dataesr/scientific-paragraphs-categorization huggingface dataset:
Consequently, the biochemical characterization of a single EXT protein is still today very challenging; (iii) large number of EXTs and EXTs-related proteins encoded in known plant genomes; and (iv) several EXT genes are expressed at the same time in the same plant tissues (see Genevestigator database, https://www. genevestigator. com). In addition, most of the available EXT mutants analyzed until now show no clear phenotype. Few exceptions are the mutants atext3 (embryo lethal), atext6, 7, 10, 12 (shorter root hairs) and lrx1, 2 (root hair morphogenesis) that showed clear phenotypes (see Table  1 ).
ACKNOWLEDGMENTS May Hijazi ,  Cécile Albenne , and Elisabeth Jamet are thankful to  Université Paul Sabatier (Toulouse, France) ,  CNRS  for supporting their research work and to the  Lebanon Ecological Association  (grant to  May Hijazi ). Part of this work has been done at LRSV which belongs to the  Laboratoire d'Excellence (LabEx)  entitled  TULIP  ( ANR -10-LABX-41 ;  ANR-11-IDEX-0002-02 ). This work was also supported by  PICT FONCyT   2011-0054 ,  Argentina (JME)  and  Mizutani Foundation  Glycoscience Grant 2013, Japan (JME). The authors wish to apologize for the papers not quoted in this review, due to lack of space.
Study Design and Sample This study was based on a cross-sectional analysis of data collected in 2010 in the Health, Inequalities and Social Ruptures (SIRS) cohort study among a representative sample of French-speaking adults in the Paris metropolitan area (Paris and its suburbs, a region with a population of 6. 5 million). At inclusion, in 2005, a 3-level random sample was constituted. First, 50 census blocks called 'IRISs' (a French acronym for blocks for incorporating statistical information, which constitute the smallest census unit areas in France whose aggregate data can be used on a routine basis, with about 2,000 inhabitants each) were randomly selected using a stratification based on their socioeconomic type and their being labelled or not labelled as 'underprivileged areas' in public (government) policies.
The individuals in each IRIS who were not re-interviewed in 2010 were replaced by a random procedure similar to the one used in 2005, up to a final sample size of 60 adults interviewed per IRIS. The refusal rate among the newly contacted people was 29% (the same as in 2005). In 2010, 3,006 adults were interviewed, and for 39 of them either weight data or height data were missing. Our study is therefore based on a sample of 2,967 individuals.
Acknowledgements This research was funded by the  French National Research Agency (ANR)  within the framework of the  Programme National de Recherche en Alimentation et Nutrition , the  French Institute for Public Health Research (IRESP)  and the  French Interministerial Committee for Urban Affairs. It also received support from  Mutualité Française. J. Martin-Fernandez  received a PhD grant from the  Île-de-France  region for this research. J. Martin-Fernandez : substantial contribution to conception and design, acquisition of data, analysis and interpretation of data and drafting the article, revising it critically for important intellectual content. F. Caillavet: revising draft critically for important intellectual content. A. Lhuissier: revising draft critically for important intellectual content.
The CaM EF-hand motif (for example that in PDB code 1RFJ)  [16]  adopts an open conformation after binding of Ca 2+ , whereas the Ca 2+ bound EF hand motif of EhCaBP5 is in a closed conformation. The r. m. s. d. between these EF-hand motifs is indeed relatively large, at 2. 38 A ˚, and the interhelical angles of the EF-hand motifs of EhCaBP5 and CaM are 64. 3 degrees and 89. 3 degrees respectively, indicative of the closed and open conformations respectively (Fig. 2A ). The overall structure of EhCaBP5 is more similar to that of the essential light chain (ELC) of myosin than to CaM. Both EhCaBP5 and the ELCs have two 4-helix globular lobes connected by a small loop. Comparison with other Ca 2+ binding proteins and.
Preparation of selenomethionine labelled protein Since the structure of EhCaBP5 (accession number EAL46660) could not be solved by molecular replacement  [15] , seleniumlabelled protein was prepared to obtain phases. For preparation of selenium-labelled protein, E. coli BL21 (DE3) cells containing EhCaBP5 plasmid were grown overnight in LB media. Cells were harvested by centrifugation at 4000 rpm for 10 minute. Harvested cells were washed with selenomethionine medium (Molecular Dimensions) twice, to take out residual LB medium, and then was suspended in the same media for inoculation for the further culture as described before  [29]. For protein expression and purification we have followed same protocol as describe earlier for native protein  [15].
Data collection, processing and structure determination SeMet-EhCaBP5 crystals were soaked in cryoprotectant solution consisting of 2. 8 M sodium acetate, 0. 1 M Bis-Tris pH 5. 5, and 20% glycerol. A single crystal was picked up in a cryo-loop and flash frozen in liquid nitrogen. A single wavelength anomalous dispersion (SAD) diffraction dataset was collected to 1. 9 A ˚resolution at the Se edge (l = 0. 9788 A ˚) on a MARCCD 165 detector at the DBT-BM14 beamline of the European Synchrotron Radiation Facility (ESRF, France). The peak dataset was then indexed, integrated, and scaled using the HKL2000  [30]. Data collection statistics are shown in Table  1   one molecule of EhCaBP5 per asymmetric unit, the crystal volume per unit of protein mass 2. 32 A ˚3/Da  [31] , which corresponds to a solvent content of 47.
3%. The sequence of EhCaBP5 consists of four SeMet residues and the positions of the Se atoms were determined using SHELXD program (correlation coefficient, CC all/weak: 34. 7/25. 4; Patterson figure of merit, PATFOM 12. 33)  [32]. The initial phases were computed and partial model was built with SHELXE program as part of the HKL2MAP package  [33, 34]. This partial model was used as a starting point for iterative automated model building and rebuilding along with sequence docking using Auto Build program in Phenix software  [35] , the remaining parts of the structure including side chains were modeled manually. The model was refined using the program REFMAC5  [36]  and iterative manual rebuilding of the model was performed in COOT  [37]. One Ca 2+ atom was identified and included in the refinement.
The translationliberation-screw (TLS) displacement parameters were determined and TLS restrained refinement was performed  [38]. For the final model, the Rwork is 18. 7% and Rfree is 22. 1%. The structure has good electron density (Figure  S2 ) and stereochemistry as indicated by program PROCHECK  [39]  with 96. 1% of residues lying in the most favoured regions of the Ramachandran plot. The final refinement statistics are shown in Table  1. The refined model of EhCaBP5 and structure factors was deposited in the Protein Data Bank under the accession code 4OCI.
Surface plasmon resonance (SPR) The E. histolytica genome codes for two myosin, myosin I (accession number EAL48894) and myosin II (accession number EAL51645). Myosin I has one IQ motif and myosin II has two IQ motifs. To check the interaction between EhCaBP5 and myosin IQ motifs, we commercially synthesized (obtained) peptides of IQ motif of myosin 1B (unconventional myosin) (IQKAWK-GYRNRKR) and second IQ motif of heavy chain myosin (myosin II) (LQACARAFAARKHFS), which is expected to bind to ELC. For the binding study we used Biacore T200 apparatus (Biacore, GE Healthcare) at National Institute of Plant and Genome Research New Delhi, India. A total of 2000 resonance units (RU) of peptides were immobilized on a research grade S series CM4 sensor chip in 10 mM sodium acetate, pH 5. 0 according to the manufacturer's amine coupling kit.
To validate EhCaBP5-IQ motif complex model, we obtained commercially synthesized two mutated Myosin 1B IQ motif peptide IQ-M1 A*A*KAWKGYRNRKR (where IQ is mutated to AA) and IQ-M2 IQKAWKGYD*ND*KD* (Where R is mutated to D). The EhCaBP5 was immobilized on sensor chip up to 500 resonance units and native myosin 1B IQ motif peptide and mutated IQ motif peptide were passed as analyte at concentration of 25, 50, 75, 100 and 125 mM. The data were recorded at 25uC and data analysis was performed using Biacore T2000 SPR Kinetics evaluation software.
Modelling and docking of EhCaBP5 with IQ motif Analysis of the crystal structure showed that the conformation of the Ca 2+ bound EF-hand motif of EhCaBP5 resembles that of myosin ELC, the coarse grained model of the EhCaBP5-peptide complex was obtained using the crystal structure of squid myosin, which contains its ELC and associated IQ motifcontaining heavy chain (PDB ID-3I5G)  [18]. The peptide bound conformation of EhCaBP5 was obtained by employing the flexible superimposition protocol of RAPIDO structural alignment software  [43]. The course grained complex model of CaBP5-IQ motif used as the starting structure was then used for the molecular docking simulations with the IQ motif peptide using Rosetta FlexPepDock web server  [44]. The Rosetta FlexPepDock protocol optimizes the protein-peptide complex using Monte-Carlo algorithm along with energy minimization  [45].
Acknowledgments We thank the staff of DBT-BM14 at the  ESRF  and the  Department of Biotechnology, Government of India , for access to the beamline. SG is grateful for the  Innovative Young Biotechnologist Award. SK thanks CSIR, SA thanks  UGC  for  D. N. Kothari  fellowship. We also thank  Nancy Guillen ,  Pasteur Institute, France  for Myosin 1B antibody.
Control CPLL-treated antiproliferative activities, the consumption of banana has been associated with reduced risk of chronic diseases such as cardiovascular diseases and cancer  [44]. Up to date, no in depth work has been focused on identifying the banana fruit proteome; since fresh banana pulp contains approximately 20% of carbohydrates and only 1% of proteins, this fruit has been traditionally considered as a difficult matrix for protein extraction, being a target in studies of optimization of protein extraction methodologies  [45]. Fruits, as every biological source, contain highly-abundant proteins, which are often of limited interest for proteome analysis, whereas other proteins may be orders-of-magnitude less abundant, although still of high importance. Here too, by using CPLLs, advanced mass spectrometry techniques and musa mRNAs database in combination with Uniprot_viridiplantae database, we could identify, for the first time, 1131 proteins  [46].
In another investigation on non-alcoholic beverages, the trace proteome of white-wine vinegar was identified again via CPLLs but under conditions mimicking reverse-phase capture, i. e. , at pH 2. 2 in presence of 0. 1% trifluoroacetic acid. A total of 27 unique gene products could be tabulated, of which 10 specific of the database Vitis vinifera, 13 found in the general database Uniprot_viridiplantae and four in Swiss Prot_all entries. The most abundant species detected, on the basis of spectral counts, appears to be the whole genome shotgun sequence of line PN40024, scaffold_22 (a protein of the glycosyl hydrolase family, indicated by an arrow in Figure  4 )  [52]. The hypothesis set forward regarding these 27 surviving proteins to the strongly acidic, pH 2. 2, environment of vinegar is that they could be the only ones resistant to denaturation, a phenomenon that typically occurs with proteins which have a tightly packed hydrophobic core and are thus insensitive to pH denaturation.
Laboratory analysis Selenium was determined in serum, milk and feces. In blood and milk samples, selenium was determined with Hybrid Vapor Generator (HVG-1, Shimadzu, Japan) according to the procedure described in detail by  Seboussi et al. (2009). The serum and milk Se data are reported as lg/100 mL. The selenium concentration in feed is generally expressed in ppm or mg/kg. Selenium content in the different components of the diet, in feces (reported as mg/kg DM) and in water was determined at IDAC laboratory (KSA) by Inductively Coupled argon Plasma -Atomic Emission Spectrometer (ICP AES), Varian Vista MPX -CCD Simultaneous. Quantification of selenium was performed by the standard addition method, using an 11 point standard curve. AccuTraceä Reference Standard solutions used were Quality Control Standard #1AccuStandardÒ and Laboratory Performance Check Standard AccuStandardÒ.
Statistical analysis The mean selenium and standard deviation were calculated for each group. The variance analysis (repeated measures ANO-VA) for time series was applied to evaluate the difference between control and treated groups all along the experiment by taking into account the time effect, the treatment effect and the interaction between repetition and treatment (control, Se-Inorg and Se-Org). Pearson correlation was determined to assess the relationships between the selenium concentrations in the different substrates. As the SCC values are generally log-normal  (Shook, 1982) , means and S. D were calculated after a logarithm transformation of the raw data. However, the values were expressed in cells/ml to be more explicit and the means were geometric means. The software XLSTAT (Addinsoftª) was used for the data analysis (module ''data modelisation'', tool ''ANOVA for repeated measures'' using estimation method based on least square).
Acknowledgements This study has been achieved within FAO camel project  UTF/ SAU/021/SAU  with the support of  Camel and Range Research Center (CRRC). The authors thank  Mr Sallal Issa Al-Mutairi , former head of the  CRRC  for his encouragement and support. We thank also the staff of the camel farm ( Mrs Hassan and Surish ) for the monitoring of the camel feeding and milking. Thanks also to FAO team leader at Riyadh,  Dr A. Oihabi  who supported this project.
Analysis of Casp7 À / À mice showed that the BMD was comparable to that of wild-type animals. However, the BMC and volume of the alveolar bone were significantly decreased, when compared with wild types suggesting an overall decrease in alveolar bone volume. Similar trends were obtained also by examination of the mandible. Thus, data from immunohistochemistry and microCT analysis pointed to the role of caspase-7 in the formation of the alveolar bone. The bones of the lower jaw form by intramembranous ossification, as a comparison we therefore also investigated long bones, which form by endochondral ossification. Figure  5  Morphological evaluation of distal femur in adult Casp7 À / À and wild-type mice. Transversal section of femur in wild type (a) and Casp7 À / À (e), longitudinal section of wild type (b) and Casp7 À / À (f), endosteal surface of wild type (c) and Casp7 À / À (g), periosteal surface of wild type (d) and Casp7 À / À (h); wt, wild type The activated form of caspase-7 was detected in long bones throughout embryonic and early postnatal development.
Two bone compartments (cortex and trabeculae) were separated by manual contouring that was outlined adjacent to endocortical boundary. Alveolar bone was analysed as one domain. Regions of interest were reconstructed and analysis of BMC, BMD, BV, and TV was carried out using the Microview 2. 2 software package (GE Healthcare). The decrease in alveolar bone was calculated from the average values (four samples in both groups) of bone volume analysed by microCT. When compared with wild type (determined as 100% volume), the alveolar bone volume of caspase-7-deficient mice was calculated as 76%. Therefore, the decrease was 24%. 3D images were post processed by the VGStudio MAX 2. 2 software (VGStudio MAX, Heidelberg, Germany). Statistical analysis was evaluated by Sigma Plot 11. 2 (Systat software GmbH, Erkrath, Germany).
Total mRNA was transcribed into cDNA and used for the investigation by Mouse Osteogenenic PCR array (PAMM-026A-24, SA Biosciences, Frederick, MD, USA). Data were statistically evaluated by PCR array Data Analysis V4 (SA Biosciences). Statistical significance was determined using a t-test (Po0. 05). The threshold of fold change was established as À 2/2 fold-change, that means decrease/increase of 100% in investigated sample. Six embryonic specimens (ED15. 5) were analysed (3 wt, 3 Casp7 À / À ).
Acknowledgements. The research was funded by the  Grant Agency of the Czech Republic   P502/12/1285  at the  UVPS (caspase research)  and  P302/12/J059  at the IAPG CAS, v. v. i. (tooth-bone research). International collaboration runs under  Academy of Sciences  (project  M200451201 ) and the  Brno labs  under RVO:  67985904. ES was supported by  EMBO   ASTF 372-2013. We also acknowledge  Chris Healy  for help with microCT analysis,  Marcela Buchtova  for PCR Array consultations,  Barbora Vesela  for technical support and  Bernard Senger  for help with statistics. TVB holds a postdoctoral fellowship from the  FWO. Research in the Vandenabeele group is funded by European grants ( FP6 ApopTrain ,  MRTN-CT-035624 ;  FP7 EC RTD Integrated Project ,  Apo-Sys ,  FP7-200767 ;  Euregional PACT II), Belgian grants (Interuniversity Attraction Poles ,  IAP 7/32 ), Flemish grants ( Research Foundation Flanders ,  FWO G.
Although the function of selenoproteins is well established, the activity of SBP1 proteins is still unclear and the link between selenium binding and SBP1 function has not yet been determined. Mammalian SBP1 was first identified in mouse liver  (14)  in experiments designed to find new selenoproteins. Two homologues are present in humans. Today, SBP genes have been identified in many organisms including plants (  14 -18)  and additional sequences of SBP homologues are available in public databases from many additional organisms. In humans, down-regulation of SBP1 expression has been correlated with rapid tumor development in many organs  (19 -27)  and SBP1 expression is considered to be a predictor of clinical outcome. Recently, interaction of SBP1 and the selenoprotein glutathione peroxidase GPx-1 was observed, revealing a cross-talk between members of distinct families of selenium containing proteins  (19, 21, 28).
EXPERIMENTAL PROCEDURES Overexpression of AtSBP1 in Escherichia coli and Purification of the Recombinant Protein-AtSBP1 cDNA contained in the entry clone (U15803, TAIR database) was cloned into the destination pGEX-3X for GST-AtSBP1 production as previously described  (35). The recombinant plasmid was used to transform E. coli strain Rosetta 2. Cell cultures were grown at 37 °C in Luria-Bertani medium until an A 600 nm of 0. 8. The temperature was then lowered to 18 °C and expression of the recombinant protein was induced by adding 0. 8 mM isopropyl ␤-D-thiogalactopyranoside to the cultured cells for 17 h. Cells were then centrifuged and stored at Ϫ80 °C. For protein purification, cells were lysed by sonication (6 ϫ 1 min, using the Branson Sonifier 250) in 20 mM HEPES, pH 7. 4, 150 mM NaCl, 0.
1% formic acid in water). The system included a 300 m ϫ 5-cm PepMap C18 precolumn for preconcentration and desalting of the peptides and a 75 m ϫ 15-cm PepMap C18 column (Dionex) for peptide separation and elution. MS and MS/MS data were acquired using XCalibur software (ThermoFisher Scientific) in the positive ion electrospray ionization mode with a resolution of 60,000 full-width half-maximum in the MS mode. Peak list generation was first performed using MASCOT Distiller and consecutive searches against a database containing the GST-SBP1 sequence were performed using MASCOT 2. 4. The parameters used with MS/MS transformed data (. mgf) were: instrument ϭ ESI-TRAP; enzyme ϭ no; oxidation (M); selenium (CDHM); deamination (NQ); disulfide (C); peptide tolerance ϭ 10 ppm; fragment tolerance ϭ 0.
6 Da. Results were filtered using IRMa software  (41). Every peptide having a Mascot score below 18 was filtered. The isotope simulation feature of Xcalibur was used to simulate the isotopic profiles of peptides of interest with and without selenium. X-ray Absorption Spectroscopy on the Selenium-AtSBP1 Complex-X-ray absorption measurements were carried out at the European Synchrotron Radiation Facility (ESRF, Grenoble, France) at a ring current of 150 -200 mA. Spectra were collected on the BM30B (FAME) beamline (42) using a Si(220) double crystal monochromator with dynamic sagittal focusing. The photon flux was 10 11 photons/s and the spot size was 300 m horizontal ϫ 100 m vertical (full width half-maximum values). Selenium K-edge x-ray absorption near edge structure (XANES) spectra were recorded for a 1.
For each sample, four to six scans of 20 min were averaged. The position of the beam on the pellet was moved between each scan to limit radiation damage. All spectra were collected in fluorescence mode measuring the selenium K␣ fluorescence with a 30-element solid-state Ge detector (Canberra). Energy calibration was achieved by measuring a selenium foil and assigning the first inflection point of the spectrum to 12658 eV for selenium. Data analysis was performed using Athena software. After normalization, the spectrum for the selenium-AtSBP1SBP1 complex was fitted by linear combination of selenium reference compounds in the 12,640 -12,700 eV range. ). We verified that the increased T m was correlated with binding of the ions to AtSBP1 by determining the ion to protein molar ratio by ICP-MS for SeO 3 2Ϫ , Cd 2ϩ , and two additional selected ionic species (Zn 2ϩ and Ni 2ϩ ) (Fig.
The three-dimensional model of AtSBP1 was modeled using the three-dimensional structure of SBP from S. tokodaii (PDB entry 2ECE) (Fig. 7 ). The model contains residues from Tyr 29 to Asp 487 , however, the first 28 residues could not be modeled as they are predicted to be disordered and are not present in the crystal structure. The CD analysis showed that AtSBP1 secondary structure was predominantly ␤-sheet, which correlates well with the predicted overall fold of AtSBP1 that is a ␤-propeller containing 7 ␤-sheets, each one composed of four antiparallel ␤-strands (Fig. 7 ). DTNB (Fig. 4A ) and nano-electrospray MS analysis (Fig. 5 ) indicated the presence of a disulfide bridge that the model predicted between Cys 97 and Cys 158 (Fig. 7 ). DTNB analysis also suggested that four cysteine residues would be reduced and accessible.
8 , supplemental Table  S1 ). The same analysis was conducted on a mutated form of the protein where Cys 21 and Cys 22  were replaced by serine (supplemental Table  S1 ). The mutated form of the peptide "TMATETEVVAPVTVSNGGSKGSSKY" did not show any binding with selenium. The involvement of Cys 21 and Cys 22 in selenium binding was further confirmed by direct measurements of selenium by ICP-MS, on the wild type and mutated version of the protein after incubation with selenium and protein purification. Altogether, these data indicate that selenium binding to AtSBP1 involved Cys 21 and Cys 22. Identification of the Local Selenium Environment in AtSBP1 by XANES Analysis-The oxidation state and local environment of selenium in AtSBP1 was further investigated by x-ray absorption spectroscopy. Fig.
This binding site has not been characterized in the human SBP1 or in any other organism. These data demonstrate that selenium binding involves a covalent reaction via two cysteine residues in the protein. In human and mouse SBP1 sequences, the two adjacent cysteines responsible for selenium binding in A. thaliana are absent and instead a Cys 5 -X 2 -Cys 8 motif is present. Based on a three-dimensional model of human SBP1 using the S. tokodaii three-dimensional structure (PDB entry 2ECE) that was missing the disordered N terminus of SBP1 containing the Cys 5 -X 2 -Cys 8 motif, it was predicted that Cys 57 was the only candidate that could be involved on selenium binding in human SBP1  (24). However, Cys 57 is not conserved among SBP homologues, it is not present in the mouse SBP1 homologue where selenium binding was first characterized nor has the involvement of Cys 57 in selenium binding been validated experimentally.