dataesr/scientific-paragraphs-categorization huggingface dataset:
Pvalues were then adjusted for multiple testing with the Benjamini and Hochberg method  (50). Temporal clustering. In order to have a better view of the changes in expression of significant genes between each time, a clustering using the Mfuzz (2. 42. 0) R package (51) has been realized. Only genes with an adjusted p-value lower than 0. 05 in the WT time-series analysis and having a |log 2 FoldChange| > 2 (calculated according to the time point having the maximum count relative to the time point having the minimum count) has been retained for clustering. To measure the transcriptomic and temporal impact of Pho92 and Ime4 deletion, the expression value of the corresponding genes in the mutants were plotted according to the clustering established for the WT strain. Heat maps were build using 'heatmapper' online tool  (52).
Flow cytometry analysis of meiotic DNA replication Two hundred microliters of meiotic cells (at 2 OD/ml) were collected at each time point, resuspended in 70% ethanol Nucleic Acids Research, 2022 5 and stored overnight at 4 • C. Samples were then spun down, resuspended in 200 l of solution A (50 mM sodium citrate, 0. 1 mg/ml RNAse A (Sigma, Cat# R6513), 0. 2 mg/ml Proteinase K (Thermo Scientific™, Cat# EO0491)) and incubated 2 h at 50 • C. Cells were pelleted again and resuspended in 500 l of 50 mM sodium citrate containing 2 M of SYTOX Green (Invitrogen™, Cat# S7020) and transferred to 5 ml FACS tubes (Becton Dickinson, Cat# 352008). After vortexing, samples were analyzed on the LSR II (BD Biosciences) instrument and BD FACS Diva software. Single cells were gated based on forward and side scattering, FITC-A, and FITC-W.
Crosslinking and analysis of cDNA (CRAC) CRAC was performed essentially as described  (56)  with minor modifications. To facilitate later normalization between samples during dataset analysis, we used an internal 'spike-in' extract of S. pombe expressing an RNA-binding protein fused to the HTP tag. The essential protein Luc7 (30. 94 ± 19. 0 kDA HTP) with a comparable molecular weight to S. cerevisiae Pho92 (36. 05 ± 19. 0 kDA HTP) was chosen in order to collect both proteins in the same fraction during the gel-free protein fractionation step of the CRAC protocol (see below). Meiosis was induced as previously described in 500 ml of SPO to OD 600 = 2. 0 at 30 • C and 5 h following resuspension in SPO (corresponding to 3 h after IME1 induction), samples were diluted to a final volume of 2 l with SPO media and UV-irradiated at 254 nm for 80 s using the Megatron W5 UV crosslinking unit (UVO3 Ltd).
CRAC peak calling CRAC datasets were analyzed as previously described  (57)  except for the normalization step. Briefly, data preprocessing steps include the 5 adapter trimming, PCR duplicates and poly-A stretch removal and the reverse complement of the reads. BAM files were generated using bowtie2 (2. 4. 1) and the S. cerevisiae genome (SK1 assembly). The peaks were detected using the extractPeaks pipeline of the PeakCcall suite after gaussian kernel smoothing of the CRAC signal  (57)  and scored according to the 'h 2 w' score, where 'h' = height, and 'w' = width of the peak. The normalization between samples was done according to the internal Luc7-HTP spike-in. For that, the reads that did not map to the S. cerevisiae SK1 genome were mapped to the Schizosaccharomyces pombe genome (version ASM294v2) after filtering for a minimal length of 40 nt to avoid cross-species mapping.
Motif discovery, metagene analysis and gene ontology De novo motif discovery was performed with the MEME suite (5. 4. 1) (58) with the default parameters except for the motifs size fixed to nine nucleotides. FASTA sequences corresponding to the different populations of extracted CRAC peaks were used as input. UTR extensions have been defined according to the file generated in another study  (21). The mean length of the 5 UTR, CDS and 3 UTR were calculated and the position of each peak relative to the corresponding mean was determined. To put together the positions of each part of the transcript into a figure, the mean length of the 5 UTR was added to the peak position on the CDS and the mean length of the 5 UTR and the CDS were added to the peak position on the 3 UTR. Gene ontology was performed either: for Figure  3C , with the GO Term Finder tool from the Saccharomyces Genome Database (yeastgenome.
To identify functional sites bound by Pho92 in an Ime4dependent manner during yeast meiosis, we performed a CRAC analysis, a strategy that bypasses possible biases associated with immuno-enrichment of m 6 A residues. The CRAC data appeared robust, with a good signal to noise ratio and with most Pho92 mRNA targets being clearly Ime4dependent. At least in the cases of SAE3 and REC8 transcripts, the presence of methylated residues at different mei-otic time points could be confirmed by independent MazF-qPCR assays. If one could have envisaged that Pho92 binds non-methylated mRNAs, our CRAC data argue against this. Indeed, in the absence of Ime4, Pho92 fails to bind to its target mRNAs even though those are expressed, and 'Ime4independent' Pho92 binding sites appear to be nearly exclusively in non-coding RNAs.
Western blots using Peroxidase Anti-Peroxidase complex to detect Pho92-TAP in total protein extracts from WT, ndt80Δ/Δ and ime1Δ/Δ cells collected at different hours following resuspension in SPO medium. Stm1 signal detected in the same extracts was used as loading control. (C) Sequence alignment of PHO92 promoters in representative species of the Saccharomycetaceae family. The positions indicated are relative to the ATG of PHO92. The consensus binding site indicated for each motif or transcription factor is extracted from the YeTFaSCo database (85). (D) Expression of Pho92-TAP in diploid strains of the SK1 background grown in rich media. Western blots using Peroxidase Anti-Peroxidase complex to detect Pho92-TAP in total protein extracts from WT, sum1Δ/Δ, ume6Δ/Δ and sum1Δ/Δ ume6Δ/Δ cells collected in log phase cultures grown in rich media (YPDA).
ACKNOWLEDGEMENTS We acknowledge our team members for support and suggestions. We also thank  N. Hollingsworth  for the kind gift of antibodies,  F. van Werven  for kindly sharing the pCUP-IME1 strain,  A. Nicolas  for the SK1 strain, IGBMC platforms particularly the GenomEast, Imaging, Mediaprep and  FACS  facilities for support, the I2BC sequencing platform, and  D. Heintz  and  C. Villette  for help with m 6 A quantification. Author contributions: Experimental design, J. S. and B. S. ; experiments realization J. S. , D. P. , M. M. T. V. , J. Z. ; writing of original draft, J. S. and B. S. ; manuscript reviewing, J. S. , D. P. , T. V. , J. Z. , D. L. , B. S. ; funding, D. L. and B. S. ; project supervision, D. L. and  B. S. Génomique' consortium  [ ANR-10-INBS-0009 ]. Funding for open access charge: Ligue contre le Cancer.
FUNDING Ligue Contre le Cancer  ( Equipe Labellisée 2020 ) [to B. S. ];  Agence Nationale pour la Recherche  [ ANR-16-CE11-0003  to B. S. ]; CERBM-IGBMC [to B. S. ];  Interdisciplinary Thematic Institute IMCBio , as part of the  ITI 2021-2028 program  of the  University of Strasbourg ,  CNRS  and  Inserm , was supported by  IdEx Unistra  [ ANR-10-IDEX-0002 ];  SFRI-STRAT ' US  project  [ANR 20-SFRI-0012 ];  EUR IMCBio  [ ANR-17-EURE-0023 ] under the framework of the  French Investments for the Future Program. The GenomEast platform is a member of the 'France.
DNA Sequencing A 766 bp partial sequence of the multicopy 28S-18S ribosomal RNA intergenic spacer (IGS) of P. destructans isolate 01NH07 (GenBank accession number JX270192;  [43] ) was downloaded from GenBank for primer design. To design an alternative primer set, from a single copy gene, the coding sequence of the P. destructans ATP citrate lyase subunit 1 gene (acl1) was retrieved from GenBank (isolate 20631-21, GenBank accession number XM_012884837). Since the P. destructans type 20631-21 was unavailable to our study, we used isolate P. destructans OT-38-2010 (isolated from Myotis mystacinus, Finnentrop, Germany; culture 'Mmys-DE-2' in  [11] ) as reference throughout the study. Presence and correctness of the acl1 sequence in the reference isolate P. destructans OT-38-2010 was checked by sequencing three overlapping portions of the gene using primers Geo-acl1-f to Geo-acl1-r2 (see Table  1  for primer sequences.
Amplification products were purified using the QIAquick PCR Purification Kit (QIAGEN, Hilden, Germany) and sent off for bi-directional Sanger sequencing using PCR primers as sequencing primers. Consensus sequences were created and aligned using the BioEdit Software package  [44]. The resulting consensus sequence was aligned to the acl1 and IGS gene sequences of P. destructans 20631-21, respectively. For verification, BLASTn  [45]  was used to search the NCBI nucleotide database for homologies with the consensus sequences from each of the two target genes (IGS and acl1). Gene copy numbers were calculated from gDNA concentrations using the calculator available at the home page of the University of Rhode Island CELS Genomics and Sequencing Center (http://cels. uri. edu/ gsc/cndna. html).
LAMP Primer Design Primers for the LAMP acl1-specific assay were designed manually while those for the IGS-specific assay were designed using the PrimerExplorer software available on the Eiken GENOME website (see http://primerexplorer. jp/e/) (see Table  1  for primer sequences). Primer sets were selected to have a dimer(minimum)dG-value close to -2. 0, respectively. Default settings were applied for all other parameters adjustable in the primer design software. In silico analysis of primer specificity was done by testing each primer in a BLASTn  [45]  search against the NCBI sequence database. Target gene sequences of several Pseudogymnoascus spp. and from other fungal species for which [ 90% similarities were found in at least three of the tested primers were extracted from the respective genome assemblies.
Results Sequence Determination of the acl1 Gene in P. destructans BLASTn  [45]  was used to search the NCBI nucleotide database for the acl1 gene in the genomic sequence of Primer Design and LAMP Product Verification Two sets of LAMP primers, including a pair of loop primers for each gene, were designed on the basis of the acl1 gene and IGS sequences (Table  1  and Fig. 1 ). Similarity analysis of acl1 and IGS sequences for each primer-binding site in P. destructans as well as other Pseudogymnoascus spp. and other fungal species that showed high in silico sequence similarities for some of the primers is shown in Figs. S1  and S2 , respectively. The binding sites of all Pd-acl1-ID30 primers were in 100% homology with the corresponding sequences of two P. destructans strains for which acl1 sequences were available (see Fig.
[50]estructans strain 20631-21. The search retrieved a 2067 nt sequence between positions 1,116,082 and 1,118,148 on the unplaced genomic scaffold_9 of the P. destructans whole genome shotgun sequence (locus_tag = VC83_04411)[49]. The coding sequence included a start and stop codon with one intron of 57 nt between nucleotide positions 481 and 537. The translated protein sequence (Expasy translate tool http://web. expasy. org/translate/)consisted of 667 amino acids. SignalP 3. 0 Server analysis[50]predicted no signal peptide providing evidence that the protein is not secreted. Sequencing of the acl1 gene of the reference isolate OT-38-2010 (GenBank Accession Number JN242242) confirmed the presence of the acl1 gene. Both sequences showed 99. 9% homology. Two nucleotide exchanges were found at positions 527 (A-T) and 540 (T-C), i.
S2 ). Although DDE transposases have a highly conserved catalytic structure, they show overall low sequence conservation  33  , which may explain the low identities found between the ISGmo1 transposase and those found in the ISfinder database (https:// www-is. bioto ul. fr/). Despite the low identities, ISGmo1 clusters with IS sequences of other Actinobacteria, suggesting a phylogenetic relationship (Fig. S2 ). In Tn6311, the inverted repeats on the left side (IRL) includes the start codon of the orfA/orfAB ISGmo1 genes and also two putative transposase promoters according to in silico identification (http:// genom e2d. molge nrug. nl/) (Fig. 2a ). In contrast, the repeats on the right side (IRR) of ISGmo1, just upstream the molA gene, includes the last three codons of orfB and the -35 region of the molA promoter.
michiganensis, closely related with G. molinativorax)  36. However, pARLON1 shared a high nucleotide identity (88. 2%) with the contig 18 of Agrococcus casei LMG 22410 T draft genome (Contig FUHU01000018. 1, GenBank FUHU00000000. 1), as determined by ANI 37 (Table  S3 ). LMG 22410 T is the type strain of Agrococcus casei, also a member of the family Microbacteriaceae, with a G+C content (65 mol%) closer to that of G. molinativorax (64 mol%) than to other Agrococcus species  7, 38. The pARLON1 genes sharing > 70% identity with genes of the A. casei contig were those belonging to the plasmid backbone (36 predicted genes), representing 46. 3 and 53. 8% of the full coverage of contig B and contig FUHU01000018. 1, respectively. In contrast, the predicted genes belonging to the adaptive module of each of these genetic elements were different (Fig.
are not available in KEGG. Nevertheless, the predicted gene products from the 335 overexpressed transcripts in ON4 T MMM were mapped to the KEGG database  52. Some of the overexpressed predicted gene products in ON4 T MMM mapped to KEGG Orthology (KO) categories (Fig. S6 ), namely to metabolism (e. g. , amino acid, carbohydrates), environmental information processing (e. g. , membrane transport) and Brite hierarchies (e. g. , signaling and cellular processes), respectively. However, no complete KEGG pathway appeared to be overexpressed in ON4  T  MMM , in particular, none that could be related to ACA mineralization. Most of the predicted gene products mapped to more than one metabolic pathway and/or different predicted gene products mapped to the same metabolic function. Thereby, genes potentially involved in ACA mineralization were identified based on homology to previously described enzymes involved in the degradation of other xenobiotics  [53] [54] [55] [56]  and on the structural similarity of the putative substrates (Fig.
Such knowledge would enrich databases such as CONJscan  40  and oriTDB  41  , contributing to better identifying this system, particularly in genomic mining studies. Additionally, this study identified seven candidate genes involved in ACA mineralization, and validated the activity of the GMOLON4_1493 product, related to the caprolactone hydrolase chnC, in the degradation of caprolactam. The future characterization of these enzymes will contribute to enlightening the molinate degradation pathway in strain ON4 T and strengthening their biocatalytic potential.
The 454 GS FLX sequencing platform (Roche) at Genoinseq (Cantanhede, Portugal) was used following the standard manufacturer's protocols (see Supplementary Material). Sequencing reads were quality trimmed and de novo assembled by GS Assembler, version 2. 9 (Roche) using default parameters. Genome resequencing was performed using SMRT technology PacBio RSII on the RS sequencer at GATC Biotech AG (Constance, Germany), according to the manufacturer's instructions  74. Genome assembly was performed on the SMRT analysis software (http:// www. pacb. com/ produ cts-and-servi ces/ analy tical-softw are/ smrt-analy sis/). The Hierarchical Genome Assembly Process (HGAP, RS HGAP Assembly. 3), which includes pre-assembly, de novo assembly with PacBio's AssembleUnitig and assembly polishing with Quiver, was used with the default parameters, except for the minimum polymerase read quality, where 0.
80 was used instead of 0. 75. Gene prediction was carried out with GeneMarkS 75 using specific parameters for prokaryotes (genetic code 11) and functional annotation was performed using the Sma3s  76. The completeness and contamination of the SMRT assembled genome of strain ON4 T were calculated with CheckM  77. For the draft genome of strain ON4 (-) a DNA library was prepared from one nanogram of high-quality genomic DNA with the Nextera XT DNA Sample Preparation Kit (Illumina, San Diego, USA), which was sequenced using paired-end (PE) 2 × 300 bp on the MiSeq ® Illumina ® platform at Genoinseq (Cantanhede, Portugal). All procedures were performed according to the standard manufacturer's protocols. Following demultiplex and quality-filter procedures, the high quality and adapter free reads were assembled with SPAdes, version 3.
7. 1  78  , using in-house defined parameters. Confirmation of the molA regulatory region. The 5′-Rapid Amplification of cDNA Ends (5′ RACE) was performed to identify the molA gene regulatory region using RNA extracted from strain ON4 T grown in MMM. For a detailed description see the Supplementary Material. Comparison of different assemblies. The assemblies obtained from all the G. molinativorax genome sequencing projects (PRJNA245014 present study and PRJNA188907) were compared using MAUVE software  79  and the RAST server  80. In addition, the raw reads of genomes ON4 T 454 (SRR6825088) and ON4 (-) (SRR6825089) were also mapped against the contigs obtained in SMRT analysis software (genome ON4 T PacBio ) (https:// www. pacb. com/ produ cts-and-servi ces/ analy tical-softw are/ smrt-analy sis/), using the BWA-MEM algorithm  81.
The alignments were evaluated using Qualimap v2. 2. 1 software 82 and were visualized in Tablet software  83. A BLASTx search of contig B against Agrococcus casei LMG 22410 T draft genome (PRJEB19012) was performed (https:// blast. ncbi. nlm. nih. gov/). In addition, the comparison (through BLASTn) between contig B and contig FUHU01000018. 1 of Agrococcus casei LMG 22410 T was carried out using the Contiguity software  84  , and their similarity was measured by the Average Nucleotide Identity (ANI) calculator (https:// www. ezbio cloud. net/ tools/ ani).
The library preparation followed the protocol for whole transcription libraries in the Ion total RNA-Seq kit v2 (Life Technologies), using 500 ng of rRNA-subtracted products, as suggested by the manufacturer. Sequences were obtained in the Ion Proton™ platform at Genoinseq (Cantanhede, Portugal). Normalization of the data from mRNA libraries. Ion Proton adapter sequences and low-quality bases were trimmed using the Torrent Suite software (Life Technologies). Trimmed reads were aligned to the strain ON4 T genome using TMAP version 4. 0. 6 (Life Technologies). Reads that mapped to the rRNA regions were excluded. The reads count was accessed using eXpress  86  and normalized using the Trimmed Mean of M values by edgeR  87. Transcript expression differences between ON4 T MMM and ON4 T LB were considered when |Log2FC|> 2, where Fold Change (FC) is the ratio of normalized expression values of ON4 T MMM over those of ON4 T LB for each transcript.
Validation of transcriptomic data by RT-qPCR. For validation of libraries data, strain ON4 T was grown in MMM and LB. Total RNA was extracted using kit NucleoSpin ® RNA (Macherey-Nagel), and the cDNA from each sample was obtained with the Maxima H Minus First Strand cDNA Synthesis Kit, (ThermoScientific) (see Supplementary Material for detailed protocol). The potential reference genes were selected among those without differences in expression between ON4 T MMM and ON4 T LB. Three reference genes (gyrA, gyrB, recA) were selected, and primers were designed using Oligo Explorer (http:// www. genel ink. com/ tools/ gl-oe. asp). For each reference gene, the primer pair specificity was assessed in silico, followed by qPCR amplification efficiency checking (Tables S10, S11) using different dilutions of DNA amplicons, and the amplification specificity was assessed using melting curves.
Acknowledgements Authors gratefully acknowledge  Mafalda Paiva ,  Márcia Duarte ,  Miguel Pinheiro  and  Miguel Vaz  for their technical support. We also acknowledge  Ana Catarina Ferreira  and  Célia Manaia  from  Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina ,  Laboratório Associado ,  Escola Superior de Biotecnologia (ESB)  and to  Nuno Pereira  from  Instituto Superior de Engenharia do Porto (ISEP)  and  António Múrias  from  CIBIO-Research Centre in Biodiversity and Genetic Resources, InBIO, University of Porto  for their valuable help in the PFGE analysis and informatics support, respectively. We are also indebted to  Patricia Siguier  from the ISFinder database for her valuable help in the identification and characterization of ISGmo1. This work was financially supported by: Base Funding  LA/P/0045/2020  ( ALiCE) , and  UIDB/00511/2020 (LEPABE) UIDB/00511/2020 , funded by national funds through the  FCT/MCTES  (PIDDAC) and  GenomePT: National Laboratory for Genome Sequencing and Analysis  ( POCI-01-0145-FEDER-022184 ).
Data availability The datasets generated and analysed during the current study are available in the respective databases. The genomes obtained were deposited in GenBank under the accession numbers PXVE00000000 (genome ON4 T 454 ), CP028427 and CP028426 (genome ON4 T PacBio ) and PXVD00000000 (genome ON4 (-)  ). The ISGmo1 sequence was deposited in the ISfinder database (https:// www-is. bioto ul. fr/). The composite transposon carrying molA was named Tn6311, according to the Tn number registry (http:// www. ucl. ac. uk/ eastm an/ resea rch/ depar tments/ micro bial-disea ses/ tn). The data from the cDNA libraries obtained in this work have been deposited in the NCBI Gene Expression Omnibus (GEO) under accession numbers GSM3307305 and GSM3307306 for ON4 T   MMM and ON4 T LB data, respectively.
In addition, we assume that association with adjacent adhesions reduces the spontaneous unbinding rate. The probability that an adhesion site unbinds thus becomes p d � jfnb2NBðxÞnfxgjAdhðnbÞ¼0gj All in all, our proposed model extension for adhesions is relatively simple and computationally light. All adhesion dynamics are governed by the four parameters p s , p e , p d and λ adh. An overview of all the relevant parameters is shown in Table  1. Estimates of length scale, time scale, and the parameter Max Act , as well as the relative magnitudes of λ Act and λ adh can be found in S1 Text. The simulations were performed using Tissue Simulation Toolkit (  [32] ; source code in S1 Data). An interactive version in Artistoo  [33]  of the model running in a web browser is in S2 Data.
Acknowledgments G. T. gratefully acknowledges the  Indian Institute of Science  to serve as Infosys visiting professor at the  Centre for Ecological Sciences in Bengaluru. We thank  SURFsara  for the support and computing time in using the Lisa cluster computer. Martijn de Jong  is thanked for his implementation of the rejection-free algorithm of the Cellular Potts model in the  Tissue Simulation Toolkit. Babette de Jong  is thanked for linguistic advice.
This work was carried out on the Dutch national e-infrastructure with the support of  SURF Cooperative  ( 2019. 001 ). L. v. S. was supported by the  French Embassy in the Netherlands with the Bourse d'Excellence Descartes de stage. I. M. N. W. was funded by a  Human Frontiers Science Program  grant ( HFSP ,  RGP0053/2020 ). R. M. H. M. was funded by the  Nederlandse Organisatie voor Wetenschappelijk Onderzoek  grant  NWO/ENW-VICI 865. 17. 004. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.