dataesr/scientific-paragraphs-categorization huggingface dataset:
Gene expression analysis RT-PCR, performed on total RNA isolated from germinating rapeseed seeds at different 'days after germination' (DAG), was used to investigate the expression pattern of the BnLIP gene during early seedling development. In imbibed seeds (0 DAG) or at one or two DAG, no transcript could be detected (data not shown). Transcription of the lipase gene seems to be specifically activated at 3 DAG, but only transiently, since the level of the BnLIP mRNA rapidly declined at later times (Fig. 5A ). Confirming previous data (Gladied  Ghram et al. 2013) , the expression of the BnLIP gene could not be detected in different organs (roots, stems, leaves or flowers) of adult plants at the reproductive stage (Fig. 5B ). The transcript of the housekeeping BnACT gene, on the contrary, was detected at similar levels in all RNA samples (Fig.
Scheme 2. Hydrolysis of compound 3. The signal of phosphorus atom in the 31 P-NMR spectrum of the substrate 3 is located at 27. 73 ppm, while the chemical shifts of the products are 18. 54 ppm and 17. 92 ppm for 4 and 5, respectively. Such a pronounced upfield shift of the 31 P signal can be caused by the unsaturation at the site of the alpha carbon  [14]. The structures of compounds 4 and 5 were confirmed by their spectral data ( 1 H-and 13 C-NMR). Comparing the 1 H-NMR spectra of both substrate (3) and products (4, 5), it is noticed that the signals from the two protons H29, presenting as two singlets (5. 07 and 5. 01 ppm) in the spectrum of 3, there is a doublet signal derived from one proton at 5. 42 ppm ( 2 J HP = 18. 6 Hz) and at 5. 28 ppm ( 2 J HP = 19. 2 Hz) for 4 and 5, respectively (Figure  S1 ).
Olefin stereochemistry of the compound 5 was determined as (Z)-isomer. For compound 4, signals of C30 and C19 are observed at δ C : 17. 5 (d, 3 J CP = 7. 8 Hz) and 51. 5 (d, 3 J CP = 24 Hz), respectively. The structures of compounds 4 and 5 were confirmed by their spectral data ( 1 H-and 13 C-NMR). Comparing the 1 H-NMR spectra of both substrate (3) and products (4, 5), it is noticed that the signals from the two protons H29, presenting as two singlets (5. 07 and 5. 01 ppm) in the spectrum of 3, there is a doublet signal derived from one proton at 5. 42 ppm ( 2 JHP = 18. 6 Hz) and at 5. 28 ppm ( 2 JHP = 19. 2 Hz) for 4 and 5, respectively (Figure  S1 ). Similarly, in the 13 C-NMR spectra, the signal of the carbon atom connected with the phosphoryl group (C29) for compound 4 is present at 111.
0 ppm in the form of a doublet with a coupling constant 1 JCP = 193 Hz, whereas in the spectrum of compound 5, a doublet is located at 111. 9 with a coupling constant 1 JCP = 189 Hz. The 1 H-and 13 C-NMR coupling constants were consistent with the values reported for the other vinyl phosphonates  [15]. The above results suggested that the performed reaction of hydrolysis of the acetyl groups additionally led to the isomerization in the isopropenyl moiety. Several literature data have shown that then allyl phosphonate diesters undergo isomerization to the vinyl phosphonate diesters. This process occurs in various palladium catalysed nucleophilic substitution reactions, thermal rearrangements and under basic conditions  [16] [17] [18] [19] [20] [21]. The stereochemical assignments of the new obtained vinylic derivatives were also determined by the carbon phosphorus coupling constants ( 3 JCP).
The structures of compounds 4 and 5 were confirmed by their spectral data ( 1 H-and 13 C-NMR). Comparing the 1 H-NMR spectra of both substrate (3) and products (4, 5), it is noticed that the signals from the two protons H29, presenting as two singlets (5. 07 and 5. 01 ppm) in the spectrum of 3, there is a doublet signal derived from one proton at 5. 42 ppm ( 2 JHP = 18. 6 Hz) and at 5. 28 ppm ( 2 JHP = 19. 2 Hz) for 4 and 5, respectively (Figure  S1 ). Similarly, in the 13 C-NMR spectra, the signal of the carbon atom connected with the phosphoryl group (C29) for compound 4 is present at 111. 0 ppm in the form of a doublet with a coupling constant 1 JCP = 193 Hz, whereas in the spectrum of compound 5, a doublet is located at 111. 9 with a coupling constant 1 JCP = 189 Hz. The 1 H-and 13 C-NMR coupling constants were consistent with the values reported for the other vinyl phosphonates  [15].
The above results suggested that the performed reaction of hydrolysis of the acetyl groups additionally led to the isomerization in the isopropenyl moiety. Several literature data have shown that then allyl phosphonate diesters undergo isomerization to the vinyl phosphonate diesters. This process occurs in various palladium catalysed nucleophilic substitution reactions, thermal rearrangements and under basic conditions  [16] [17] [18] [19] [20] [21]. The stereochemical assignments of the new obtained vinylic derivatives were also determined by the carbon phosphorus coupling constants ( 3 JCP). For the olefin phosphonates, this constant is typical and dependent on the spatial structure. It has been reported that for various vinylphosphonates, the cis 3 JCP coupling constant is generally smaller than trans 3 JCP in the 13 C-NMR and they are equal to 6-8 Hz and 20-25 Hz, respectively  [22, 23].
Crystal Structure Determination The X-ray diffraction data were collected on a Bruker D8 venture diffractometer equipped with an PHOTON100 CMOS detector using a Mo-Kα radiation source (λ = 0. 71073 Å) at 100 K under a continuous flow of cooled nitrogen gas. The structure was solved by direct methods using SHELXT  [32]  and refined by full-matrix least-squares fitting on F 2 using MoPro program  [33]. All non-hydrogen atoms were refined anisotropically. The hydrogen atoms were refined isotropically using X-H bond length restraints and X-H distance similarity restraints to favor their placement in the ideal position. The thermal motion parameters U iso of hydrogen atoms were restrained to ride on 1. 2 × U eq for C-H and CH 2 hydrogen atoms and 1. 5 × U eq for CH  3  and OH hydrogen atoms. The O-H proton of compound 8a was located from difference Fourier map.
Biological Activity of Compounds The antiproliferative effect of the synthesized compounds was determined using the Cell Proliferation Reagent WST-1 assay (Roche Diagnostics, Mannheim, Germany). The assay principle is based upon the reduction of the tetrazolium salt WST-1 to formazan by mitochondrial dehydrogenases in viable cells. The tested compounds were exposed at various concentrations of each compound (0. 1-100 µg/mL), and then cell viability was quantified by a cell proliferation assay. The generation of the dark yellow colored formazan was measured at 450 nm. The experiments were repeated in triplicate for each tested compound concentration. Calculations of the IC 50 values were performed using GraphPad Prism 6 (GraphPad Software, San Diego, CA, USA). The cytotoxic effect of test compounds was compared with cisplatin (positive control).
The sequestrate false truffles Elaphomyces favosus, E. iuppitercellus, and E. labyrinthinus spp. nov. are described as new to science from the Dja Biosphere Reserve, Cameroon. Elaphomyces adamizans sp. nov. is described as new from the Pakaraima Mountains of Guyana. The Cameroonian species are the first Elaphomyces taxa to be formally described from Africa, occurring in lowland Guineo-Congolian tropical rainforests dominated by the ectomycorrhizal (ECM) canopy tree Gilbertiodendron dewevrei (Fabaceae subfam. Caesalpinioideae). The Guyanese species is the third to be discovered in lowland tropical South America, occurring in forests dominated by the ECM trees Pakaraimaea dipterocarpacea (Dipterocarpaceae) and Dicymbe jenmanii (Fabaceae subfam. Caesalpinioideae). Macromorphological, micromorphological, habitat, and DNA sequence data are provided for each new species.
Taxa used, sequence alignment, and phylogenetic analysis All Elaphomycetaceae (e. g. Elaphomyces, Pseudotulostoma) ITS and 28S sequences derived from ascomata and ECM root tips available in GenBank were downloaded. Each gene region was aligned separately with the sequences from our new species using the RNA structure-based algorithm Q-INS-i implemented in MAFFT v7. 023b  (Katoh et al. 2002 , Katoh & Toh 2008 , Katoh & Standley 2013). After correcting the orientations of four ITS sequences, removing one short sequence (GenBank accession AM087442) and one sequence with substantial numbers of ambiguous bases (GenBank accession AB161194), the uneven ends were trimmed and alignments refined with a second round of alignment in MAFFT, as above, and refined alignments concatenated into a single dataset.
Phylogenetic analysis under the maximum likelihood criterion was performed using the Pthreads parallelised version of RAxML v7. 0. 3  (Stamatakis 2006 , Ott et al. 2007 ) with a GTRGAMMA model, allowing model parameters to be estimated for each gene partition separately. Branch support was assessed using nonparametric bootstrapping with the autoMRE option. Geographic sources of sequences used from GenBank were determined primarily from locality information in GenBank records. The alignment and tree have been accessioned in TreeBase at http://purl. org/phylo/treebase/phylows/study/ TB2:S18165.
REsULTs Final alignments consisted of 82 sequences and 832 positions for the ITS (381 parsimony informative, 361 constant, 90 autapomorphic), and of 18 sequences and 887 positions for the 28S (145 parsimony informative, 712 constant, 30 autapomorphic). All 28S sequences had corresponding ITS sequences derived from the same source, except for Elaphomyces digitatus where they were derived from two separate conspecific sources and subsequently combined in the dataset. All characters were included in the analysis. RAxML rapid bootstrapping terminated after 550 replicates (WRF average of 100 random splits = 2. 319227) and the.
JN168718 uncultured Elaphomyces NR_121522 Elaphomyces compleximurus   (-ln = 10065. 206922 ) of a combined analysis of ITS and 28S sequences of Elaphomycetaceae taxa in RAxML using a GTRGAMMA substitution model. Tree is midpoint rooted. Numbers on or next to branches are nonparametric bootstrap supports >70 % from 550 bootstrap replicates. For terminals downloaded from GenBank, labels begin with GenBank accession number and are colour-coded by geographic origin of the sources of the sequences as determined by GenBank records. Terminal labels for taxa generated in this study begin with the collection number. Terminals in bold are represented by both ITS and 28S sequences. Those beginning with a 'C' had their sequence orientation corrected for phylogenetic analysis. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 i m a f U N G U S Table  1.
GenBank accession numbers ITS: KT694138; 28S: KY694149. Description: Ascomata 6-20 mm tall (without basal attachment) × 7-27 mm broad, subglobose to ovate or somewhat lobed, black overall, with a distinct subturbinate base encompassing dark brown to black ectomycorrhizas, dense extramatrical mycelium, and sand; peridial surface nearly smooth on immature ascomata, on larger, mature ascomata verrucose throughout; warts 0. 1-0. 2 mm tall and 0. 6-0. 8 mm broad, polygonal, 4-5-6-sided, with flattened apices. Peridium in section subcartilaginous, three-layered; outer layer black, carbonaceous, < 0. 25 mm thick, underlain by a greyish tan second layer with occasional reddish tones, to 0. 5 mm thick, with embedded, black ectomycorrhizas; inner third layer dark grey to black, to 0. 75 mm thick. Gleba initially off-white to pale grey, greyish black at maturity, somewhat powdery but mostly arranged in irregular moist masses, with fine, grey hyphae particularly near gleba-peridium interface.
dewevrei monodominant forest, 25 Aug. 2014, Henkel THDJA 39 (YA 0063175 -holotype; HSC G1178, OSC 149782, K(M) 200226). GenBank accession numbers ITS: KT694139; 28S: KT694143. Description: Ascomata 4-8 mm tall and 6-12 mm broad, subglobose to ovate, without a distinct base, dark brown to black overall under scattered adherent soil, debris, and ectomycorrhizas; peridial surface somewhat smooth macroscopically but close inspection reveals low warts covering the entire surface; warts subcircular, to 150 µm tall and 400 µm broad, blunt at apex. Peridium in section subcartilaginous, with two distinct layers; outer first layer ~ 0. 15 mm thick, black, carbonaceous; underlying second layer to 0. 5 mm thick, greyish to grey-brown, with an apparent "third" inner layer appearing as a thin band of white cottony hyphae emanating from the outer gleba and contiguous at irregular intervals with white glebal veins.
The phylogenetic relationships, if any, between these species could not be assessed here as ITS and 28S sequence data for E. spirosporus, E. striatosporus, and E. virgatosporus are lacking in GenBank. Elaphomyces iuppitercellus has larger ascospores (mean diameter = 24. 7 µm) than E. guangdongensis (mean diameter 17. 8 µm), E. spirosporus (mean diameter 20. 5 µm), E. striatosporus (mean diameter = 17. 5 µm), and E. virgatosporus (mean diameter = 20. 2 µm); additionally, each of the European species has a grey-toned gleba, which contrasts with the pinkish brown gleba of E. iuppitercellus. Also, the striate ornamentation walls of E. iuppitercellus are much thinner than those of all other striate-spored Elaphomyces species. Elaphomyces iuppitercellus ascomata had an identical ITS sequence with that obtained from a G.
GenBank accession numbers ITS: KT694137; 28S: KT694148. Description: Ascomata to 13 mm tall and 20 mm broad, broadly ovate to depressed ovate, with a distinct, slightly tapered base composed of ectomycorrhizas, sand, and dense, dark brown to nearly black mycelium; peridium slightly thickened in this area; peridial surface verrucose beneath a turf of erect, dark brown hyphae; warts black, polygonal, 4-6-sided, with uneven side lengths, 100 µm tall and ± 300 µm broad, flattened, on close inspection appearing finely ridged. Peridium in section subcartilaginous, five-layered; outer layer ± 0. 05 mm thick, dark brown; second layer ± 0. 1 mm thick, black, carbonaceous; third layer 0. 35-0. 60 mm thick, pale tan, with scattered embedded, black-mantled ectomycorrhizas across the lower portion of the ascoma, these more dense near the basal attachment; fourth layer ± 0.
It is clear from the detailed descriptions and illustrations of P. japonicum from  Kawamura (1954) ,  Otani (1960), and Asai et al. (2004)  that the species shares the unusual macromorphological structure with P. volvatum, and both species have key micromorphological features shared with Elaphomyces. Masuya & Asai (2004)  stated "…the fact that unopened ascomata of P. japonica are highly similar to the fruit-body found in the genus Elaphomyces suggests that this species, which we believe should be treated as Pseudotulostoma, may also exist as a species of Elaphomyces". It should be noted that during the time of both  Miller et al. (2001)  and  Masuya & Asai (2004)  very few Elaphomyces sequences were available in GenBank, so taxon sampling for the genus was low in both studies. Subsequently,  Reynolds (2011)  provided unpublished data suggesting a congeneric relationship of Pseudotulostoma and Elaphomyces, a relationship also suggested by our phylogenetic analysis (Fig.
Additional specimens examined: Cameroon: East Province: Dja Biosphere Reserve, Northwest Sector near the village of Somalomo, Upper Dja River Basin, within 2 km radius of Dja base camp located at 3°21'29. 8" N 12°43'46. 9" W, ~1. 4 km WNW of base camp on trail between Gilbertiodendron plots 1 & 2, in semi-inundated G. dewevrei monodominant forest, 20 Aug. 2014, Henkel 9874 (YA, HSC G1175, OSC 149786, K(M) 200224; GenBank accession numbers: ITS KT694135; 28S KT694147); 28 Aug. 2014, Henkel 9897 (YA, HSC G1176, OSC 149788, K(M) 200219; GenBank accession numbers ITS: KT694136; 28S: KT694146); ~2 km WNW of base camp in vicinity of Gilbertiodendron plot 3, in G. dewevrei monodominant forest, 26 Sep. 2014, Henkel 10015 (YA, HSC G1177, OSC 149787, K(M) 200220, GenBank accession numbers ITS: KT694134; 28S: KT694145).
Additional specimens examined: Cameroon: East Province: Dja Biosphere Reserve, Northwest Sector near Somalomo Village, Upper Dja River Basin, within 2 km radius of Dja base camp located at 3°21'29. 8" N 12°43'46. 9" W, ~1. 5 km WNW of base camp in Gilbertiodendron plot 2, in G. dewevrei monodominant forest, 4 Sep. 2014, Henkel 9934 (YA, HSC G1179, OSC 149783, K(M) 200221; GenBank accession numbers ITS: KT694141; 28S: KT694142).
Guyana: Region 9 Cuyuni-Mazaruni: Pakaraima Mountains, Upper Mazaruni River Basin, ~10 km west of Mt Ayanganna, within 0. 5 km of a base camp at 5° 26' 21. 3" N 60° 04' 43. 1" W, 100 m north of base camp in savanna fringing forest dominated by Pakaraimaea dipterocarpacea and Dicymbe jenmanii, 2 Jun. 2012, Henkel 9660 (BRG 41125 -holotype; HSC G1181, OSC 149784, K(M) 200222 -isotypes). GenBank accession numbers ITS: KT694133; 28S: KT694144.
Type: Guyana: Region 9 Cuyuni-Mazaruni: Pakaraima Mountains, Upper Mazaruni River Basin, ~10 km west of Mt Ayanganna, within 0. 5 km of a base camp at 5° 26' 21. 3" N 60° 04' 43. 1" W, 100 m north of base camp in savanna fringing forest dominated by Pakaraimaea dipterocarpacea and Dicymbe jenmanii, 2 Jun. 2012, Henkel 9660 (BRG 41125 -holotype; HSC G1181, OSC 149784, K(M) 200222 -isotypes). GenBank accession numbers ITS: KT694133; 28S: KT694144.
The BAC names given here are abbreviations from the complete clone names (e. g. , Tae-B-82036-ng-235H14). Raw 454 read data were processed and assembled using Newbler (version 2. 7). Resulting contigs were preliminary ordered by mapping BAC end sequences and genetic markers on the contigs to the published homologous region on 3B of the reference cultivar Chinese Spring (GenBank accession: FN564434). The contig order was refined and remaining gaps were closed by sequencing equimolar pooled BACs 217J06, 235H15, 18G11, 114J13 and 90G13 on one PacBio SMRT cell (GATC, Konstanz, Germany) cells using AHA scaffolding  (Bashir et al. 2012)  for orientating and ordering contigs and PBJelly  (English et al. 2012 ) for filling gaps. Ab initio gene models refined by BLASTx and protein domain prediction algorithms were retrieved using the semi-automated annotations pipeline TriAnnot  (Leroy et al.
RNA sequencing For RNA profiling, frozen tissue samples were ground under sterile conditions and pooled to comprise a single sample/data point as described in  Kugler et al. (2013). 100 mg frozen tissue was used to extract RNA using the RNeasy Plant Mini Kit (Qiagen, Venlo, Netherlands). Quality and quantity were checked on an automated electrophoresis-system (Experion, #701-7000, Bio-Rad, Hercules, CA, USA). Samples were sequenced on Illumina HiSeq 2000/MiSeq machines (Eurofins MGW, Ebersberg, Germany) yielding at least 20 M 100 bp paired-end reads per sample (Supplementary Table  S2 ). The respective data sets are available in the EBI ArrayExpress (http://www. ebi. ac. uk/arrayexpress/) repository under the accession number E-MTAB-4222. Tophat  (Trapnell et al. 2012 ) was used to assign reads from the susceptible and resistant genotype to the Fhb1 contig (Supplementary Table  S2 ).
Reads were kept which showed at maximum one error in the alignment over its entire read length. Next, the contig-mapped reads were compared to the same data set mapped to the high confidence and low confidence gene sets generated from all 21 chromosomes of Chinese Spring  (Mayer et al. 2014 ) to detect falsely mapped reads. Reads were removed from the contig alignment when they found better matches to contigs from 20 Chinese Spring chromosomes excluding chromosome 3B. HTSeq  (Anders et al. 2015)  was used to extract the reads counts for annotated gene models. Significant differences between treatments and lines were obtained using the exactTest function in the R package EdgeR  (Robinson et al. 2010). SNP in CDS regions were detected by searching for polymorphisms present only in mapped reads from CM-NIL51, which includes the Remus susceptible Fhb1 region compared to reads originating from the CM-82036 Fhb1-region (CM-NIL38).
Ultimately, ten BACs of which five cover the entire contig were sequenced and assembled to form a contig of 1029 kb (Fig. 1a , GenBank accession: KU641029). The distance between flanking markers sts32 and sts189 stretches 800. 5 kb compared to 752 kb of the same interval in the Chinese Spring. While markers sts32 and UMN10 are evenly spaced in both cultivars, the distance between UMN10 and sts189 is around 49 kb larger in CM-82036. A dot plot analysis using a 100 bp word size to compare collinearity between the Fhb1-contig and the respective region in Chinese Spring showed more extensive rearrangements. Both sequences are highly dissimilar between positions 143 and 517 kb of the Fhb1-contig, which also includes UMN10 at position 426. 0 kb, but high similarities exist in the flanking regions (Fig.
Yet two of the four ab initio pipelines employed by TriAnnot suggest a gene model, which finds no further evidence in database comparisons to expressed genes. At the distal end of the sequenced contig around marker sts189 genes #28 to #33 find best matches in the Chinese Spring reference sequence. The Fhb1 region seems to lack TAA_ctg0954b. t00480. 1, an F-box domain-containing protein located between genes #32 and #33, for which no gene models were predicted. This highly colinear region to Chinese Spring also covers the two remaining small gaps in the sequenced contig with no predicted Chinese Spring genes mapping therein. Relative positions in the direction of markers sts32-sts189 a BLASTn against CDS sequences of ctg954b. If no hits were retrieved sequences were additionally used as query to search the ctg954b genomic DNA sequence, yielding "no gene annotated" as a positive or "no hit" as negative result.
Gene expression profiles in the Fhb1 region in response to F. graminearum We added expression data to the sequenced contig to further substantiate gene predictions and to gain an impression of expression dynamics in this region in the presence or absence of the pathogen. Expression profiles were generated from 72 RNA-seq libraries originating from F. graminearum and mock-inoculated wheat head tissues sampled in a dense time-course series from three to 48 h after inoculation. The sampled tissue derives from a newly developed NIL pair with the resistance donor CM-82036 as the recurring parent containing either Fhb1 and Qfhs. ifa-5A (CM-NIL38) or susceptible alleles originating from the German spring wheat cultivar Remus (CM-NIL51). To account for polymorphisms in CM-NIL51 to the sequenced contig, we allowed one mismatch per read when mapping reads to the Fhb1 region.
We controlled falsely mapped reads by mapping reads also against the IWGSC high and low confidence gene sets. About 10 % of the mapped reads found better matches in these data sets excluding genes from chromosome 3B and were excluded from any further analysis. Despite these considerations, only few genes in the central segment of the sequenced contig were hit by reads originating from the susceptible CM-NIL51 (genes #8-#27), while genes in the flanking non-divergent regions are generally expressed at comparable levels in either NIL (Fig. 2a ; Supplementary Tables  S4  and S5  including raw read counts and significant changed genes, respectively). Other large constitutive expression differences have only been detected for gene #3, encoding a protein of unknown function, for which we find higher transcript abundances in the susceptible CM-NIL51.