dataesr/scientific-paragraphs-categorization huggingface dataset:
Gene functions were identified by the aid of a manually annotated T. reesei genome database proprietary to IFPEN. Comparison of the gene expression in QM9978 to QM6a identified a total of 785 genes differentially expressed (DE) in at least one time point. The number of down-regulated genes slightly increases during the time course, whereas the number of up-regulated genes remains stable. Interestingly, DE genes are mainly downregulated, meaning their expression is lower in QM9978 then in QM6a. We compared the gene expression data with our sequencing results and identified five DE genes, which were affected by mutations. The genes were characterized by homology search using the NCBI BLASTp tool (https://blast. ncbi. nlm. nih. gov/Blast. cgi) and the Joint Genome Institute genomics resource database (http://genome.
jgi. doe. gov). The annotation was additionally verified manually using the FUNGIpath database (http://embg. igmors. u-psud. fr/fungipath/). This way we identified ID51893-an orthologue of the lipid body protein ppoC (A. nidulans) involved in coordinating sexual and asexual sporulation  [28] , ID54675-a homologue of the transcription factor vib-1 involved in vegetative incompatibility and cellulose utilization in N. crassa  [29] , ID68803-a predicted RTA1-domain protein, and ID108418 and ID122376-two hypothetical proteins of unknown function. From the total of 785 genes, only 153 genes (23%) were DE at all time points. In this gene set, we find 14 glycoside hydrolases (including cbh2, xyn2, and agl1), eight putative transporters (including crt1), and four transcription factors including vib1 (ID54675) and azf1/sah-1 (ID61055) as identified by homology search as described above  [30].
" Indeed, analysis of the genomic landscape led to the identification of a translocation between chromosomes V and VII. It has been shown that DNA damage such as Fig. 6  VIB1 is required for cellulase production and signaling. Expression levels for the cellulase gene cbh1 a, the transcription factor vib1 b, and the main positive regulator xyr1 c were assessed in -/+vib1 strains versus WT after a shift from glycerol to 1% (v/w) lactose. Gene expression levels were measured by relative quantitative PCR using tef1 and sar1 as a control and normalized to expression level at time point zero (24 h growth on glycerol) for cbh1 and xyr1 or to expression level in QM9978 for vib1. Samples were taken 5 h (black), 16 h (light gray), and 24 h (dark gray) after replacement. Mean values ± standard error of triplicate data from two biological replicates are shown.
Statistical analysis of the results was performed with the Prism GraphPad software (https://www. graphpad. com/ scientific-software/prism/). For transcriptomic studies 50 mL of minimal medium (5 g/L (NH 4 ) 2 SO 4 , 5 g/L KH 2 PO 4 , 11. 7 g/L trisodium citrate, 0. 6 g/L MgSO 4 , 0. 6 g CaCl 2 , 20 g/L glucose) were prepared in a 250-mL Erlenmeyer flask. The medium was supplemented with the following trace elements: 0. 5 mL/L FeSO4•7H 2 O, 2 mL/L CoCl 2 , 0. 16 mL/L MnSO 4 , and 0. 14 mL/L ZnSO 4. Prior to sterilization, the pH of the medium was adjusted to 5. 4. Strains QM6a and QM9978 were inoculated in duplicate with approx 10 6 conidia/mL. Cultivation was carried out at 30 °C at 150 rpm. When the glucose was close to depletion (<3 g/L), 5 mL of a lactose solution was added (25 g/L lactose, 6 g/L (NH 4 ) 2 SO 4 , 5 g/L trisodium citrate).
Gene expression analysis by real-time qPCR DNase treated (DNase I, RNase free; Fermentas) RNA (5 mg) was reverse transcribed with the RevertAidTM First Strand cDNA Kit (Fermentas, Germany) according to the manufacturer's protocol using a combination (1:1) of the provided oligo-dT and random hexamer primers. All assays were carried out in 96-well plates, which were covered with optical tape, as previously described  [70]. Primers, amplification efficiency, and R-square values are given in Additional file 4: Table  S3. The amplification efficiency was determined using triplicate reactions from a dilution series of cDNA, and then calculated from the given slopes in the IQ5 Optical system Software v2. 0. Expression ratios were calculated using the REST 2009 Software (Quiagen, Germany). All samples were analyzed in two independent experiments with three replicates in each run.
Reads were then aligned against the T. reesei genome (version 2 from the JGI website) using the Bowtie mapper (version 0. 12. 7) [72]. Alignments from reads matching more than once on the reference genome were removed using Java version of samtools  [73]. To compute gene expression, the T. reesei genome annotation from JGI (version 2) was used. All overlapping regions between alignments and referenced exons were counted. The sample counts were normalized using DESeq 1. 8. 3  [74]. Statistical treatments and differential analyses were also performed using DESeq 1. 8. 3. A threshold of two for the log2 ratios with an adjusted p value <0. 001 was used to identify genes differentially expressed (DE). Gene functions were identified by the aid of a manually annotated T. reesei genome database proprietary to IFPEN.
Sequence alignment and analyses Illumina short reads from QM9978 were mapped onto the T. reesei genome (http://genome. jgi-psf. org/Trire2/), using the Maq 0. 6. 6 software solution  [75]. Mapping was done with two maximum mismatches. InDels and SNVs were identified using Maq 0. 6. 6. Homozygous mutations were selected and filtered on genomic context (complexity = 1, uniqueness > 15. 8, GC percentage between 0. 31 and 0. 74). Each mutation was manually checked using the Integrative Genome Viewer and compared to the sequence of the Rut lineage to remove the false mutations coming from initial QM6a error sequencing. Large structural variations were searched using the BreakDancer software and filtered on the reads number covering the genomic variations  [76]. We evaluated the location of SNVs and deletions according to gene annotations using the "filtered models" from the JGI website.
From this annotation, we calculated the position of intron, promoter (using an 800 bp upstream region), and terminator (using a 200-bp downstream region). Functions of genes were predicted by similarity to orthologous genes when found in other fungal taxa using the FUNGIpath database (http://embg. igmors. u-psud. fr/fungipath/). If no orthologous gene function could be identified but a gene with a homology e-value superior to e-10 was identified, the product of this gene was annotated as "similar to. " Conserved domains were identified either by interproscan (http://www. ebi. ac. uk/interpro/ search/sequence-search) or by NCBI BLASTp search (https://blast. ncbi. nlm. nih. gov/Blast. cgi). To validate the translocation between chromosomes V and VII, we amplified the region around genes encoded by the protein IDs 80028 and 54675 by PCR using oligonucleotides up and downstream of the coding region (Primer 54675_MutaC_F + 54675_MutaC_R and 80028_ MutaC_F + 80028_MutaC_R Fig.
Funding This work has been supported by the  Austrian Science Fund  ( P24219-B21 ) to BS. JR was further supported by the  TU Wien Ph. D. program molecular and elemental imaging in biosciences MEIBio. The École normale supérieure genomic platform was supported by the  France Génomique national infrastructure , funded as part of the  "Investissements d' Avenir" program  managed by the  Agence Nationale de la Recherche  (contract  ANR-10-INBS-09 ). This work was in part supported by the " Fondation Tuck" research fund  (Grant  2009-03 ) to AM,  SLC , and  FBM.
Availability of supporting data The whole genome sequence of T. reesei QM9978 is deposited at the Sequence Read Archive (SRA; https://www. ncbi. nlm. nih. gov/sra) under the Accession Number SRX2015251. The RNA-Seq gene expression data and raw fastq files are available at the GEO repository (http://www. ncbi. nlm. nih. gov. gate1. inist. fr/geo/) under the Accession Number GSE89199.
12 Detailed information on these and other protease inhibitors can be retrieved from the PLANT-PI database at http://www. plantpis. ba. itb. cnr. it/. Water-soluble chlorophyll proteins (WSCPs) constitute a small Kunitz PI sub-family. WSCPs are unique amongst chlorophyll (Chl) binding proteins in that they are hydrophilic proteins that do not contain carotenoids. 13 WSCPs are present in only a limited number of plant species belonging to the Amaranthaceae, Brassicaceae, Chenopodiaceae, and Polygonaceae. 2, 3 Based on their unique photochemical properties, WSCPs are grouped into photoconvertible (class I) and non-photoconvertible (class II) WSCPs. Class II WSCPs can be further subdivided into class IIA and class IIB, using their affinities for chlorophyll (Chl) a and Chl b and the resulting Chl a:Chl b ratio.
Plant serpins Serpins constitute another family of plant PIs. The Arabidopsis genome contains 41 potential PI genes, belonging to 8 of the 67 known protease inhibitor families in the MEROPS peptidase database. Serpins are grouped in family I4. Their name was originally derived from the fact that they are active as serine PIs,  27  although some e1368599-2 serpins inhibit cysteine proteases, whilst others have bifunctional activity or are non-inhibitory. All serpins displaying PI activity contain flexible bait loops and form covalent complexes with their target proteases. In this respect, serpins differ from other PIs, such as those in the Kunitz PI and potato PI families, which display 'standard' or 'Laskowski' mechanisms and from noncovalent, reversible complexes with their targets. The unique reaction mechanism of serpins explains why these P € Is produce dead-end complexes with their target proteases.
Many complete S. aureus genome sequences are available in the NCBI database (currently 116). These genomes were obtained from isolates from patients with sepsis and also from laboratory strains or have been generated with molecular tools. Several transcriptomic analyses have been conducted under various conditions by different laboratories (3-8) using the standard model HG001 strain, a derivative of the RN1 (NCT8325) strain with repaired rbsU (a positive activator of SigB). The strain still contains a mutation at tcaR, a transcriptional regulator involved in teicoplanin susceptibility and biofilm  (9). Nevertheless, a complete genome sequence of this commonly used S. aureus laboratory strain is not available. Here, we present the draft genome sequence of the reference strain HG001. Chromosomal DNA was extracted using the Gentra Puregene kit (Qiagen) following the manufacturer's guidelines.
Whole-genome sequencing was conducted with the PacBio RS platform (GATC, Biotech SARL, Germany). Two single-molecule real-time (SMRT) cells were used to sequence the genome (mean coverage of 78 times the genome), which was assembled de novo from 6 contigs with the SMRT portal (PacBio). The pseudomolecule was constructed by referring to the NCTC8325 genome sequence (GenBank accession no. CP000253, NCBI reference sequence no. NC_007795). The Seaview tool  (10)  has been used to manually align contigs. The final genome assembly consists of a 2,819,767-bp-long DNA molecule. Genome annotation has been done using Prokka v1. 10 (11), which predicted 2,617 coding sequences (CDS), 62 tRNAs, 15 rRNAs, 1 transfer-messenger RNA (tmRNA), and 59 other noncoding RNAs. This annotation has been manually curated, with the addition of 4 more peptides and 418 noncoding RNAs from the Staphylococcal Regulatory RNAs Database (http://srd.
Results Structures of P core from two new crystal forms. We have previously reported the crystallographic structure of the HMPV P core domain (P residues ~169-194) at an intermediate resolution of 3. 1 Å  37. Serendipitously (see Materials and Methods), we obtained two additional crystal forms of P core with improved resolution, allowing us to build a higher quality model (100% Ramachandran favoured, see Table  1 ). The first crystal (form 1, space group P2 1 ) diffracted to a resolution of 1. 6 Å, while the second crystal (form 2, space group P2 1 2 1 2 1 ) gave rise to diffraction data up to 2. 2 Å. In all of the crystal forms, including the original crystal (PDB ID: 4BXT)  37  , the asymmetric unit is composed of two tetrameric, helical coiled-coils packing against each other in varying orientations (Fig.
Material and Methods Protein cloning, expression and purification. The regions of the HMPV P gene (strain NL1-00, A1, GenBank: AAK62966. 1) encompassing phosphoprotein residues 1-60, 135-237, 135-294, and 1-294 were amplified by polymerase chain reaction and cloned into pOPINF (P 1-60, 135-237 and 135-294) or pOPINE (P1-294) plasmids  78  using the In-Fusion system (TAKARA CLONTECH) following the instructions of the manufacturer. Recombinant proteins expressed from pOPINF feature a N-terminal (His) 6 -tag followed by a 3C protease site, while pOPINE has a C-terminal (His) 6 -tag. All constructs were verified by nucleotide sequencing. The (His) 6 -tagged constructs were transformed into Rosetta2 E. coli cells for recombinant expression. E. coli were grown at 37 °C in terrific broth (TB) in presence of appropriate antibiotics to an OD 600 of ~0.
5, 150 mM NaCl. For small-angle X-ray scattering experiments, proteins were concentrated on-site with centrifugal filter units (MILLIPORE). Small angle X-ray scattering experiments. SAXS measurements were performed on beamline BM29 (P 1-60 , P 135-237 and P 135-294 ) and former beamline ID14-3 (P 1-294 ) at the European Synchrotron Radiation Facility (ESRF), Grenoble, France. Samples were kept at 20 °C and data were collected at a wavelength of 0. 0995 nm and a sample-to-detector distance of 1 m. 1D scattering profiles were generated and buffer subtraction was carried out by the automated data processing pipeline available at BM29 (ID14-3). The radius of gyration was determined with the program PRIMUS  79  according to the Guinier approximation at low Q values, and molecular weights were estimated based on  44.
In the case of P 135-294 and P 1-294 , which displayed concentration dependent changes in the SAXS profile at low Q values, a merged curve was produced by combining the low Q region of data measured at low concentration with the high Q region of the high concentration SAXS profiles. These particle interference-free merged curves were used for subsequent analysis. Structural modelling and molecular dynamics simulations. Different strategies were used to obtain all atom models for each construct. 1000 models of the backbone of monomeric P 1-60 were obtained using the program flexible-meccano  47  , with an α-helical propensity of 50% for residues 14-26 which were observed to form an α-helix when complexed with the HMPV N protein  32. Protein side chains were then added using the program SCCOMP  80.
Ensemble optimization. For each model from each ensemble, theoretical SAXS patterns were calculated with the program CRYSOL  87  and ensemble optimization fitting was performed with GAJOE  88, 89. GAJOE uses a genetic algorithm to select from a large pool of conformers optimized sub-ensembles that minimize the discrepancy between the experimental and calculated curves χ exp according to the following equation: ( ) ( ) ( ) where K is the number of points in the experimental curve, σ is the standard deviation and µ is a scaling factor. The optimum selected ensemble size and relative weights of the models were determined automatically by GAJOE. For each curve, the ensemble optimization procedure was repeated for a minimum of 20 times, from which the Rg distributions of the optimized ensembles were built.
K I Q I Q Q exp 1 1 (1) Crystallization and data collection. Our initial goal was the crystallization of a complex of the HMPV M2-1 protein bound to a P construct including the putative M2-1 binding region. The expression and purification of HMPV M2-1 has been described previously  30. In an attempt to crystallize the M2-1 -P 135-237 complex, vapour diffusion crystallization trials of a 1:1 mixture of these two proteins at 7 mg/ml in 20 mM Tris, pH 7. 5, 150 mM NaCl were set up using a Cartesian Technologies pipetting system  90. Although we were not able to grow crystals of a complex, crystals which later proved to harbour only the P oligomerization region could be obtained after extended time periods. The P2 Structure determination and refinement. The HMPV P core data sets were phased by molecular replacement with PHASER 92 using the previously published structure (pdbID:4BXT).
The structures from both crystal forms were subjected to multiple rounds of manual building in COOT  93  and refinement in PHENIX  94. We made use of translation-libration-screw (TLS) parameters and 8-fold torsion-angle non-crystallographic symmetry (NCS) restraints as implemented in PHENIX  94. For the 1. 6 Å data of crystal form 1 we additionally carried out anisotropic atomic displacement parameter (ADP) refinement. The structures were validated with the wwPDB Validation Service (https://validate-rcsb-1. wwpdb. org/). Refinement statistics are given in Table  1. The final coordinates and structure factors have been deposited in the PDB with accession codes 5OIX and 5OIY. Structure and sequence analyses. Structure-related figures were prepared with the PyMOL Molecular Graphics System (DeLano Scientific LLC).
Strictly conserved residues (coloured in deep purple) are explicitly labelled. E. B-factor putty representation of a single P core tetramer from crystal form 2. Red and thick regions of the putty represent high B-factors (~50 Å 2 ), whilst thin and blue regions indicate low B-factors (~20 Å 2 ). A solvent accessible helix displayed significantly higher B-factors that the rest of the coiled-coil (indicated by arrow). F. Structural superposition of six P core tetramers taken from crystal forms 1 and 2 and the previously published crystal (PDB ID: 4BXT).
Acknowledgements The research leading to these results has received funding from the  European Union Seventh Framework Programme  (FP7/2007-2013) under SILVER grant agreement n ° 260644, and  MRC grant  ( MR/L017709/1 ). MR is funded by a  Wellcome Trust  Fellowship ( 204703/Z/16/Z ),  CMG  benefited from the support of the  Labex EpiGenMed , an  « Investissements d'avenir » program , reference  ANR-10-LABX-12-01 , and JMG by the WT ( 200835/Z/16/Z ). This work was supported by a  Wellcome Trust  administrative support grant ( 203141/Z/16/Z ). The authors would like to thank the staff of beamline BM29 and former beamline ID14-3 at the  European Synchrotron Radiation Facility (Grenoble, France)  for assistance with SAXS data collection. The authors would also like to thank  Diamond Light Source  for beamtime (proposal  MX10627 ), and the staff of beamlines I03 and I04 for assistance with crystal testing and data collection.
core form 1 (PDB ID: 5OIX) P core form 2 (PDB ID: 5OIY) Data collection Space group P 1 21 1 P 21 21 21 Cell dimensions a, b, c (Å) 29. 0, 110. 4, 38. 7 37. 8, 45. 4, 116. 8 α, β, γ (°) 90, 95. 6, 90 90, 90, 90 Resolution (Å) 36. 4-1. 6 (1. 67-1. 61)* 42. 4-2. 2 (2. 28-2. 20) CC (1/2) 1. 0 (0. 5) 1. 0 (0. 7) R merge 4. 6 (101. 4) 11. 0 (275. 8) R pim 2. 9 (65. 3) 3. 3 (81. 0) I/σI 13. 9 (1. 4) 11. 9 (1. 3) Completeness (%) 99. 3 (99. 7) 98. 7 (97. 1) Redundancy 3. 3 (3. 3) 12. 2 (12. 4) Refinement Resolution (Å) 36. 4-1. 6 42. 4-2. 2 No. reflections 31086 (3078) 10636 (1033) R work /R free 17. 9/20. 3 24. 8/26. 5 No. atoms Protein 1640 1586 Ligand 6 0 Solvent 242 67 B-factors (Å2) Protein 34. 6 51. 6 Ligand 71. 1 - Solvent 51. 0 51. 2 R. m. s. deviations Bond lengths (Å) 0. 009 0. 007 Bond angles (°) 1.
Gal4 Lines Screen for the Study of VAMs Function Our aim was to study specifically the VAMs to pinpoint their function in adult fly. In the search for a behavior associated to the function of the VAMs, we needed specific genetic tools to allow the manipulation of the corresponding motor neurons (the Ventral Abdominal Motor Neurons, VAMNs) as well as tool for the VAMs themselves. Recently, thousands of transgenic Gal4 lines have been generated and are known as the Janelia FlyLight stocks. In this collection, the Gal4 open reading frame is under the control of different short intronic (or noncoding) regions of genes known to have a patterned expression in the adult nervous system  (Pfeiffer et al. , 2008; Jenett et al. , 2012). For each line the expression pattern is described and available on Janelia FlyLight database (http://flweb.
janelia. org/cgi-bin/flew. cgi). Using this database, we first selected the enhancer Gal4 stocks that drive the expression of the GFP reporter in a subset of cells located in the abdominal ganglia, assuming that the cell bodies of the VAMNs are positioned in the abdominal ganglia of the ventral nerve cord (VNC). We eliminated all the lines showing too broad GFP expression pattern in the brain or in the entire VNC. We then screened the selected lines by crossing (F) The Tdc2 Gal4 line allows the GFP expression exclusively in the smallest population of boutons (see merge in F"). This octopaminergic/tyraminergic innervation is closely associated to glutamatergic boutons as showed in zoomed images. For all conditions, motor neurons are stained with HRP (Horse Radish Peroxidase is a neuronal membrane marker,  Jan and Jan, 1982) , images of abdominal segments A3-A5 are represented.
In this case, the tip (or the extremity) of the abdomen reaches a position perpendicular to the resting position (the horizontal position, parallel to the microscope slide) (Figure  3A ). Thus, the abdomen of a fly is able to perform different folding movements detectable on movie analyses. We quantified these movements in two ways: (1) the number of occurrence of each type of movement (small, large, curving) during a 1-min period and (2) the relative percentage of time when the abdomen is not in a resting position during the 1min video recording (the percentage of activity). To perform this, we used the Fiji software and analyzed each individual fly movement by measuring the displacement over time of the abdomen relatively to a drawn basal line corresponding to the resting position (yellow line in Figure  3B ).
Genetic New Tools: The Flylight Gal4 Collection The Enhancer Gal4 lines of the Janelia Light Project provide to the community a huge collection of Gal4 lines. This collection offers several interesting particularities. The small size of the enhancer-DNA fragments cloned upstream of the Gal4 gene result in restricted expression pattern, allowing ectopic gene expression specifically small tissue regions or within a small number of cells. In addition, the full expression pattern (in embryo, larva and adult) of these different Gal4 lines is documented and available on line. We have selected from the database, accordingly to their expression profile in the abdominal ganglia, nearly 200 enhancer Gal4 lines. These lines have been screened for their expression pattern in the MNs of the VAMs. Only one line, 24G08 Gal4 allows the expression of the GFP reporter specifically in the MNs innervating the VAMs of the abdomen.
ACKNOWLEDGMENTS We thank the  Bloomington Drosophila Stock Center  ( NIH P40OD018537 ) and the  Janelia consortium  for flies and the  DSHB (Developmental Studies Hybridoma Bank , created by the  NICHD  of the  NIH  and maintained at The  University of Iowa, Department of Biology, Iowa City, IA 52242 ) for the antibodies. We want to thank  Jean-Maurice Dura  for the strain white outcrossed by  Canton S, Alain Garces  for antibody gift and  Olivier Bricaud  for comments on the manuscript. We also thank the  Montpellier Ressources Imagerie  ( MRI ) for the microscopes facilities.