dataesr/scientific-paragraphs-categorization huggingface dataset:
Establishment success and invasiveness To date, 29 out of 43 alien taxa (~ 69%) are considered to be established. The established status of Malleus regula (Forsskål in Niebuhr, 1775) and of Isognomon legumen (Gmelin, 1791) were here updated based on the unpublished data gathered and the critical analysis of the literature. The former species was previously reported from Greece based on an empty shell from Symi (Dodekanisa)  (Giannuzzi-Savelli et al. 2001) , as the specimens from Astypalaia (Dodekanisa) recorded as such by Angelidis in  Lipej et al. (2017)  are instead I. legumen. We now report M. regula as a common presence in Astypalaia (Dodekanisa), where several specimens were collected in 2011-2013 in three bays (Panormos, Micro Vai and Vai: Appendix 1). However, this taxon is also well known from nearby Turkish shores, where it colonizes most of the crevices of the infralittoral fringe (FC and LPT, personal observations); therefore, its establishment in Greece was expected.
Acknowledgements The study of the alien species from Greece was partially funded by the  East and South European Network for Invasive Alien Species  -a tool to support the management of alien species in Bulgaria (ESENIAS-TOOLS) (EEA funded -Contract No. Д-33-51/30. 06. 2015 ) (FC and AZ), the  DEVOTES (DEVelopment Of innovative Tools  for understanding marine biodiversity and assessing  Good Environmental Status , funded by the  European Union  under the seventh  Framework Programme, 'The Ocean of Tomorrow' Theme - grant agreement no. 308392; http://www. devotes-project. eu)(AZ) and the  COST (European Cooperation in Science and Technology) Action TD1209 Alien Challenge (FC)  projects. John Mark Hanson  and  Brian Morton  kindly proofread the present article and offered insight and support.
First, a baseline survey was undertaken in July 2014 to elicit household information: demographics, farm characteristics, use of financial services, asset ownership and market conditions. The questionnaire was piloted, revised and then implemented by trained enumerators through face-to face interviews with 25 of the 38 households. Two short surveys of a panel of 20 randomly selected irrigators were undertaken, and two focus groups were held in January and July 2015 aiming to evaluate the progress of the project activities and the farmers' engagement, when possible with different farmers; however, the small number of households meant this was not always possible. Data collection also included observations by two project officers regularly visiting the scheme; reports from the meetings of the Agricultural Innovation Platform; and discussions with irrigators and scheme leaders.
Market segments and price fluctuations To explore how crop price and price fluctuations influence cropping decisions and to identify potential cropping strategies, seasonal variations in crop price were analyzed for the wholesale market and the retail markets in Maputo City and Boane from September 2012 to May 2015. The analysis used weekly data from Sistema de Informação de Mercados Agrícolas  (SIMA, 2015). Of the crops grown at the scheme, wholesale prices were available for three crops and retail prices for eight crops (Table  2 ). Not surprisingly, vegetable prices fluctuate more than maize and other staple foods, such as cowpea in Maputo and beans in Boane. The retail price of vegetables tends to be more variable in Boane than in Maputo, with the exception of potatoes and beans. Potatoes are more often available at Boane than at Maputo, probably because potatoes are grown locally.
| Analyses Irrigation being applied at the block level (i. e. , whole plot), the ORPHEE experiment is a split-plot experiment which requires adapting the calculation of degrees of freedom and mean sum of squares of residuals. This was achieved using linear mixed effect models (LMM), with Block and Block × Irrigation as random factors (1|Block:Irrigation in R syntax). Herbivory and leaf trait data were analyzed at the tree level. Nonindependence of individual oaks within plots was accounted for by defining plot as a random factor, nested within blocks  (Schielzeth & Nakagawa, 2013). For each test, we first built a full model including all fixed effects and their interactions (see details for each response variable below). The full model was then simplified by sequentially dropping nonsignificant terms, starting with highest-order interactions.
ACKNOWLEDGMENTS The research in ORPHEE was funded by the  GIP-ECOFOR program  from the  French Ministry of Ecology , under the project  BIOPICC ECOFOR-2014-15. The work was supported also by a grant overseen by the  French National Research Agency (ANR)  as part of the  "Investissements d'Avenir" program  ( ANR-11-LABX-0002-01 ,  Laboratory of Excellence ARBRE ). We thank  Rosalie Lefeu ,  Inge van Halder ,  Fabrice Vétillard ,  Bruno Garnier ,  Bastien Gravellier , and  Mélanie Thiery  for their help with field work. We thank  Nicolas Angeli  and  Christian Hossann  for the isotope and elementary analyses ( INRA Nancy Technical Facility of Functional Ecology-OC 081 ). Thanks to the experiment unit  UE Forêt-Pierroton (INRA) , and especially to  Bernard Issenhuth  for yearly management of the ORPHEE experiment.
The aim of the present study was to investigate, in Brevibacterium strains, key genetic determinants known to be important for growth in cheese: the catabolism of energy compounds present in cheeses, iron acquisition, salt tolerance and bacteriocin production. For that purpose, we sequenced the genome of 13 Brevibacterium strains, including eleven strains isolated from cheeses. We performed comparative analyses of these genomes and of ten other Brevibacterium genomes from strains isolated from diverse environments and already present in the Integrated Microbial Genomes (IMG) database  [18].
Genome sequencing, assembly and annotation Libraries were generated using the TruSeq DNA Sample Preparation Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions. Sequencing was carried out on an Illumina MiSeq apparatus at the INRA GeT-PlaGE platform (http://get. genotoul. fr) in order to generate paired-end reads (250 bases in length). For each strain, the paired-end reads were merged using FLASH  [19]. De novo assembly was performed using SPAdes version 3. 1. 1 [20]. Only contigs with length > 1000 bp were considered for further study. Gene predictions and annotations were performed automatically using the Integrated Microbial Genomes (IMG) database and comparative analysis system  [21] , as described in the corresponding standard operating procedure  [22]. PHA-STER  [23]  was used to predict prophages.
Comparative genomic analysis and phylogenetic classification Comparative genomic analyses were performed considering the 13 genomes sequenced in the present study as well as the ten other Brevibacterium genomes present in the IMG database in September 2016 (   The "Brevibacterium linens BL2" genome in the JGI database is in fact the genome of strain ATCC 9174  [95]  phylogenetic analysis was performed for the 23 Brevibacterium genomes using the sequences of 40 marker genes, as described by Mende et al. [27]. The genomes of Glutamicibacter arilaitensis Re117  [16]  (Project accession number PRJEA50353) and Corynebacterium casei LMG S-19264  [28]  (Project accession number PRJNA186910) were used as outgroups. An in-house database of the 40 marker genes present in 388 bacterial strains, which included 117 strains isolated from dairy products  [29] , was used to detect the 40 marker genes in the Brevibacterium genomes using tBlastN  [30].
The best hits were selected with at least 60% sequence identity and 80% coverage. Each marker gene was translated into an amino acid sequence using T-Coffee  [31]  and aligned using MUSCLE  [32]. The 40 individual alignments were then concatenated to a single one, which was used to build the tree using FastTree 2  [33]  with the following parameters: -gamma -pseudo -mlacc 3 -slownni and the default bootstrap procedure (1000 resamples). The tree was visualized and annotated using MEGA7  [34]. Homologous gene families were computed using the OrthoMCL procedure implemented in GET-HOMOLO GUES software  [35]. Amino acid sequences of the CDSs from the 23 Brevibacterium genomes were grouped into clusters using 75% identity and 75% coverage thresholds with a BlastP cutoff E value <1e-05. The inflation index of OrthoMCL algorithm was set to 1.
5, as recommended by Li et al. [36]. Strain ATCC 9175 T was set as the first reference genome, the subsequent ones were randomly chosen by GET-HOMOLOGUES. Functional category assignment to each cluster was done according to the Clusters of Orthologous Groups (COG) database  [37]. The Average Nucleotide Identity (ANI), implemented in GET-HOMOLOGUES software, was computed on homologous genes for all possible pairs of genomes.
Phylogenomic analyses and orthology The genomic data from the 23 Brevibacterium strains were used to assess their intra-genus phylogenetic relationships. The phylogenomic tree partitioned the strains into two major lineages (Fig. 1 ). Lineage 1 contains two Brevibacterium strains isolated from human-associated samples, i. e. , B. mcbrellneri ATCC49030 T   will be referred to as group "aurantiacum/sandarakinum/ antiquum", group "linens/siliguriense/iodinum" and group "casei", respectively. The taxonomy of the Brevibacterium genus is still in process of reclassification  [11]. According to Stackebrandt et al. [38] , 16S rRNA (rrs) gene sequences and DNA-DNA hybridization (DDH) should be considered as molecular criteria for species delineation. However, the Average Nucleotide Identity (ANI) has recently been proposed to replace DDH values  [39] [40] [41].
The second type is a glycerophosphoryl diester phosphodiesterase [EC 3. 1. 4. 46], which was identified only in the strains of the phylogenetic groups aurantiacum/sandarakinum/antiquum and linens/siliguriense/iodinum. Uptake of fatty acids can be done by passive diffusion through the membrane lipid bilayer or by proteinfacilitated transfer  [49]. Genomic analysis revealed the presence of short-chain fatty acid uptake (AtoE) family proteins (TC no. 2. A. 73) in all of the 23 Brevibacterium strains and it is noteworthy that Brevibacterium strains have a greater number of transporters from this family than other Actinobacteria strains (1. 7 vs. 0. 1 genes per genome), based on assignations to the COG2031 for the 5726 Actinobacteria strains present in April 2017 in the IMG database. A complete beta-oxidation pathway for fatty acid degradation was identified in all of the investigated strains, except in strains ATCC 49030 T and 5401308 T , for which genes encoding L-3-hydroxyacyl-CoA dehydrogenase or 3-ketoacyl-CoA thiolase seemed to be lacking.
Interestingly, analysis of the genomes present in the IMG database also revealed that four gene clusters involved in iron acquisition were shared between Brevibacterium strains isolated from cheeses and cheese isolates belonging to other genera (Glutamicibacter, Microbacterium and Corynebacterium). This corresponded to recent HGT events since the percentages of identity at the amino acid level between the genes in Brevibacterium and the genes in the other genera were typically ~95-100%. In most cases, transposase genes were located close to the clusters. These clusters were denoted Iron-Brev1, Iron-Brev2, Iron-Brev3 and Iron-Brev4 (Additional file 9). The cluster Iron-Brev1 corresponds to the ActinoRUSTI region that was recently described  [17].
9 and 4. 0 genes per genome, respectively, based on assignations to the COG0025, COG1055, COG1757, COG3004, COG3067 and COG3263). It is noteworthy that Brevibacterium strains have a greater number of transporters from the Sodium Solute Symporter (SSS) family than other Actinobacteria strains (7. 3 vs. 1. 7 genes per genome, based on the number of proteins matching the PF00474 Hidden Markov Model).
Bacteriocines and phenazines In cheese, bacteriocin producers can inhibit other microbial groups that share the same ecological niche, which confers them a selective advantage. Genomic analysis predicted the production of several bacteriocins in Brevibacterium strains (Additional file 11). Linocin M18related bacteriocins (PF04454) were identified in 15 genomes, including five of the nine strains of the phylogenetic group aurantiacum/sandarakinum/antiquum, all six strains of the group linens/siliguriense/iodinum and four of the eight other strains (B. album DSM 18261 T , B. senegalense JC43 T , B. jeotgali SJ5-8 T and B. sp. Mu109). Five groups of ribosomally synthesized and posttranslationally modified peptides (RiPPs)  [62]  were predicted in the 23 Brevibacterium strains. The first group corresponds to lanthipeptides, which are characterized by the presence of lanthionine (Lan) and/or methyllanthionine (MeLan) and/or labionin (Lab) residues  [62, 63].
Many lanthipeptides have an antimicrobial activity, mainly against Gram-positive bacteria  [64] , and are referred to as lantibiotics. Lanthipeptide gene clusters were predicted in seven strains, of which six are cheeseassociated (Additional file 11). Even if they have different structures, these clusters contain one or two putative lanthipeptide synthetases, one or two putative precursor peptides, one to three putative ABC transport system components and, in some cases, a prolyl oligopeptidase (PF00326) (Fig. 3A ). Protein sequence analysis of the predicted lanthipeptide synthetases suggests that all of them belong to class III, corresponding to a trifunctional enzyme LanKC  [65]. The sequences of all putative precursor peptides (Fig. 3B ) contain two characteristic and conserved Ser/Ser(Thr)/Cys motifs necessary for the formation of (Me)Lan and/or (Me)Lab.
3C  and Additional file 11). Integration of this ICE occurred at the 3′ end of a gene encoding a class Ib ribonucleotide reductase beta subunit, resulting in a 12-bp perfect repeat sequence, present at the two borders of BreLI. It is noteworthy that, in comparison to the four other strains, a segment containing three genes of the lanthipeptide gene cluster region is lacking in the ATCC 9174 BreLI Island (compare clusters (a) and (b) in Fig. 3A ). The second group of predicted RiPPs is related to lactococcin 972 (PF09683), which has been characterized in Lactococcus lactis IPLA 972  [69, 70]. Genes with a weak homology with the lactococcin 972 precursor peptide were identified in six cheese-associated strains from the phylogenetic group aurantiacum/sandarakinum/antiquum, corresponding to two different putative prepeptides, one of them being present only in strain 239c, and the other in five B.
The lactococcin 972-related bacteriocin biosynthesis gene cluster in strains ATCC 9174 and CNRZ 920 is also flanked by a tRNA-val gene. The third group of predicted RiPPs corresponds to linear azol(in)e-containing peptides (LAPs), which are characterized by the presence of multiple thiazole and (methyl)oxazole heterocycles, and sometimes by their corresponding 2-electron reduced azoline state. LAP gene clusters were predicted in four B. aurantiacum cheese-associated strains (Additional file 11). One cluster is present in strains 6(3), ATCC 9175 T and ATCC 9174, and another is present only in strain 8  (6). All these clusters contain putative precursor peptides, a SagB-type dehydrogenase domain-containing protein (TIGR03605), one or two YcaO cyclodehydratases (PF02624) and a cyclodehydratase-docking fusion protein (TIGR03882), representing the critical components in LAP biosynthesis  [62, 71].
Acknowledgments We are grateful to the  INRA MIGALE bioinformatics platform  (http:// migale. jouy. inra. fr)for providing computational resources, and the IMG-ER system (https://img. jgi. doe. gov/cgi-bin/mer/main. cgi)for generating annotations. Funding N-P. P. is the recipient of a doctoral fellowship from the  AgroParisTech Foundation  and the  INRA MEM metaprogram. This work was supported by  France Génomique National  infrastructure, funded as part of " Investissement d'avenir" program  managed by  Agence Nationale pour la Recherche  (contrat  ANR-10-INBS-09 ).
linens ATCC 9172 T Harzer cheese PRJEB19834 FXYY01000001-FXYY01000080 Permanent draft This study B. linens Mu101 Munster cheese PRJEB19836 FXZA01000001-FXZA01000081 Permanent draft This study B. sp. 239c Camembert cheese PRJEB19828 FXZH01000001-FXZH01000068 Permanent draft This study B. sp. Mu109 Munster cheese PRJEB19840 FXZF01000001-FXZF01000126 Permanent draft This study B. iodinum ATCC 49514 T Cow milk PRJEB19872 FXYX01000001-FXYX01000065 Permanent draft This study B. jeotgali SJ5-8 T Seafood PRJEB19841 FXZM01000001-FXZM01000047 Permanent draft This study B. aurantiacum ATCC 9174 a Romadur cheese PRJNA405 AAGP01000001-AAGP01000076 Permanent draft DOE JGI, 2005 (direct submission) B. album DSM 18261 T Soil PRJNA195785 AUFJ01000001-AUFJ01000016 Permanent draft Kyrpides et al. , 2013 (direct submission) B.
sandarakinum DSM 22082 T Wall surface PRJEB16423 LT629739 Complete Varghese, 2016 (direct submission) Kämpfer et al. , 2010 [91] B. linens AE038-8 Fresh water PRJNA268212 JTJZ01000001-JTJZ01000029 Permanent draft Maizel et al. , 2015 [92] B. siliguriense DSM 23676 T Fresh water PRJNA303729 LT629766 Complete Varghese, 2016 (direct submission) B. sp. VCM10 Fresh water PRJNA234061 JAJB01000001-JAJB01000141 Permanent draft Muthukrishnan et al. , 2014 (direct submission) B. casei S18 Human associated PRJNA174308 AMSP01000001-AMSP01000043 Permanent draft Sharma et al. , 2012 (direct submission) B. ravenspurgense 5401308 T Human associated PRJNA159637 CAJD01000001-CAJD01000026 Permanent draft Roux et al. , 2012 [93] B. mcbrellneri ATCC 49030 T Human associated PRJNA34583 ADNU01000001-ADNU01000096 Permanent draft Qin et al.
Bioinformatics analysis reveals that DHBN is the only highly conserved domain in N-terminal domains of the vertebrate BLM homologues-To probe whether the N-terminal domains are evolutionarily conserved in sequence and structure, we performed multiple-sequence alignment of most homologous proteins of BLM (BLMs) in the reference proteome database (see "Experimental Procedures") and constructed a phylogenetic tree (supplemental Fig. S1 ). These data reveal that the N-terminal domain of BLM displays three striking features. (i) It lacks sequence conservation among orthologs. By scanning over 78 BLM sequences from different species, we found that the sequences of the helicase core region were highly conserved with an average 81. 7% identity and 89. 9% similarity, whereas those of the N-terminal domain varied greatly within and across species.
3E ). The V-shape with the interhelical angle of 120°between the helices ␣1 and ␣3 is reminiscent of the helix-turn-helix (HTH)  (32)  and EF-hand motifs  (33) , which are 110°(Trp repressor, PDB code 1TRO) and 117°(S100A10, PDB code 1BT6), respectively. However, when the structures are superimposed on the first helix, the second helix has a different spatial location. The DHBN has, therefore, a different conformation from those of the HTH and EF-hands (Fig. 3F ). A search of structural homologs of the dimeric DHBN with DALI gave a significant hit (Z-score 7. 4) with Syngap, a Ras GTPase-activating protein (PDB code 3BXJ) (Fig. 3G ). The homolog structural elements found in Syngap are in the GAPex domain between GTPase domain and C2 domain  (34). When superimposed, the r. m. s. d. is 3. 7 Å calculated on 94 C␣.
Gel filtration studies showed that BLM has a native molecular mass of ϳ700 kDa, consistent with an olig- A 100 nM concentration of each gBLM truncate protein and 4 nM DNA, 1. 0 mM ATP were simultaneously preincubated at 25 °C for 5 min, respectively. Data were collected and fitted as described under "Experimental Procedures. " D, kinetics of conformational transition of the full-length and truncated gBLM proteins determined by DLS. The assays were performed as described under "Experimental Procedures. " E, comparative limited proteolysis of gBLM(1-1300), gBLM(294 -1258), gBLM(360 -1258), and gBLM(610 -1258). A 6. 5 M concentration of each gBLM truncate protein was cleaved with ␣-chymotrypsin at 0, 5. 0, 2. 5, 1. 3, 0. 6, and 0. 3 g/ml (lanes 1-6) at 18 °C for 1 h, respectively. The corresponding protein marker M is shown in lane 7.
Experimental Procedures Bioinformatics analysis of the conservation of the DHBN-All BLM homologous protein sequences have been downloaded from the Reference Proteomes database by hmmsearch. First, the sequences were aligned with the online MAFFT program after the truncated sequences were removed manually. Then the maximum likelihood phylogenetic tree was constructed by PhyML (JTT model, default parameters)  (47) , and the final tree with domain organization information was manipulated and rendered with evolview  (48, 49). The disorder tendency of each residue of each sequence was calculated by IUPred, a web-based tool for the prediction of intrinsically unstructured regions of a protein. The coverage, identity, and average values of disorder tendency of each residue site of the multiple-sequence alignment were integrated with python scripts.
Plasmid construction, protein expression, and purification-According to the NCBI amino acid sequences of G. gallus bloom syndrome protein (accession number NP_001007088. 2, gBLM for short), gBLM(1-1300) without the nuclear localization signal was amplified and constructed into pET21a-sumo vector. Then by taking the positive pET21a-sumo gBLM (1-1300) as the template, gBLM(1-612), gBLM(294 -1258), gBLM(360 -1258), and gDHBN(294 -359) were amplified by the corresponding forward and reverse primers and constructed into pET15b-sumo plasmids and transformed into the expression strain of 2566, respectively. Similarly, gBLM(610 -1258) consisting of the gBLM helicase core was amplified, constructed into pTWIN1 (New England Biolabs), and transformed into BL21 (DE3). Likewise, pET15b-sumo hDHBN (residues 362-414) and pET15b-sumo pDHBN (residues 1-66) were constructed according to the NCBI amino acid sequences of H.
sapiens BLM helicase (accession number P54132, hBLM for short) and P. crispus bloom syndrome protein (accession number XP_009483195. 1, pBLM for short). In the experiment, expression of all BLM truncated proteins were induced by 0. 3 mM isopropyl 1-thio-␤-D-galactopyranoside at 18 °C for 16 h. Because gBLM(1-612), gBLM(294 -1258), gBLM(360 -1258), and gBLM(1-1300) showed lower stabilities than gBLM(610 -1258) and the DHBN proteins, they were purified to homogeneity sequentially by affinity chromatography with cOmplete His tag purification resin (CHTPR, Roche Applied Science) column and ion exchange chromatography on SP Sepharose Fast Flow (GE Healthcare) and Q Sepharose Fast Flow (GE Healthcare), respectively. Similarly, purification of gBLM(610 -1258) was carried out through chitin affinity chromatography and SP ion exchange chromatography, substituting KCl for NaCl in the buffers.
1 M trisodium citrate, pH 4. 4, 12% PEG 1500, and 15% glycerol. As expected, the homologous pDHBN gave out high resolution crystals from the optimal condition of 0. 2 M ammonium acetate, 0. 1 M trisodium citrate, pH 3. 6, and 16% PEG 3350. Crystals were loop-mounted, cryo-protected, and diffracted on BL18U1 and BL19U1 beamlines at SSRF (Shanghai Synchrotron Radiation Facility). Once data were collected and processed, the structures extending to 2. 7 Å resolution of gDHBN and 1. 4 Å resolution of pDHBN were ascertained by selenium and by the molecular replacement phasing method, respectively  (50). Moreover, by following the similar sitting drop crystallization and optimization methods of gDHBN and pDHBN, optimized crystals of hDHBN exhibited higher diffraction resolution in well conditions of 0.