dataesr/scientific-paragraphs-categorization huggingface dataset:
MrModeltest selected HKY+G, GTR+I+G, SYM+G and SYM+G as the best-fit models for the ITS, 28S, rpb2 and ITS-28S-rpb2 datasets for the BI analyses. ML and BI analyses of the respective ITS, 28S and rpb2 datasets produced almost identical topologies with comparable support values. The ITS, 28S and rpb2 phylogenetic analyses inferred all identical deep and middle rank relationships but their respective topology solved different terminal relationships for M. furcata, M. mesoamericana, M. orientalis and M. pseudofurcata (refer to S2 Fig). However no significant conflict was detected between the topologies inferred by individual locus. Bootstrap proportions higher than 70% in the ML analysis (ML-BP) and posterior probabilities of the Bayesian Inference (BI-PP) higher than 95% are indicated above and below the branches respectively or as ML-BP/BI-PP by the node.
New species are in bold. Initials proceeding sample numbers refer to the collectors (see Table  1 ). https://doi. org/10. 1371/journal. pone. 0205840. g002 as in the three-locus phylogeny, where they formed a clade sister to that formed by the North American M. ochricompacta and Asian M. roxburghiae. Compared to the species of clade A, relationships among all the species of clade B are well resolved. Distance analysis on the ITS-28S-rpb2 combined dataset showed that the within-group mean distance of clade B (0. 035 ± 0. 003) is almost double that of clade A (0. 018 ± 0. 002).
Species delimitation Using the two criteria for determining evolutionary lineages in GCPSR, i. e. genealogical concordance and/or genealogical non-disconcordance  [40] , ten terminal independent evolutionary lineages were recognized. The tenth lineage, only supported by ITS analyses (ML-BP/ BI-PP 98/1. 00), comprised four out of the eight M. pseudofurcata sampled in this study (S2 For the ITS dataset (S1 Text), the highest within-group mean distance (0. 005) was for M. aurantiophylla. The lowest between-group value for the Malaysian sample 2676 (ITS: KP071201) is 0. 022 (between M. mesoamericana) and based on this, we took it as a distinct species (Multifurca sp). For the ITS-28S-rpb2 dataset (S1 Text), the highest within-group mean distance (0. 003) is for M. pseudofurcata group 2. The lowest between-group value for the Australian sample RH10009 is 0.
Morphologically, species from Australasia and Asia show higher morphological diversification than those in North America. For instance, the Asian M. zonaria is the only species in the genus that has both hymenial pseudocystidia and gloeocystidia  [3, 14, 19]. New Caledonian M. aurantiophylla is the only species in the genus that has mucronate pileocystidia  [3, 15]. In the lactarioid clade, the Australian M. stenophylla is the only one that can be morphologically recognized by the larger spores with a well-developed ornamentation  [16]. Moreover, in this clade an ITS sequence of a Malaysian sample (GenBank accession KP071201) shows relatively bigger genetic distance than those between the other Asian species and even Asian and American species. All these facts make us believe that tropical Asia, Australasia or somewhere between the two regions might be the key region in the early divergence of Multifurca and its two major clades.
Halling et al. [23]  suggested three possible hypotheses that could account for such a distribution: i) long distance dispersal by basidiospores, ii) post-Cretaceous migration of co-symbionts over land bridges with a change or shift in symbiotic partners, and iii) an ancient, Pangaean distribution with little migration since the breakup of Pangaea in the Cretaceous. Previous molecular studies have suggested that these three scenarios are all possible, e. g. Pisolithus and some species pairs of Hysterangiales for the first hypothesis, Solioccasus and Hydnum p. p. for the second, and Cyttaria and Tuberaceae for both the first and third)  [65] [66] [67] [68] [69]. Our analysis using a more ancient calibration point (500-560 Ma for the stem base age of Ascomycota) estimated the origin of Multifurca to be centered at the early Paleocene, well after the breakup of Gondwana.
Our estimated ages of Multifurca and its relatives in Russulaceae and Russulales are slightly older than those given by Looney et al. [63]  and Wisitrassameewong et al. [46] , although those of the mycenoid and suilloid clades, Agaricales and Boletales are largely in line with the mininum age of the corresponding fossils and estimated ages of these orders using genome data  [47, 48, 70]. Even with these older ages, the third hypothesis, i. e, an ancient, Pangaean distribution with little migration still does not currently fit Multifurca. The decrease in genetic distance from Australasia across Asia to North America argues against a panmictic distribution, and thus against random long distance spore dispersal as the sole mechanism (hypothesis one). Following our AAR results, the corresponding times of divergence and the symbiotic relationships with hosts, we have to accept a complex mechanism that incorporates both medium distance dispersal and post-Cretaceous migration to explain the current distribution pattern.
Similarly some published data may suggest the same mechanism in ectomycorrhizal fungi between the islands in the South Pacific and other landmasses. For instance, in Lactifluus, some samples from American Samoa are found as conspecific with a Papua New Guinean environmental sample  [72]. Wang et al. [25]  showed that in the Lactifluus leoninus lineage, southern China-Thai L. aff. leoninus and a Papua New Guinean environmental sample shared 97% similarity in ITS sequences. In the genus Hydnum, it was found that one sample from Papua New Guinea is nearly identical to some Chinese samples  [70]. More recently Han et al. [73]  showed at least three independent dispersal events for ancestors of Strobilomyces from Southeast Asia to Australasia. Considering the relatively low host specificity of Multifurca species or species pairs  [3, 16, 19]  we postulate that the dispersal of M.
furcata shares the same habitat and area of distribution with M. ochricompacta, it is much rarer than the latter species. Buyck et al. [3]  discussed M. furcata on the basis of sequence data obtained for M. mesoamericana, which is described as a new species below. Given the prevalence of cryptic species in the M. furcata species complex and even several ITS types of M. furcata in North America, to fix the precise application of the name M. furcata, epitypification based on DNA data is needed. When studying the mycelium-stipe transition, we found long and slender pseudocystidia with apices reminiscent of the typical aculeate-mucronate gloeocystidia in below-ground parts of species of subg. Multifurca. However, we were unable to find well-developed rhizomorphs. So far, there are no other observations made for below-ground structures of species in subg.
The aligned ITS dataset includes 43  sequences and 938 characters: 345 bp of ITS1, 155 bp of 5. 8S, and 438 bp of ITS2. The two ITS copies (GenBank accessions MH063850 and MH063851) of XHW2844 differ in six INDELs (Fig 1). Three of the six INDELs (sites: 700-701, 702, 816-819) are identical with those of M. mesoamericana and M. stenophylla, one (sites: 812-815) highly homogeneous with those of M. furcata and M. stenophylla and two (sites: 721, 755-756) unique. One of the two ITS copies of DPL4293 (GenBank accession MH063859) is homogeneous with that of M. mesoamericana at site 824 and with M. pseudofurcata and M. stenophylla at sites 914-916 and the other copy (MH063860) is the same as those of two samples of M. furcata (DPL6743 and DPL6495) (Fig 1). In addition, all taxa of the lactarioid clade more or less share INDELs with at least one of the other species (Fig 1).
Acknowledgments The curators of herbaria PC, F, NY and MEL generously provided loans of valuable specimens. J. Justice  and  D. P Lewis  provided recent collections of M. furcata (the epitype) and M. ochricompacta. Dr. F. Li ,  Sun Yat-Sen University , China generously provided a specimen of M. orientalis. The authors thank  Mrs. X. J. Wang ,  Baotou Normal University  and  S. C. Li , The  Union Medical University, Beijing  for help on the lab work. Dr. B. Feng  and  Dr. T. S. Yi ,  Kunming Institute of Botany, Chinese Academy of Sciences  gave direction on biogeographic analyses.
FUNDING Research in the Maroteaux laboratory has been supported in part by funds from the  Centre National de la Recherche Scientifique , the  Institut National de la Santé et de la Recherche Médicale , the  Sorbonne Université Sciences -Pierre et Marie Curie , and by grants from the  Fondation pour la Recherche sur le Cerveau , the  Fondation de France , the  Fondation pour la Recherche Médicale "Equipe FRM   DEQ2014039529 , " the  French Ministry of Research (Agence Nationale pour la Recherche   ANR-17-CE16-0008  and the  Investissements d'Avenir programme   ANR-11-IDEX-0004-02 ) and the  DIM Cerveau et Pensée  from  Region Ile de France. LM's team is part of the  École des Neurosciences de Paris Ile-de-France network and of the Bio-Psy Labex  and as such this work was supported by  French  state funds managed by the  ANR  within the  Investissements d'Avenir programme  under reference  ANR-11-IDEX-0004-02.
) for 3 h at room temperature. The cleaved sample was applied on a nickelnitrilotriacetic acid column, and the protein of interest was collected in the flowthrough and concentrated in a final buffer using Vivaspin TM ultrafiltration columns (GE Healthcare). The protein concentration was determined by measuring the absorbance at 280 nm using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and an ⑀ value of 1490 M Ϫ1 cm Ϫ1. MD simulations were carried out with the program Amber12 and using the all-atom ff03 force field in explicit solvent, represented by the TIP3P water model. A representative structure of the ensemble of NMR structures for the p8 homodimer (  7 ) was used as the initial structure (PDB code 2JNJ) as well as the yeast Tfb5-Tfb2C (p8/p52C) crystal structure (PDB code 3DOM).
The tleap module of AMBER12 software  (46)  was used to create a periodic box containing the complex, six Na ϩ ions, and 25,134 water molecules. The system minimization and the molecular dynamics simulations were performed with the parallel version of the PMEMD module of AMBER12, as described previously  (16). A total of 20 ns of MD were run at 300 K at constant pressure of 1 bar with the atomic coordinates saved every 1 ps. All of the calculations required over 56 CPU hours on an Intel Xeon E5540 at 2. 53 GHz. The fragment libraries were docked against the representative NMR structure of human p8 and the crystallographic structure of yeast Tfb5-Tfb2C. The docking calculations were performed using Autodock Vina version 1. 1. 2 (47). The pdbqt coordinates of the proteins were built with the addition of explicit polar hydrogen and Gasteiger partial charges.
The grid module of AutoDockTools was used to define the docking active site, by considering either the full structure or the residues located at the interface. The docking studies were performed on human p8, employing either a grid box with sizes of 74, 46, and 50 Å in the x, y, and z dimensions for the full protein or a smaller grid (28, 52, and 32 Å) restricted to the residues at the interface between the two monomers. The same procedure was used to perform docking against the p8 -p52 complex, with a grid box of dimensions set to 54, 52, and 58 Å in x, y, and z dimensions, respectively. For the interface, a grid box was built with x, y, and z sizes of 13, 15, and 4 Å. The pdbqt files of the fragments were translated into three-dimensional coordinates using the Open Babel version 2. 2. 3 program  (48).
1. 5) and drawn using Chemwindow. DSF experiments were carried out using a CFX96 real-time PCR detection system (Bio-Rad), and the fluorescence of the SyproOrange dye (Invitrogen Life Technology) as a function of temperature was recorded using the HEX channel (excitation, 450 -490 nm; emission, 560/580 nm). The samples were submitted to a temperature ramp from 20 to 95 °C with a heating rate of 0. 3 °C/min and 0. 5 °C increments. Data were analyzed using the CFX Manager TM software (Bio-Rad). A total of four measurements were recorded for each condition. The T m value was estimated from the transition midpoint of the fluorescence curve. The stability of p8 was monitored in different buffers distributed in 96-well plates (200 mM acetate (pH 5. 5), 200 mM MES (pH 6. 0 and pH 6. 5), 200 mM phosphate (pH 6.
The p8 (histidine tag-cleaved) protein sample buffered in 50 mM Tris, pH 7. 4, 150 mM NaCl, and 0. 25 mM TCEP was loaded on a Superdex 200 Increase 5/150 column (GE Healthcare) using an Agilent 1260 Infinity LC chromatographic system (Agilent Technology) coupled to a multiangle light scattering (MALS) detection system. The column was equilibrated with a 0. 1-mm filtered 50 mM Tris buffer, pH 7. 5, 150 mM NaCl, 0. 5 mM TCEP buffer. Data were collected using a DAWN HELEOS 8ϩ (8-angle) and Optilab T-rEX refractive index detector (Wyatt Technology). 100 l of protein sample at 140 M were loaded on the column, and the separation was performed at a flow rate of 0. 4 ml/min at 15 °C. Results were analyzed using ASTRA version 6. 1 software (Wyatt Technology). All NMR experiments were recorded at 298 K with 3-mm NMR tubes on a Bruker Avance 600-MHz spectrometer (Wissembourg, France) equipped with a proton-optimized triple resonance cryoprobe.
2% FA) and 5% solvent B (0. 2% FA in ACN). Proteins were eluted using the following gradient of solvent B at a 300-nl/min flow rate: 5-40% during 0. 5 min; 40 -99% during 7. 5 min, followed by 6 min at Targeting TTD-A to reduce transcription 99% and 2 min at 5%. The LTQ-Orbitrap Velos was operated either in single MS or in data-dependent acquisition mode with the XCalibur software. MS scans were acquired in the 500 -2000 m/z range with the resolution set to a value of 60,000. For top-down experiments, survey scan MS were acquired in the same way, with a resolution at 60,000. Precursor ions were selected from an inclusion list established thanks to previous MS analyses and were fragmented by collision-induced dissociation or higher-energy collisional dissociation, and the resulting fragment ions were analyzed in the Orbitrap, at a resolution of 60,000.
In brief, cells expressing XPB-YFP were imaged using a Zeiss LSM 710 confocal microscope with a ϫ40, 1. 3 numerical aperture oil immersion objective. All images were obtained at constant acquisition parameters so as to preserve relative fluorescent quantities within a given set of experiments. The resulting images were analyzed using the ImageJ program (53) as follows; after background subtraction, the total fluorescence signal present in the nucleus of individual cells was estimated and then averaged along with more than 90 cells over two or three independent experiments. The resulting data for the different conditions were then normalized to the compound 10 (mock)-treated case. RNA detection was performed using the Click-iT RNA Alexa Fluor imaging kit (Invitrogen), according to the manufacturer's instructions.
Acknowledgments-We acknowledge the use of PICT-Genotoul -Ibisa facility, funded by  Ibisa ,  CNRS , European structural funds, and the  Region Midi-Pyrenees  and the use of the imaging facility  CIQLE (Centre d'imagerie quantitative Lyon-Est, UniversiteClaude Bernard Lyon 1, Lyon, France). We are grateful to  M. Trivedi  and  K. Rottier  for input at the beginning of the project,  O. Saurel  for NMR support, and  L. Mourey  for insightful comments during the study. We acknowledge  B. Brutscher  for support with TRACT experiments, and we thank  B. Kieffer  and  A. Poterszman  for stimulating discussions and the generous gift of plasmids.
Edited by Karen G. Fleming This work was funded in part by the  RITC Foundation  and in part by  French Ministry of Research  ( Investissement d'Avenir Program ,  Proteomics French Infrastructure)  Grant  ANR-10-INBS-08  (to O. B. -S. ), the  FEDER (Fonds Europeens de developpement Regional) ,  Toulouse Me  ´tropole, and the  Region Midi-Pyrenees. The authors declare that they have no conflicts of interest with the contents of this article. This article contains supporting information and Figs. S1-S8.
The abbreviations used are: TTD-A, trichothiodystrophy group A; MD, molecular dynamics; DSF, differential scanning fluorimetry; TRACT, TROSY for rotational correlation times; c, rotational correlation time; SEC, size- exclusion chromatography; MALS, multiangle light scattering; STD, saturation transfer difference; ES cells, embryonic stem cells; PPI, protein-protein interaction; 2D, two-dimensional; CSP, chemical shift perturbation; HSQC, heteronuclear single quantum coherence; TEV, tobacco etch virus; TCEP, tris(2-carboxyethyl)phosphine; PDB, Protein Data Bank; ACN, acetonitrile; FA, formic acid; YFP, yellow fluorescent protein.
| Statistics To compare food collection on each diet, we used a Kruskal-Wallis ). The red central mark is the median, the edges of the box are the 25th and 75th percentiles, the whiskers extend to the most extreme data points not considered outliers, and outliers are plotted individually. Refer to Table  1  for the definition of each diet regression (using the function fitlme) were done in Matlab, with colony as a random factor. All consumptions were standardized ((value -mean)/standard deviation). This procedure reduces the covariation between linear variables and their interaction terms  (Aiken, West, & Reno, 1991). All statistical tests were performed using Matlab.
Response surfaces were visualized using the function tps in the package fields in the statistical software r. Red indicates the highest values for tunnelling activity, while blue regions are associated with the lowest values. The tunnel length was measured for each colony every 6 days until the end of the experiment and associated with the consumption of food over those 6 days (N = 562). We adjusted intake to the number of termites still alive when food was offered (i. e. , every 3 days), and tunnelling activity (cm dug per day) to the number of workers (as soldiers do not dig) still alive in each colony, to take into account differences in mortality between colonies. Adjusted R 2 of surface regression of tunnelling as a function of nutrient collected are, respectively, 0. 3, 0. 28 and 0. 11 (SI, Tables  S12-S14 ) in agreement with these predictions, termites kept food collection constant across a wide range of P:C:L ratios.
Effects of nutrient collection on termite survival (days). Daily consumption per individual (μg) was recorded for each experimental colonies of termites (70 workers and 30 soldiers in each colony) confined for the whole duration of the experiment to one of 11 diets varying in macronutrient content and composition. Response surfaces were visualized using the function tps in the package fields in the statistical software r. Red indicates the highest values for the life span, while blue regions are associated with the lowest values. Black circles indicate the mean intake per individual on each of the diet. (a) Effects of nutrient intake on workers survival (Mean life span for each experimental colony). (b) Effects of nutrient intake on soldiers survival (Mean life span for each experimental colony).
Mass spectra were recorded with an Agilent Technologies 5975C inert MSD with triple axis detector. The mass spectrometer was operated under electron impact ionization conditions (electron energy 70 eV, source temperature 230 • C). Data were obtained in the full scan mode with a mass range of m/z 50-550 atomic mass units (amu), using the MSD Chemstation software E. 02. 02. 14. 31 (RRID:SCR_015742). Identification of the FA methyl esters was based upon retention times obtained for a homemade pool of FA methyl ester commercial standards with a purity >99% (Sigma) when available. The National Institute of Standards and Technology database (version 2. 0, RRID:SCR_006440) was also sometimes used to identify unknown FA. All identified FA with a signal/noise> 10 were considered in the analysis of the proportions, FA identified with a signal/noise between 3 and 10 were marked as a trace.
Statistical Analysis We combined the results of experiments 1 and 2 in order to present and analyze the data (Figure  1B ). FA composition of tissues, plasma assays, and organs weight were statistically analyzed with a linear mixed-model with 2 fixed factors (lipid quality, DHA supplementation) and 2 hierarchized random effects (experimentation/duration of diet). The major aim was to compare the potential effect between lipid quality effect (VO and VO+DHA vs. DL and DL+DHA) and DHA supplementation effect (VO and DL vs. VO+DHA and DL+DHA) on tissues FA composition. Consequently, the diet duration effect was included as a random effect, as no interaction was found between lipid quality effect and diet duration effect. Body weight and food consumption were analyzed with the same linear mixedmodel for repeated measures.
Multiple comparisons between groups were performed by Tukey-Kramer procedure adjusted with false discovery rate method (fdr). Prior to analysis, the model was assessed by verifying the normality of the model and the normality of the residuals graphically, homoscedasticity was supposed true. When normality of model was not validated, groups were compared by non-parametric ANOVA using Kruskal-Wallis test followed with Dunn's post-hoc test (PCR and enzymatic activity results). For all procedures, p < 0. 05 was considered as significant. All data were reported as mean ± SEM. To identify fatty acid biomarkers across groups, multivariate analysis was used in this study on FA composition of rats fed for 6 weeks. First, principal component analysis (PCA) was performed to study the model overview. Secondly, redundancy analysis (RDA), a variant of partial least square analysis (PLS-DA), was used  (47).
RDA was performed to assess differences in FA metabolic profiles, considering as constraints the lipid quality effect, the DHA supplementation effect and the interaction between these two factors. The analysis was assessed separately for each tissue. As FA compositions were presented as the percentage of total detected FA, and that the FA proportion took place in a large range of values (0. 10-56. 74), the data were transformed by centering log-ratio (clr), then by centeringscaling  (48). A permutation test was used to consider the significance of these three terms (49). This test was followed by pairwise comparisons using factor fitting to an ordination adjusted with fdr method to assess the significance of the 4 diets. FA explaining most of the variability between lipid quality effect (LQ, DL and DL+DHA vs.
ACKNOWLEDGMENTS We would like to thank  Océane Sence  and  Coline Devillechabrolle  for their technical assistance. The authors are indebted to  Xavier Blanc  ( UPAE, INRA Jouy-en-Josas, France ) for the preparation of the lipid-free base necessary for the realization of the diets. We are grateful to  Maxime Hervé  for his assistance in the multivariate statistical analysis. We would also like to thank  Josephine Aronica  for proofreading the English editing and academic writing of the paper.
5, plus 12. 5 or 100 mM CaCl 2. Cells were then incubated for 48 h at 30° C prior to growth assay results being recorded. Quinacrine staining of live yeast cells was conducted as previously described using a final concentration of 200 mM  (Conibear and Stevens, 2002). The addition of Concanavalin A tetramethylrhodiamine conjugate (ConA-TRITC; ThermoFisher) to final concentration of 50 mM allows fluorescence visualization of the yeast cell surface. Images were acquired using a Zeiss Axioplan 2 fluorescence microscope with a 100× objective and captured using Zeiss AxioVision software.