dataesr/scientific-paragraphs-categorization huggingface dataset:
Impairment of cpDNA Replication in Maize cptk1 Plants As noted above, qPCR data indicated positiondependent differences in the magnitude of the cpDNA deficiency in cptk1 mutants. These results were reminiscent of those seen previously in maize mutants deficient in chloroplast DNA polymerase  (Udy et al. , 2012)  and suggested that the loss of CPTK1 causes a defect in cpDNA replication. To explore this possibility, the relative stoichiometry of cpDNA regions across the genome was scanned by qPCR using a set of primer pairs spaced several kb apart. DNA was examined from apical, middle, and basal sections of the leaf, which in wild-type plants harbor mature, young, and immature chloroplasts, respectively (Supplemental Fig. S6 ;  Leech et al. , 1973). The magnitude of cpDNA deficiency in cptk1 mutants varied along the genome (Fig.
Several showed no repeated bases or just one at the junction border, suggesting they were produced by nonhomologous end joining. Very few such junctions were found in sequences derived from wild-type plants as compared to cptk1 (Supplemental Fig. S8 ). Importantly, the majority of these sequences in cptk1 mapped just upstream of the genomic region that is most strongly reduced in abundance, near the rRNA transcription unit (Fig. 6D ). Thus, our data support the conclusion that collapse of cpDNA replication early in leaf development in cptk1 mutants leads to broken chloroplast genomes that are then repaired by MHMR or nonhomologous end-joining pathways. These truncated genomes are deficient in various essential genes and are therefore incapable of supporting chloroplast biogenesis. A, Representative plastidial transcripts were quantified by RT-qPCR and normalized against a set of nuclear housekeeping genes.
Phylogenetic and Bioinformatics Analysis Bacterial and plant sequences were identified in the databases by BLASTP and TBLASTN with maize and Arabidopsis sequences as queries. Alignments were constructed with ClustalW implemented in the Macvector package using the GonneT matrix. Phylogenetic trees were built with PhyML v3. 1 online software (www. phylogeny. fr) using the neighbor-joining method implemented in the BioNJ program. Graphical representations were performed with TreeDyn (v198. 3). Subcellular targeting predictions were obtained with TargetP, Predotar, and MultiLoc2 (http://urgi. versailles. inra. fr/predotar/predotar. html, http://www. cbs. dtu. dk/services/TargetP, http://abi. inf. uni-tuebingen. de/ Services/MultiLoc2). GC skew plots were calculated with GCSkew (http:// genskew.
qPCR Analysis qPCR experiments were performed in a LightCycler480 (Roche) in a total volume of 6 µL containing 0. 5 mm of each specific primer and 3 µL of SYBR Green I Master Mix (Roche Applied Science). The thermocycling program was as follows: a 7-min denaturing step at 95°C followed by 40 cycles of 10 s at 95°C, 15 s at 60°C, and 15 s at 72°C. The second derivative maximum method was used to determine Cp values, and PCR efficiencies were determined from DNA serial dilution curves or using LinRegPCR software (http://LinRegPCR. nl). Three technical replicates were performed for each experiment. Results of qPCR and RT-qPCR analysis of maize and Arabidopsis sequences were standardized as previously described  (Udy et al. , 2012; Wallet et al. , 2015). Quantification of cpDNA copy numbers used a set of primer pairs located along the organellar genomes whose sequences and coordinates are given in Supplemental Table  S1.
A non-parametric test produces the nominal p-value for each tested target gene set. False-discovery rate (FDR) was used to correct for multiple testing (P FDR ). For secondary analysis of the significantly enriched pathways, we applied Gene Set Analysis SNP (GSA-SNP;  (Nam et al. , 2010) ) on the same input data. GSA-SNP uses p-values of SNPs to calculate enrichment scores by using the Z-statistic method. But instead of using the maximum effect per gene as a proxy for the respective gene, we chose the second-best p-value to represent the effect of each gene to avoid spurious associations  (Kwon et al. , 2012). For pathways, we used curated target gene sets (pathways) from Reactome as available through the Molecular Signature Database (v6. 0;  (Subramanian et al. , 2005). Their sizes were restricted from 20 to 200 to avoid overly narrow or broad gene sets.
Gene expression data BrainScope enables interactive visual exploration of spatial and temporal human brain transcriptomes from the Allen Institute for Brain Science  (Huisman et al. , 2017). Here we focused on the dataset Developmental Transcriptome from the BrainSpan atlas that had been pre-processed and re-analyzed by BrainScope's developers resulting in the dataset Developing human (comparative explorer) with RNA expression levels of 18,233 genes (Entrez Gene definitions) that were z-score normalized, to have a zero mean and a standard deviation of 1. To explore changes of co-expressed genes in brain regions and time windows, we used heat maps of the comparative explorer from BrainScope under default settings. Each square of a heat map displayed the average regional expression of the selected gene(s) across pooled tissue samples (replicates, developmental stages) from donor brains (controls).
Exploration of gene expression in BD-associated pathways To assess patterns of co-expressed genes from both pathways in the developing and adult brain, we used data from BrainSpan accessed through BrainScope and screened (i) expression of each single associated gene, (ii) expression of the combined set of associated genes (Combined), and (iii) expression of associated genes in context of target gene sets (Whole pathway). We found that five of the six genes enriched in GRB2 events in ERBB2 signaling demonstrated expression peaks during fetal development and infancy, while MAPK1 expression was lower during prenatal stages and higher during postnatal stages. The combined pattern of the six genes emphasized neural development and was similar to the whole pathway pattern. In NCAM signaling for neurite out-growth, four of the ten enriched genes (NCAN, FYN, NRAS, CREB1) revealed high expression during fetal and early postnatal development.
ACKNOWLEDGMENTS We are grateful to all patients and control subjects who contributed to this study. We thank the  Bipolar Disorder Working Groups of the MooDS and PGC consortia  for providing access to the relevant data. C. L. is the  Canada Research Chair in Environment and Genetics of Respiratory Disorders and Allergy , Director of the  Asthma Strategic Group of the Respiratory Health Network (RHN) of Fonds de la recherche en santé du Québec (FRSQ)  and researcher of the  CHILD Study.
Prognostic value of epigenetic genes in DLBCL We defined as epigenetic genes, genes belonging to the following families: DNMTs, methyl-CpG-binding domain (MBD) proteins, histone acetyltransferases (HATs), HDACs, HMTs, histone demethylases and bromodomain (BRD) and extra-terminal motif (BET) proteins  [20]  (Supplementary Table  1 ). We then investigated the prognostic value of their expression in DLBCL in two independent cohorts of patients with newly-diagnosed DLBCL (accession number GSE10846  [21] ): 233 patients treated with R-CHOP (rituximab-cyclophosphamide, hydroxydaunorubicin, vincristine, and prednisone) (Lenz R-CHOP cohort) used as training cohort and 181 patients treated with CHOP (cyclophosphamide, hydroxydaunorubicin, vincristine, and prednisone) (Lenz CHOP cohort) used as validation cohort.
Gene expression data of patients with DLBCL Gene expression microarray data from two independent cohorts of patients diagnosed with DLBCL were used. The first cohort (n = 414 patients; Lenz cohort)  [21]  was further divided in two cohorts, according to the patients' treatment. The first one, used as training cohort, included 233 patients treated with R-CHOP, whereas the second one, used as validation cohort, comprised 181 patients treated with CHOP. A third cohort (69 patients treated with R-CHOP; Melnick cohort) also was used as validation cohort  [86]. The pre-treatment clinical characteristics of the Lenz and Melnick cohorts were previously published by G. Lenz and R. Shaknovich's groups, respectively  [21, 86]. Affymetrix gene expression data (obtained using Affymetrix HG-U133 plus 2.
0 microarrays) are publicly available via the online Gene Expression Omnibus (http://www. ncbi. nlm. nih. gov/geo/) under the accession numbers GSE10846 and GSE23501. We also used GSE56315 data to compare gene expression profiles between DLBCL and normal centrocyte and centroblast samples  [24]. They were analyzed with Microarray Suite version 5. 0 (MAS 5. 0), using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
The study was approved by the ethic committee of Montpellier and patients provided a written informed consent (DC-2010-1185 and DC-2013-2027). For protein expression evaluation, slides were digitized using an iScan Coreo scanner (Ventana, Roche, France) to generate images. The Ventana image analysis algorithm, which is integrated in the Ventana Virtuoso image and workflow management software, was used for detection and semi-quantitative measurement of each protein (Ventana, Roche, France). Immunostaining results (i. e. , percentage of positive cells) were evaluated by two pathologists. P53 and MYC expression were considered positive if nuclear staining was respectively observed in 10% or more and in 40% or more of tumor cells  [90] [91] [92] [93] [94]. BCL2 expression was scored as positive if 50% or more of tumor cells showed cytoplasmic staining  [90].
ACKNOWLEDGMENTS This work was supported by grants from  French INCA (Institut National du Cancer) Institute  ( PLBIO15-256 ),  Languedoc Roussillon Region and FEDER (Hemodiag 2020) ,  ITMO Cancer (MM&TT)  and  Siric Montpellier  ( INCa-DGOS-Inserm 6045 ). JD is supported by a grant from  ARC  foundation.
RNA-seq and bioinformatics High-throughput sequencing of RNA libraries was performed following the standard protocol from Fasteris (www. fasteris. com). All sequencing runs were performed on an Illumina HiSeq 2500 with a minimum percentage of bases above a quality score of 30 (Q30) of about 90%. Sequencing length was 100 bases for siSOX9 RNAseq and 125 bases for siY14. Raw sequences were evaluated with FastQC for the quality of the sequencing and for sequencing adaptor contamination. Low quality sequencing reads were trimmed and sequencing adaptor sequences were removed with fastq-mcf (www. expressionanalysis. github. io/ea-utils/) (Parameters: -D 100 -l 50 for siSOX9-RNA-seq experiments and -l 125 for siY14 RNA-seq experiments). High quality sequencing reads were then aligned with Tophat2 (Bowtie1) (https://ccb.
jhu. edu/software/ tophat/index. shtml) and Hisat2 (https://ccb. jhu. edu/ software/hisat2/index. shtml) for siSOX9 reads and siY14 reads, respectively. The BAM files produced by the aligners were sorted with samtools. Differential alternative splicing events were quantified with rMATS (http://rnaseq-mats. sourceforge. net/) (parameters: -t single -len 100 for siSOX9 or -len 125 for siY14). Aligned reads (BAM files) were converted into SAM format with samtools view (http://samtools. sourceforge. net/), and read counting of transcripts was performed with htseqcount (http://chipster. csc. fi/manual/htseq-count. html). Differential expression analyses were then performed with DE-Seq on three replicates per condition (http://bioconductor. org/packages/release/bioc/html/DESeq. html). ChIP-seq data from Shi Z.
3e-142. (C) Functional interaction between SOX9 and Y14. HEK293T cells were co-transfected with control, anti-PSF or anti-Y14 siRNAs, together with either a control plasmid or wt SOX9. The levels of mRNA variants of the endogenous PTBP2 and ZDHHC16 reporter minigene were quantified by RT-PCR. PSI and PSE were then calculated for PTBP2 and ZDHHC16, respectively. Data are presented as means ± SEM (n ≥ 5). ****P < 0. 0001 with a one-way ANOVA test with Bonferroni's multiple comparison test. Mechanistic analyses of the role of SOX9 in alternative splicing suggest a model in which SOX9 is recruited to promoters of specific target genes to either activate transcription or modulate alternative splicing of target mRNAs. Mining of published ChIP-seq data  (19)  revealed an enrichment of SOX9 peaks close to promoters of its splicing targets, rather than in gene bodies, close to alternatively spliced exons.
3e-142. (C) Functional interaction between SOX9 and Y14. HEK293T cells were co-transfected with control, anti-PSF or anti-Y14 siRNAs, together with either a control plasmid or wt SOX9. The levels of mRNA variants of the endogenous PTBP2 and ZDHHC16 reporter minigene were quantified by RT-PCR. PSI and PSE were then calculated for PTBP2 and ZDHHC16, respectively. Data are presented as means ± SEM (n ≥ 5). ****P < 0. 0001 with a one-way ANOVA test with Bonferroni's multiple comparison test.
ACKNOWLEDGEMENTS We are grateful to  Dr D. Lleres  ( IGMM, Montpellier, France ) for providing anti-PSP1 antibody and to  Dr V. Gire  and  F. Tomas  for their help in western blot analyses. We thank  Dr D. Helmlinger  for discussion and critical reading of the manuscript. We also thank  V. Georget  and  S. De Rossi  from  Montpellier RIO Imaging  microscopy facility and  S. Fromont  and  F. Lionneton  from  Montpellier Genomic Collection facility  for the quantification with the Caliper LabCHIP.
Illustrations using a protein model As a more realistic example, we selected the model of IgGbinding domain III (PDB entry 2igd; S. Butterworth, V. L. Lamzin, D. B. Wigley, J. P. Derrick & K. S. Wilson, unpublished work) refined at 1. 1 A ˚resolution using individual anisotropic ADP values. We chose the core of this model as a single TLS group containing residues 6-61 (leaving out the flexible N-terminus). We considered two models derived from these data. One model contained C atoms only (56 in total) and the other model included all main-chain atoms (C , O, C and N). Each of the two models was treated as a single TLS group. For each model we fitted TLS matrices to individual anisotropic U n values (ANISOU records from the PDB file) using the phenix. tls tool; we refer to these matrices as TLS CA and TLS MC , respectively.
TLS Method R U (all) R U (no V) R U (d x , s x ) R U (d y , s y ) R U (d z , s z ) R U (d x ) R U (d y ) R U (d z ) PDB entry 2igd from the corresponding TLS matrices as described in  Urzhumtsev et al. (2015). Here, and in the following, to simplify the text we drop the parameters l x , l y , l z ; w x , w y , w z ; v x , v y , v z from the list in (5) since they are invariant within these tests. Then, using the parameters in (5) (Table  2 ) and the C -only model, we calculated U ensemble,n and U TLS,n for the following different scenarios. Firstly, we considered a scenario where all three librations are used together, including their screw components, while vibrations are excluded: MP no V ¼ ðd x ; d y ; d z ; s x ; s y ; s z ; 0; 0; 0Þ: Excluding vibrations led to an increase in R U for both TLS MC and TLS CA ; the values in the R U (no V) column in Table  1  are $1.
5 times larger 2  than those for R U (all). Secondly, we calculated R U separately for each individual libration, including its corresponding screw component (Table  1   1 ]. These tests let us draw two conclusions. Firstly, the ensemble size required for reliable calculation of U ensemble,n does not depend on the model size and, similarly to the oneatom case (x2. 2), 5000-10 000 models are sufficient. Secondly, large values of the screw components are responsible for the disagreement between U ensemble,n and U TLS,n and the large reesulting R U. This conclusion prompted us to revisit the TLS Components of the elemental motions. The four upper blocks correspond to the TLS matrices for PDB entry 2igd calculated for C atoms only (TLS CA ) and for the main-chain atoms (TLS MC ). The TLS matrices were decomposed with (10) or (11) using the constraints described in  Urzhumtsev et al.
(2015). The two bottom blocks correspond to the model for PDB entry 4muy. The vectors v x , v y , v z and l x , l y , l z of the vibration and libration bases, respectively, are given in Cartesian coordinates in the principal basis  [M]  with the origin at the group centre of mass and with the axes parallel to the crystal axes. The points w x , w y , w z (in A ˚) are given in the orthonormal basis [L] composed of the principal libration axes l x , l y , l z and describe the shift of these axes from the origin. The libration amplitudes d x , d y , d z are given in radians and the vibration amplitudes t x , t y , t z and the screw components s x , s y , s z are in A ˚. For details of the definitions, see  Urzhumtsev et al. (2013)   (2015).
3. For each set of matrices, TLS MC or TLS CA , we extracted elemental motions using (11), generated U ensemble,n using corresponding models and then computed R U values using the previously obtained U TLS,n. Table  1  shows that the updated R U values calculated using (11) to adjust S are acceptably low not only for the total motion but for each of the individual components, both for TLS CA and for TLS MC. Fig. 3(a)  shows R U plots as a function of the number of generated models. The curves are nearly identical for both models, showing even lower values for R U than the original curve for the C -only model. A more striking result is obtained when applying the new correction method to a real-life example: PDB entry 4muy  (Span et al. , 2014). In all tests TLS groups were used as defined in the PDB file.
Model selection and analysis setup The PDB (as of 14 November 2016) contains 123 954 entries, of which 32 162 contain TLS records. Since each PDB entry may contain more than one TLS record, a total of 260 353 TLS groups are available in the PDB. For each of these groups we tried to determine the corresponding elemental motions. This was performed using phenix. tl-s_as_xyz as described in  Urzhumtsev et al. (2015). 88 697 groups could be interpreted in terms of elemental motions. In 263 of these cases all three matrices were composed of zeros. Some further 314 groups were excluded because the deposited TLS information was corrupted in a number of different ways (missing TLS group origin, noninterpretable atomic or TLS records etc. ). The remaining 88 120 TLS sets were subjected to three independent rounds of decomposition into elemental motions, each applying corrections to the S matrix using (9), (  10 ) and (11), respectively.
When using (10) and (11) the constraints on described in  Urzhumtsev et al. (2015)  were applied. For each set of extracted parameter values we analyzed the following motions. (i) A combination of three screw rotations and the vibration component, i. e. the overall motion (5). (ii) A combination of the screw rotations with no vibration components (6). Table  3  Number of TLS groups with ADP matrices that are reproducible by explicit group motions (R U 0. 05). PDB content (November 2016): 32 162 entries containing TLS records, 260 353 TLS groups in total. For 263 TLS groups all three matrices were zero and these groups were excluded from further work. Decomposition of TLS matrices into parameters of elemental motions was performed using (  9 ), (  10 ) and (  11 ). The 'Extracted groups' column shows the total number of TLS groups for which parameter extraction was possible and 'Extracted entries' shows the number of PDB entries for which this was possible for all of the groups.
Discussion Validation of atomic models is now routine in macromolecular crystallography and is an integral part of structure submission to the Protein Data Bank  (Read et al. , 2011; Gore et al. , 2017). It requires nomenclature compliance and fit to experimental data. Atomic coordinates are subjected to validation that includes analysis of stereochemistry and molecular packing. Atomic displacement parameters (ADPs) are also subjected to validation. For isotropic ADPs the existing validation criteria are rather simple: their values must be positive, not excessively large and not vary too much between neighbouring atoms. For anisotropic ADP values the criteria are somewhat more complex  (Hirshfeld, 1976; Schneider, 1996). Similarly to atomic coordinates and displacement parameters, TLS matrices are model parameters and therefore should be subjected to some form of validation.
12 and later. Data and scripts that can be used to reproduce the figures and tables are available at http://phenix-online. org/ phenix_data/afonine/tls2/. DE-AC02-05CH11231. AU acknowledges the support and the use of the resources of the French Infrastructure for Integrated Structural Biology (FRISBI; ANR-10-INBS-05) and of Instruct-ERIC.
TLS t x , t y , t z v x , v y , v z d x , d y , d z l x , l y , l z w x , w y , w z s x , s y , s z decomposition algorithm described in Urzhumtsev et al. PDB entry 2igd TLS CA (10) 0. 163 (À0. 085, 0. 437, 0. 896) 0. 011 (À0. 262, 0. 915, À0. 308) (À12. 67, À0. 39, 16. 71) À2. 07 0. 278 (0. 905, 0. 410, À0. 114) 0. 019 (À0. 067, 0. 301, 0. 951) (1. 65, 0. 97, 8. 55) À0. 88 0. 304 (À0. 417, 0. 801, À0. 430) 0. 027 (0. 963, 0. 270, À0. 017) (À4. 67, À3. 47, 0. 76) 0. 80 TLS MC (10) 0. 089 (À0. 082, 0. 334, 0. 939) 0. 010 (À0. 272, 0. 943, À0. 193) (À14. 16, À1. 74, 22. 42) À5. 70 0. 277 (0. 948, 0. 316, À0. 030) 0. 020 (À0. 113, 0. 168, 0. 979) (0. 49, 0. 11, 11. 77) À0. 24 0. 314 (À0. 306, 0. 888, À0. 343) 0. 027 (0. 956, 0. 288, 0. 061) (À4. 92, À3. 54, À0. 25) 0. 89 TLS CA (11) 0. 163 (À0.
As for regions of Stylin-01 other than the C terminus, the labeling of Stylin-02 with anti-1-07 seemed stronger after an extended treatment (15 to 60 min) with chitinase, indicating that this motif is poorly accessible at the surface (Fig. 3B ). Based on these results, it is impossible to conclude about the relative contribution of Stylin-01 or Stylin-02 to the strong labeling at the surface of the acrostyle observed with anti-1-11. Stylin-01 and Stylin-02 are conserved among aphid species. A comparative analysis was conducted on Stylin-01 and Stylin-02 homologs found in several aphid species (see Fig. S1A  and B in the supplemental material), through BLAST searches or direct sequencing of aphid colonies maintained in our laboratory (accession numbers are given in Table  S1  in the supplemental material).
Investigating whether these subtle differences could explain the lack of effect of Stylin-02 on CaMV transmission will require a technical means (not yet defined) to distinguish between the C-terminal domains of these proteins. Recently, Liang and Gao (54) reported a positive interaction in the yeast-two-hybrid system between the coat protein of a noncirculative virus, Cucumber mosaic virus (CMV; isolate SXCH [GenBank JX993913]), and Mpcp4 of their M. persicae colony from southeastern China. Mpcp4 was first identified in 2007 by Dombrovsky et al. (37)  during a search for extractible cuticular proteins in whole aphids. This protein actually corresponds to the protein we identified in this study as Stylin-01. Liang and Gao (  54 ) a The percentage of maxillary stylets labeled out of the total number of maxillary stylets observed is indicated in parentheses.
Expression levels were normalized with two internal reference genes encoding actin and elongation factor 1␣ (EF1␣) from M. persicae  (58). RT-qPCRs were performed in duplicates. Amplification efficiencies were analyzed with LinRegPCR free software (v. 2014. 5) (59). Expression ratios were calculated using the threshold cycle (2 ϪΔΔCT ) method  (60). Transmission tests. Cohorts of aphids fed for 72 h on artificial diets supplemented with siRNA were collected and starved for 1 h in glass tubes. They were allowed a 5-min acquisition access period (AAP) on CaMV-infected turnips (Brassica rapa cv. Just Right) 23 days postinoculation, followed by a 2-h inoculation access period (IAP) on 8-day-old turnip test plants, before insecticide spray was applied. In Stylin-01 silencing experiments, 2 biological replicates were performed using 2 aphids per test plant and 48 test plants per treatment.