dataesr/scientific-paragraphs-categorization huggingface dataset:
To rule out any artifact due to the assembly process, we confirmed the sequence by PCR amplification and Sanger sequencing of that region. The Cas7 sequence was registered in GenBank (BankIt2035475 Seq1 MF564202). It is quite divergent from the previously identified cassicolin genes, with only 72. 3-76. 7% nucleotide sequence identity and 71. 9-77. 8% deduced amino acid sequence identity. However, we were not able to amplify Cas7 transcripts from germinating spores of the Cas2+7 isolates IA, JQ and PB. RT-qPCR analysis of Cas2+7 isolates during interactions with plant hosts may demonstrate the functionality of Cas7 and confirm its protein sequence. Cassicolin is the perfect illustration of a species-specific effector responsible for intraspecific diversity due to sequence polymorphism, presence/absence and copy number variations.
ACKNOWLEDGMENTS We thank the  Metatranscriptomics of Forest Soil Ecosystems consortium  for access to unpublished genomes of Colletotrichum gloesporioides and C. acutatum,  Irina S. Druzhinina ,  Tu Wien  and  Christian P. Kubicek  for access to the unpublished genomes of Trichoderma asperellum and T. harzianum, and  Michel Dron  for scientific advices and support.
FUNDING DL's salary was funded by  IFC  ( Institut Français du Caoutchouc, Paris, France ) and  Michelin, SIPH and Socfin Companies. C. cassiicola isolate CCP sequencing, assembly, and annotation were performed by  U. S. Department of Energy Joint Genome Institute. The work conducted by the  U. S. Department of Energy Joint Genome Institute , a  DOE Office of Science User Facility , is supported by the  Office of Science  of the.
Each cDNA was initially cloned into pGEM-T Easy and then the binary vector pMOGORFLAUX1 14 , which contains the 2 kb promoter region, start codon and the 3′UTR of the Arabidopsis AUX1 gene. Constructs were then transformed into the Arabidopsis mutant aux1-22 using the floral-dip method  26. Primers used for cDNAs amplification are listed in Supplementary Table  1. Root growth and gravitropism analyses were performed on vertical agar plates and quantified as described earlier  27. Characterization of osaux1 root architecture. Two independent T-DNA insertion mutant lines of Osaux1 were identified using OryGeneDB software  28. In line 3A-51110, the T-DNA was inserted within intron 5, while in line 3A-01770 the T-DNA was inserted in exon 6 (and termed osaux1-1;1 and osaux1-1;3, respectively). T-DNA insertions were confirmed using the site-finder approach  29.
6 with 1% agar) containing 1 µM, 31 µM, or 312 µM P. Low P media were complemented with equimolar concentration of KCl. Seedlings were grown vertically in 12-inch square plates in growth chamber maintained at 28 °C with 12 h of light and 12 h of darkness. After 9 days of growth seedlings were transferred to glass tubes filled with same media without agar (hydroponic system). Liquid media was changed every day and root hair growth was recorded on nodal roots of 15 days old seedlings using a Zeiss stereo zoom microscope (optical zoom ×2. 5, digital zoom ×1. 2). Experiments were repeated three times. RH length was measured as the average of 30-60 fully elongated root hairs from one seedling. Data from >10 seedlings were used to calculate the final RH length. Split root experiments. Rice seeds (DR5:VENUS3X) were dehusked and were cut into halves to retain only embryo portions (onwards referred as seeds).
Root tips were mounted in low melting agarose (0. 5%) and were scanned typically using a two photon laser scanning microscope. The GFP and PI emissions were collected in separate channels with excitation at 836 nm (Chameleon Ultra II) and 1096 nm (Chameleon Compact OPO), respectively, with a gain set at 600 nm using 2 PMT NDD and 2 PMT BiG detectors. All images were processed using Zeiss ZEN software. For images stack, the auto brightness correction was applied. In some cases, roots were scanned using Leica SP5 confocal microcope with 1. 5 μm step size for Z-stacks. Maximum projections were generated using Leica SP5 software, RT-qPCR and reporter imaging. qRT-PCR was performed in three biological and four technical replicates per sample. Total RNA (2 µg) was used for cDNA synthesis using transcriptor first-strand cDNA synthesis kit (Roche)  14.
Acknowledgements This work was supported by the awards from the  Biotechnology and Biological Sciences Research Council  [grant numbers  BB/G023972/1 ,  BB/R013748/1 ,  BB/L026848/1 ,  BB/M018431/1 ,  BB/PO16855/1 ,  BB/M001806/1 ,  BB/P010520/1 ]; the  European Research Council   FUTUREROOTS Advanced Investigator grant  [grant number  294729 ];  Leverhulme Trust  [grant number  RPG-2016-409 ];  Royal Society  [grant number  WM130021 ,  NA140281 ];  Newton International Fellowship  ( NF140287 ) and  British Council Newton Bhabha  ( 228144076 ). This work was also supported by funds from the  University of Nottingham Future Food Beacon of Excellence Nottingham Research and PhD+ fellowship schemes ; the  Interuniversity Attraction Poles Program  initiated by the  Belgian Science Policy Office  [ P7/29 ]; the  Swedish Governmental Agency for Innovation Systems (VINNOVA) , and the  Swedish Research Council  (V.
Gas chromatography coupled to mass spectrometer (GC-MS) was used to identify and to quantify neutral sugars that constitute the water soluble polysaccharides from Zizyphus lotus fruit. The trimethylsilyl (TMS) method was successfully used for derivatization of the monosaccharides units of extracted polysaccharides that were released by hydrolysis method. Sugars were identified based on their retention times compared with those of standards and the NIST MS Spectral Library. All sugars were quantified in TIC (Total Ion Current) mode using calibration curves. Data is related to "Optimization extraction of polysaccharide from Tunisian Zizyphus lotus fruit by response surface methodology: Composition and antioxidant activity" (Mkadmini Hammi et al. ,.
Image Processing Most of the image processing was performed using the ImageJ public domain software. The orientation field was obtained by computing the local structure tensor with ImageJ plugin OrientationJ 34,35. For representation purposes, we occasionally used a Line Integral Convolution (LIC) under Matlab (MathWorks). The velocity field was mapped by particle image velocimetry (PIV) analysis. Stacks of images were analyzed with a custom made PIV algorithm based on the MatPIV software package for MatLab (MathWorks Inc. ) 7. The window size was set to 32 pixels = 23. 75 µm with a 0. 5 overlap for L>30µm and 16 pixels = 11. 9 µm with a 0. 5 overlap for L=20µm and L=30µm. The friction screening length λ was measured by fitting two decreasing exponential curves to the V y velocity profiles.
Statistical analysis Statistical analysis was performed with Matlab (Mathworks) or Origin (Originlab). Experiments were performed in at least 2 replicas, each using 6 well plates with stripes of two distinct widths per well (for L=50µm, 100µm and 200µm to 1200µm) or five distinct widths (for L=10 to 200 µm). The number of analyzed FOVs for each width is reported in the list below. Error bars represent the SDs over all the FOVs analyzed (pooling all experiments in a single set). FOVs presenting topological defects were excluded from the analysis. The orientational profiles are all acquired 50h after confluence. The velocity profiles obtained from the PIV velocity maps are averaged over time (0 < t < 50h postconfluence). Both profiles were averaged along the direction of the stripe. Middle angle distribution measurement and PIV analysis of HT1080 cells were obtained from 28 stripes of 125±5 µm width in course of 25 hours, starting from confluency.
Acknowledgements It is a pleasure to thank the members of the  Biology-inspired Physics at MesoScales (BiPMS) group  and in particular  Floriana Ascione ,  Trinish Sarkar  and  Hannah G. Yevick. We thank  Leo Valon  for suggesting the use of RPE1 cells. VY gratefully acknowledges the  CelTisPhyBio Labex  and the  EU PRESTIGE program  for financial support. GS is supported by the  Francis Crick Institute  which receives its core funding from  Cancer Research UK  ( FC001317 ), the  UK Medical Research Council  ( FC001317 ), and the  Wellcome Trust  ( FC001317 ). The  BiPMS group and the Physical Approach of Biological Problems  group are members of the  CelTisPhyBio Labex. The BiPMS group is a member of the  Institut Pierre-Gilles de Gennes.
Aggression assays We tested microbiota-remodelled and untreated ants against nestmates and non-nestmates from the original colonies, in both experimental rounds  (3) (4) (5)  replicates/combination, total=260 tests; Figure  1 , Data set S1). Assays consisted of dyadic encounters in Petri dishes with clean filter paper on the bottom. For two minutes after first contact, an observer (blind with respect to ant treatment and original colony) used the software Etholog 2. 25  (26)  to quantify the frequency and duration of biting, mandible opening, antennation and absence of contact (Figure  S3 ). For statistical analyses, we excluded the mandible opening behaviour (usually considered as aggressive) because pooling it with biting produced similar results (Supplementary Information). In addition, because keeping ants in the same Petri dishes for three weeks resulted in a significant effect on aggression (Binomial GLMM with 'Petri dish' as fixed and 'colony' as random variables, z=3.
21, Df=141, p=0. 001), we considered only interactions between nestmates kept in different Petri dishes. We analysed data in R using the packages lme4, car and multcomp (27-29), fitting generalized linear mixed models (GLMMs). Classifying biting as aggressive behaviour and antennal contact as non-aggressive allowed measures to be analysed as a single binomial response variable. For Round 1, the initial model included biting/antennation frequencies as response variable, whereas. CC-BY-NC 4. 0 International license a certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under The copyright holder for this preprint (which was not this version posted May 31, 2018. ; https://doi. org/10. 1101/335521 doi: bioRxiv preprint nestmate, diet treatment and their interaction were included as fixed factors.
The elongation factor 1 alpha (EF-1α) was used as a reference gene  (34). Each run included two negative controls with no added template for each gene used. Data were ordinated using an unscaled principal coordinate analysis (PCoA) and intersample distances were again calculated using Canberra, Hellinger and Bray-Curtis methods. We estimated the difference in variation among groups using the HOMOVA command (with Bonferroni-adjusted alpha-values) implemented in mothur  (35). For analysis, we initially used a standard curve with PCR products in tenfold dilution series of known concentration (fold change method) to calculate the PCR efficiency using the REST software  (36). Data were imported in R and expressed as ΔΔC T values, i. e. as the fold change relative to the EF-1α control gene  (37) , always using zero as reference.
16S rRNA MiSeq analyses To investigate whether novel OTUs appeared with the dietary treatment, we screened ant worker guts individually with 16S rRNA MiSeq sequencing. Amplicons were generated using the 515F/806R primers targeting the 16S rDNA V4 region  (42) , purified using the Agencourt AMPure XP (Beckman Coulter) and quantified using Quant-iT dsDNA High-Sensitivity Assay Kit and Qubit fluorometer (Invitrogen) to allow for dilution and mixing in equal concentrations before sequencing. Sequencing (for details see the Supplementary Information) took place in the Section of Microbiology at the University of Copenhagen using an Illumina MiSeq. Data [Genbank: SAMN04261407 -SAMN04261536 and SAMN05362797 -SAMN05362832] were analysed using mothur  (35). Details on the mothur procedure are given in the Supplementary Information.
After filtering/processing the sequencing data and clustering at 97%, rarefaction tables were constructed using pseudo-replicate OTU datasets containing 1-272000 sequences with 1000 iterations/pseudo-replicate, and the resulting curves were visualized in Microsoft Excel 2013. The final OTU Table was rarefied at 5000 reads after manual inspection of the rarefaction curves, which reduced the number of OTUs to 1500. We used the MiSeq data to calculate Canberra and Bray-Curtis distances, after which we used Non-metric MultiDimensional Scaling (NMDS) to ordinate and visualize the effects. We used GLMs to pair aggression data with Bray-Curtis or Canberra distances calculated from the 16S rRNA.
1. 0 (using package xcms, script available upon request) and normalized using a Z-transformation  (43). To compare odour profiles among different rounds, we used linear mixed models (LMM) with the relative abundance of each compound as the response variable, 'diet treatment' and 'experimental round' as fixed variables, and 'colony' as a random variable. We conducted linear hypotheses using the multcomp R package (44) function glht to evaluate differences between diet treatments in the same Rounds, and between the same diet treatments across Rounds. All p-values were corrected for false discovery rate (FDR) given that we had conducted 73 separate tests per contrast. We used a coinertia analysis  (45)  to check for correlations between CHCs (transformed to logarithmic data) and qPCR measures (ΔCt values) of the.
Sample size and statistical analysis. The sample size of 236 participants was calculated using an estimated prevalence of brucellosis of 15%  31  with a 5% precision at a 95% confidence interval after a 20% inflation for non-response rate using Epi Info(version 7. 1. 4. 0, CDC, Atlanta US). Data was entered in EpiData3. 1software (EpiData, Odense, Denmark), then exported to STATA version 13 (StataCorp, College Station, Texas, USA) for analysis. Descriptive analysis of independent variables namely (participant's age, gender, education level, marital status, religion, income status, occupation, family history of brucellosis, consumption of raw milk and other products) was done. Prevalence of brucellosis was the ratio of the number of patients with fitting definition of probable or confirmed brucellosis by the total number of included patients tested for brucellosis.
05) with brucellosis. Ethical approval to conduct the study was obtained from Mbarara University of Science and Technology Research and Ethics Committee (MUST-REC) and the Faculty Research Committee (FRC). The study was given study number 02/03-17 by the REC. We respected the guidelines of Helsinki and CIOMS-2002 (Council for International Organizations of Medical Sciences) regarding research with humans, avoiding any type of physical or moral damage. Written informed consent was obtained by research assistants from all adult participants (18 years and above) and in case of minors (below 18 years) from their parents or guradians. Assent was obtained from children who were older than 7 years. The datasets generated and analysed during the study are available from the corresponding author on request.
Acknowledgements We thank the patients who participated in the study and the staff of Rushere community hospital who contributed in various ways towards the success of the study. We are very grateful to  Epicentre Mbarara  for funding the study. The contribution of funders of the  Institute for Tropical Health (Obra Social la CAIXA, Fundaciones Caja Navarra and Roviralta, PROFAND, Ubesol, ACUNSA and Artai)  is also gratefully acknowledged. We also thank  Moriyon Ignacio  from  Institute for Tropical Health, University of Navarra (ISTUN), Pamplona, Spain and Francis Bajunirwe of Mbarara University of Sciences and Technology, Mbarara, Uganda  for their technical input into the study.
At least two to three biological replicates were performed for each experiment. As described previously, after comparing the variance in oocyst numbers between different replicates, equal numbers of midguts from the various replicates were selected randomly and pooled for producing dot-plots using GraphPad Prism 7 software  [25, [46] [47]. A published method  [25, 48]  was used, with some modifications, to determine the sporozoite loads in the salivary glands of the infected mosquitoes. Salivary glands were dissected, and individual glands were placed in Eppendorf tubes with 30 μl of PBS, followed by homogenization on ice. A sample (10 μl) of this homogenate was placed in a Neubauer counting chamber and counted after 5 min using a Leica phase-contrast microscope at 400x magnification. The dot plots of oocyst and sporozoite numbers in each individual gut and salivary gland were generated using GraphPad Prism 7 software, along with the median values, represented as red bars.
They were held there until all the mosquitoes in that cup died, and the number of dead mosquitoes in the cup was recorded and the dead mosquitoes removed daily  [25, 44]. For the life span assays of mosquitoes receiving a single blood meal (blood-fed on mice), the mosquitoes were offered a blood meal 5 days after emergence, and only mosquitoes taking a blood meal on day 5 were kept for the rest of the study. The survival percentage represents the mean survival percentage for all three biological replicates of 35 mosquitoes each. Statistical significance was determined by Kaplan-Meier survival analysis with pooled data from three replicates by using GraphPad Prism 7 software, and p-values were determined by Wilcoxon test as described in  [25, 29]. For the fecundity assay, approximately 50 7-day-old adult female wt X1, Vasa-Cas9, FREP1-gRNA, and heterozygous or homozygous FREP1 knockout mutant mosquitoes were allowed to feed on mice.
Acknowledgments We would like to thank the  Johns Hopkins Malaria Research Institute Insectary and Parasitology core facilities , and especially  Dr. Mlambo  for providing P. berghei-infected mice and  Dr. Tripathi  for providing P. falciparum gametocyte cultures. We thank  Dr. Jun Li  for sharing FREP1 antibody. We also thank  Dr. Deborah McClellan  for editorial assistance.
EF1α (AT5G60390) and SAND family protein (AT2G28390) were used as internal reference genes. Realtime RT-PCR was performed using SYBR Green Master mix I (Roche) and specific primers, CHLI-245-Fw and CHLI1-340-Rev and Tu-3694-Fw and Tu-3830-Rev, respectively, for CHLI1 mRNA and TuYV detection (Supplementary Table  S1 ), on a Lightcycler LC480 apparatus (Roche) according to manufacturer's instructions. Relative gene expression levels of CHLI1 and TuYV were calculated by means of the linear regression of efficiency method using LinRegPCR software (version 7. 4) and averaged over three technical replicates. After normalization with the reference genes, values were further normalized with two pools of mock-inoculated samples for CHLI1 expression and three pools of TuWT-infected plants for viral RNA accumulation.
For Tu-RTM1 VIGS experiments, non-inoculated leaves from TuYV-inoculated plants were randomly collected at 36 dpi. Total RNA was extracted as indicated above from individual plants and treated as before. Primers RTM1-189-Fw and RTM1-319-Rev were used for RTM1 mRNA detection and Tu-3694-Fw and Tu-3830-Rev for TuYV detection (Supplementary Table  S1 ). Realtime RT-PCR was performed on RNA from individual treated plants (5 or 6) and quantification was performed as described above and data normalized using, as references, Tu-WT for virus quantitation or mock for RTM1 transcript quantitation.
In summary, the VIGS experiments performed with the silencing suppressor defective mutants showed no intensification of the silencing effect on the endogenous CHLI1 in the absence of P0. We then analyzed the speed and the durability of the vein yellowing phenotype induced by the TuYV-recombinant viruses by performing a time course experiment on plants infected with two of the TuYV vectors exhibiting the strongest phenotype, TuM1hp and TuM1s81. The silencing phenotype on TuM1hpinfected plants was visible after a week and slightly faster (1 or 2 days earlier, data not shown) compared to TuM1s81-infected plants and appeared on new developing leaves until 18 dpi (Supplementary Figure  S2 ). For both viruses, source leaves or leaves that were at the source/sink transition state at the time of virus inoculation remained symptomless (Supplementary Figure  S2 , see red arrows).
Conversely, the viral offspring that was efficiently transmitted by aphids from TuM1hp-infected plants developed symptoms in only 4 out of 10 infected plants and the symptoms remained fainter when compared to those exhibited by the TuM1s81 progeny (Supplementary Figure  S5A ). This observation suggests that only a fraction of the TuM1hp progeny that was taken up by the aphid from the infected source plants still contained the CHLI1 insert able to induce silencing. The genome stability of the recombinant viruses inoculated by the aphids was analyzed by RT-PCR and sequencing as described earlier. Five aphid-inoculated plants were analyzed for each recombinant virus. The viral progeny in all five TuM1s81 infected-plants gave a single PCR fragment of the expected size which sequence was identical to that of the agroinoculated virus (Supplementary Figure  S5B ) except one nucleotide deletion also found in the source plant that was again observed in the progeny (data not shown).
, 1998; Whitham et al. , 1999; Cosson et al. , 2012; Revers and Garcia, 2015). An 80 bp fragment from RTM1 cDNA was inserted in sense orientation into the previously described TuM2 (Figure  1A ) resulting in the recombinant Tu-RTM1. The control viruses TuWT and TuM2 and Tu-RTM1 were agroinoculated to Col-0 plants and infection was assessed by DAS-ELISA and real-time RT-PCR on systemically infected leaves of individual plants 4 weeks pi. The recombinant virus was fully infectious as 95% of the inoculated plants were infected (ELISA, data not shown) and the viral titer was in the range of that measured for TuWT and TuM2 (Figure  6A ). While accumulation of RTM1 transcripts in TuWT and TuM2-infected plants was similar to mock-inoculated plants, a statistically significant decrease in RTM1 mRNA accumulation was observed in Tu-RTM1-infected plants (Figure  6B ) reaching 88.
FUNDING This work was financed by the  Centre National de la Recherche Scientifique  and the  French National Agency for Research (ANR)  in the frame of  P0-SUPP  ( ANR-06-BLAN-0009-01 ) (DB-B), and  VIROMOUV  ( ANR-08-GENM-016-003 ) (BM, SC, and KH). DB-B was the recipient of a Ph. D. grant given by the  French Ministère de l'Education Nationale, de l'Enseignement Supérieur et de la Recherche.
FROM PUTATIVE TO GENUINE MAPK SUBSTRATES Usually, putative MAPK substrates are initially identified from systematic approaches, such as phosphoproteomics, protein array or yeast two-hybrid screening. However, much more evidence is necessary to qualify a protein as a genuine MAPK substrate. At the biochemical level, the protein should be phosphorylated in vitro by the MAPK. This may be achieved for instance by a classical kinase assay using radiolabeled ATP or by a non-radioactive kinase assay followed by mass spectrometry analysis. Whatever the approach, the identification of the precise phosphorylation site(s) on the protein is required. A proof of the existence in planta of the phosphosite(s) identified in vitro is necessary as well. This proof may be found in databases such as PhosPhAt  (Durek et al.