonas reinhardtii (PDB ID code: 7ASW). Structural analysis reveals that chloroplastic CrTRXz is a classical TRX with an atypical electronegative surface conserved in plant homologs. We dissected TRXz surface properties to assess its putative specificity over known target proteins of AtTRXz. Moreover, based on structural features, we proposed the Calvin-Benson enzyme CrPRK as being recognized by CrTRXz, which was confirmed by our in vitro activity assays.
Cloning Nuclear encoded amino acid sequence of Chlamydomonas reinhardtii thioredoxin z (UniRef100 entry A8J0Q8, thioredoxin-related protein CITRX) was analyzed by TargetP2. 0 (Emanuelsson et al. , 2007 , Almagro Armenteros et al. , 2019) , ChloroP  (Emanuelsson et al. , 1999)  and Predalgo  (Tardif et al. , 2012)  to predict the transit peptide cutting site and the subsequent mature sequence of chloroplastic protein. The sequence coding for amino acids 56-183 was PCR-amplified from Chlamydomonas reinhardtii EST database plasmid AV642845 with DNA primers 5'-TGTCGCCATATGGTCATTAGCCATGGAAAG-3' and 5'-CTCCTTAAGCTTCTACTGCTGCGGCGCCTCGGG-3'. The PCR product was inserted into pET28a by restriction with NdeI and HindIII and subsequent ligation, yielding pET28a-His 6 -CrTRXz. Recombinant protein is a fusion of Met-HHHHHH-SSFLVPRGSHM-and TRXz residues 56 to 183, as validated by plasmid Sanger sequencing.
Small angle X-rays scattering Diffusion curves were collected from BioSEC3-300 size-exclusion chromatography in line with X-ray exposure capillary at beamline SWING of synchrotron SOLEIL (Saint-Aubin, France). Data were processed with FOXTROT (Xenocs, Grenoble France) using CLEVERAVG algorithms and interpreted with ATSAS  (Petoukhov et al. , 2012 , Franke et al. , 2017).
Crystallization and structure determination Purified CrTRXz was tested for crystallization on commercial sparse-screening conditions (Qiagen, Hilden Germany) of the Joint Center for Structural Genomics screens  (Lesley and Wilson, 2005)  with a mixture of 30 nL protein and 30 nL precipitant equilibrated against a reservoir volume of 30 µL mother liquor. 30 µm sided monocrystals grew in one week in condition 38 at position D2 of screen IV (0. 1 mol. L -1 HEPES pH=7,5; 1,26 mol. L -1 ammonium sulfate). Crystals were transferred in mother liquor supplemented with 12. 5% glycerol and flash-frozen in liquid nitrogen for diffraction experiments at micro-focused beamline PROXIMA-2A at SOLEIL synchrotron (Saint-Aubin, France). A 99. 36 % complete dataset was collected at 2. 444 Å resolution. Data was indexed in space group P3 2 21, integrated, scaled and converted with XDSME  (Legrand, 2017).
Acknowledgements This work was funded by  CNRS ,  Sorbonne Université , and  Agence Nationale de la Recherche  grants  LABEX DYNAMO 11-LABX-0011 ,  CALVINDESIGN  ( ANR-17-CE05-001 ) and  CALVINTERACT  ( ANR-19-CE11-0009 ). Libero Gurrieri  was supported by grant  PON ARS01 00881 "ORIGAMI"  ( Italian Ministry of University and Research ). Fernanda Pires Borrega  and  Sandrine Hoang  contributed to the preparation of recombinant thioredoxin z. The  Institut de Biologie Physico-Chimique  ( FR 550 CNRS ) provided access to crystallization facilities. We acknowledge SOLEIL for provision of synchrotron radiation facilities. We thank  Martin Savko ,  Serena Sirigu , and  William Shepard  for assistance in using beamline PROXIMA-2a, and  Aurélien Thureau  and  Javier Perez  for assistance in using beamline SWING.
Conflict of Interest Statement The authors have no conflicts of interest to declare. Supplementary figures Supplementary figure 1. Sequence alignment of CrTRXz homologs. Sequence alignment was performed by Clustal Omega with homologs from different species. Residues with more than 50% conservation are colored in red, strictly conserved residues are in white with a red background. Numbering is according to the sequence of TRXz from Chlamydomonas reinhardtii. TRX sequences were retrieved from UniprotKB database for the following species: Chlamydomonas reinhardtii (A8J0Q8), Gonium pectorale (A0A150FZQ6), Tetrabaena socialis (A0A2J7ZQ73), Volvox carteri f. nagariensis (D8TVT1), Ostreococcus tauri (A0A1Y5IIS5), Arabidopsis thaliana (Q9M7X9), Synechocystis sp. PCC 6714 (A0A068MSG5), Glycine max (I1JW39).
5-50 μM) of CrTRXz (white bars), CrTRXf2 (light grey bars) and CrTRXm (dark grey bars) in presence of 0. 2 mM DTT. TRX:PRK molar ratios (n:n) are indicated for each tested condition. Control sample (CTR, black bar) shows the activity after incubation with 0. 2 mM DTT without TRXs. All the activities were normalized on fully activated PRK obtained after 4 h of reduction with 40 mM DTT. Data are reported as mean ± standard deviation (n=3). Crystallographic diffraction data and model statistics. Statistics for the highest-resolution shell are reported in parentheses. of CrTRXz crystal structure. (F) Electrostatic potential of AtTRXz Phyre2 model. Potential is colored from red (negative) to blue (positive). (PDB identifier 1DBY).
Phenotype and genotype geographical distribution mirrors past human migrations and natural selection  [4] [5] [6] [7]  and comparison with primates makes it possible to evoke their evolutionary and migration trajectory with accuracy  [8, 9]. Red cell blood groups are also crucial in medicine to ensure transfusion safety, transplants, and foeto-maternal compatibility  [10]. To date, the International Society of Blood Transfusion (retrieved from the ISBT website, http://www. isbtweb. org) has recorded more than 380 blood group specificities grouped into 40 systems. In transfusion, it is routine practice to scrutinize six blood groups: ABO, Rh, Kell, Duffy, Kidd and MNS (reviewed in  [10] ). Curiously, despite their significance and the amount of available genotypic data on modern Humans that is continuously accumulating  [11] , almost no attention has been paid to these major red cell blood polymorphisms in palaeogenetic studies  [12].
3C ). No differences in species abundance were identified with a range of shotgun metagenomics taxonomic classifiers, such as IGGsearch, MetaPhlan2 or Kaiju (Supplementary Data 1). There was a large intragroup variability by comparison to the variability observed between the two groups of rats (species-level operational taxonomic units of IGGsearch shown in Fig. 3B ), which prevented reaching definitive conclusions. This was also the case when we measured pathway abundances for tryptophan (Fig. 3D ) and nicotinamide metabolism (Fig. 3E ). Since the low levels of pesticides that comprise the mixture studied here had limited effects on gut microbiome composition, we further evaluated if the mixture and the tested pesticide individually affected bacterial growth in vitro at a broad range of concentrations.
We finally compared our transcriptome findings to a list of gene expression signatures collected from various rat tissues after treatment with various drugs from the drugMatrix toxicogenomics database (Table  S2 ). The alterations in the liver transcriptome we observed correlated well with those of livers from a study in which nicotinamide was administered to rats at a dose of 750 mg/kg (adj-p = 1. 6e-7). This correlates well with the changes in the biochemical composition of the serum-gut microbiome axis. Reduced representation bisulfite sequencing (RRBS) of the liver samples was also performed to assess if alterations in epigenetic (DNA methylation) status may be responsible at least in part for the treatment-related changes in gene expression patterns. There were no differences in the percentage of methylated cytosines in CpG islands (42.
We assessed the significance of our classification using permutation tests. The number of variables investigated (n) is also shown. New estimates of R2Y and Q2 values were calculated from this 1000 times permuted dataset (p values pR2Y and pQ2 for permuted R2Y and Q2, respectively). methylation per base. Since a given base is generally either methylated or not in a given cell, it is expected that the distribution of percentage DNA methylation per base has a bimodal distribution, which is the case in our study (Fig. 6A ). We also annotated the methylation calls. DNA methylation patterns in relation to gene transcription start sites (TSS) showed that CpG dinucleotides near TSS tend to be unmethylated, which confirmed that our RRBS analysis is of a good quality (Fig. 6B ). We We presented fold changes (FC) for the metabolites that were found to have their variable importance in projection (VIP) scores > 2 in the OPLS-DA analyses.
No deviations from the above-mentioned values were registered. Cages were identified by a card indicating study protocol code, experimental and pedigree numbers, and dosage group. The cages were periodically rotated on their racks to minimize effects of cage positions on animals. Diet and treatments. Experimental groups consisted of 12 female Sprague-Dawley rats of 8 weeks of age, treated for 90 days. Female animals were chosen to make the results of this investigation comparable to our previous studies, showing that the longterm exposure to a glyphosate-based herbicide was associated with the development of liver disease  73, 74. Animals received ad libitum a rodent diet supplied by SAFE (Augy, France). The feed was analysed to identify possible contaminants or impurities and these were found to be below levels of detection for all substances tested (Supplementary Data 4).
Briefly, DNA was digested with MspI prior to end repair, adapter ligation and size selection. Products were then amplified by qPCR and pooled in equal amounts. Pooled libraries were bisulphite converted and PCR enriched following a second qPCR amplification. Libraries were quantified using the Qubit® 2. 0 Fluorometer (Life Technologies) followed by quality assessment using the Agilent 2200 Tapestation and DS1000 screentape (Agilent Technologies). Pooled libraries were loaded at 1. 1 M with 20% standard PhiX library (Illumina, CA, USA) and sequenced to 75 base pair single end on a NextSeq 500 (Illumina, CA, USA). Data were aligned to the rat reference genome Rn6 with Bismark  76. A total of 407,904,185 reads (average of 16,996,008 ± 4,648,420 reads per sample) were generated for the 24 liver samples.