dataesr/scientific-paragraphs-categorization huggingface dataset:
nanK (RGNV35913_01289) is the last gene of the cluster, coding for a predicted ManNAc kinase, involved in the phosphorylation of ManNAc into ManNAc-6-P. Previous data showed that the transcription of nanH was up-regulated when R. gnavus ATCC 29149 was grown in presence of mucin, as determined by microarrays and qPCR. 10 Here we analyzed the transcriptional activity of this cluster by RNAseq analysis in both R. gnavus mucin-degrader strains grown on mucin as sole carbon source. We confirmed that all the genes involved in the release and transport of sialic acid -nanH and the 3 genes coding for an ABC transporter -as well as all the genes putatively involved in sialic acid metabolism inside the cell-were upregulated when R. gnavus ATCC 29149 and ATCC 35913 were grown with mucin (Fig. 4B  and C ).
Acknowledgments The authors gratefully acknowledge the support of the  Biotechnology and Biological Sciences Research Council (BBSRC). Sequencing was conducted at The Genome Analysis Center (TGAC). We would like to acknowledge  Simon Anders  and  Michael Love  for their help with the analysis of RNASeq data-The genome sequence of R. gnavus ATCC35913 has been deposited in the European Nucleotide Archive (ENA-EMBL) with the study accession number,  PRJEB12317 ; and annotated contigs are available with accession numbers  FCFA01000001-FCFA01000241.
In the remaining subjects (n0835, group IV), the plasma glucose concentration recorded during the OGTT never fell below the fasting concentration. The results showed that subjects whose post-load plasma glucose concentration returned to fasting level more quickly had greater insulin sensitivity, a higher insulinogenic index, and a lower risk of developing T2DM after 8 years of follow-up compared with subjects whose post-load glucose concentration returned to baseline more slowly. The incidence of T2DM was 0% in group I and increased progressively to 6. 4% in group IV. Ning et al. (  44 ) performed a similar study to investigate the association between fasting, 2-h glucose levels and the risk of cardiovascular disease (CVD). This study used data from 19 European cohorts that included 12,566 men and 10,874 women with normal fasting plasma glucose (FPG) and 2-h glucose levels.
16 to 1. 02% from wk 1 to 3, in agreement with the recommendations of the breeder  (Aviagen, 2009). Diets dl-Met-and HMTBAprovided 26% and 33% TD Met:Lys for wk 1 and wk 3, respectively, and 52% and 59% TD TSAA:Lys for wk 1 and 3, respectively, which are 30% and 45% lower than the supply of these AA in diets dl-Met+ and HMTBA+. All diets were offered in pelleted form. Because the TSAA concentration in the diet may affect voluntary feed intake  (Picard et al. , 1993; Bunchasak, 2009) , the daily food allowance of TSAA+ was below the anticipated ad libitum intake capacity (reduction of approximately 12%; data not shown) to ensure a similar feed intake between both treatments. Feed intake in TSAAbirds was close to their ad libitum intake capacity because feed refusals were systematically observed.
ACKNOWLEDGMENTS We thank  Rebeca Alonso-Olalla ,  Nadine Mézière ,  Colette Mustière ,  Yolande Jaguelin ,  Philippe Ganier  ( INRA, Saint-Gilles, France ),  Jean-Marc Hallouis ,  Fréderic Mercerand ,  Isabelle Jottreau ,  Sabine Crochet ,  Thierry Bordeau ,  Estelle Cailleau-Audouin , and  Cécile Berri  ( INRA, Nouzilly, France ) for their collaboration in this experiment.
a b s t r a c t Ni is recognized as an element that is toxic to humans, acting as an allergen and a carcinogenic agent, and it is also toxic to plants. The toxicity of Ni has been understudied in microorganisms. The data presented here were obtained by submitting the model bacterium Escherichia coli K-12 to nickel stress. To identify expressed genes, RNA-Seq was performed. Bacteria were exposed to 50 mM NiCl 2 during 10 min. Exposure to Ni lead to the deregulation of 57% of the E. coli transcripts. Further analysis using DAVID identified most affected biological pathways. The list of differentially expressed genes and physiological consequences of Ni stress are described in "Ni exposure impacts the pool of free Fe and modifies DNA supercoiling via metal-induced oxidative stress in Escherichia coli K-12" (M.
Data The RNA-Seq and gene expression datasets were deposited in NCBI's Gene expression Omnibus  [2] , accessible through GEO series accession number GEO: GSE76176. Fig. 1  shows the distribution of deregulated genes in E. coli upon exposure to 50 mM Ni. 2545 genes were deregulated considering a Fold-Change (FC) of 1. 5, representing 57 % of the 4440 annotated transcripts of E. coli K-12 strain W3110. Gene Ontology was applied to classify differentially expressed genes according to their biological function (see Fig. 1  in  [1] ). GO Terms that were enriched in the list of differentially expressed genes were identified using the DAVID tools (Database for Annotation, Visualization and Integrated Discovery)  [3, 4]. Pathways that were significantly affected were mapped using KEGG and are listed in Table  1.
Data analysis Strand-orientated RNA-Seq was performed on Illumina Hiseq2500. Basecalls were performed using HCS 2. 0. 5 and RTA 1. 17. 20. Reads were aligned to whole reference genome Escherichia coli K-12 W3110 NC_007779 using CASAVA v 1. 8. 2 software (Illumina). Gene expression was determined using Cufflinks v. 2. 0. 2. software. Differentially expressed genes were identified as described in  [1]. The diagrams show the number of genes whose synthesis was increased or decreased after metal exposure. 57 % of the 4440 E. coli transcripts were differentially expressed using expression ratio of 1. 5 (po 0. 05). Among these 57 %, 16 % had expression ratios superior to 4. 5. The functional analysis was performed on these 16% that represent 196 down-regulated and 148 up-regulated genes.
"Microbiologie, Adaptation et Pathogénie", UMR5240, INSA Lyon, France Data accessibility Data are with this article and deposited in NCBI's Gene Expression Omnibus (GEO), accessible through GEO Series accession number GEO: GSE76167 http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc ¼GSE76167.
"Microbiologie, Adaptation et Pathogénie", UMR5240, INSA Lyon, France Data accessibility Data are with this article and deposited in NCBI's Gene Expression Omnibus (GEO), accessible through GEO Series accession number GEO: GSE76167 http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc ¼GSE76167 Value of the data Ni, as many transition metals, is essential as a trace element to living organisms whereas it becomes toxic when present in excess. At present, the description of Ni toxicity in bacteria is under-studied although this metal is a widespread element bacteria are in contact with.
Primer design and specificity assessment Primer Express 3. 0 (Applied Biosystems, California, USA) was used for the design of a S. thermophilus specific primer, based on its tuf gene sequence and on the tuf gene sequence of other LAB species, which were all retrieved from GenBank. These sequences were aligned with Clustal W2 and BLAST software was used to check in silico specificity. The nucleotide sequence of the primer pair was as follows: CGC GAC ACT GAC AAA CCA T (Stherm f), and CCA CGA CCA GTG ATT GAG AAT ACA (Stherm r). Our primer pair was compared against previously designed primers (Tuf) targeting this same gene of S. thermophilus  (Falentin et al. , 2012). Since these primers are used with the same annealing temperature as our primers, they allowed direct comparison under the same qPCR amplification conditions.
Real-time qPCR and RT-qPCR amplification conditions Assays were performed in a StepOnePlus Real-Time PCR System (Applied Biosystems) and the data were analyzed with StepOne software v2. 2. Different Stherm primer concentrations, from 40 to 600 nM were evaluated. Based on the results obtained, a concentration of 400 nM was selected. Amplifications were done in a final volume of 25 μL, containing 12. 5 μL of QuantiTect SYBR Green PCR Kit (Qiagen), 5 μL of DNA or cDNA (0. 2 ng/uL), 1 μL of each 200 nM primer (final concentration of 400 nM) and 5. 5 μL of GIBCO ultra-pure water (Invitrogen). No-template controls as well as positive controls with known Ct values were included in every PCR run. Different thermal cycling conditions were evaluated and a working protocol was established as follows: one uracil-N-glycosylase preincubation step at 50 °C for 2 min, one cycle at 95 °C for 15 min followed by 40 cycles at 94 °C for 15 s, 60 °C for 30 s and 72 °C for 1 min.
The efficiency (E%), slope and correlation coefficient R 2 values of each standard curve were calculated with StepOnePlus software version 2. 2 (Applied Biosystems). The limit of detection (LOD) was defined as the highest template dilution at which linearity was maintained and corresponded to the lowest value for which copy number calculation was accurate. Results for all samples analyzed are expressed as DNA/cDNA copy number/ng of total DNA/cDNA extracted. 2. 12. Evaluation of free DNA and RNA detection threshold PM samples (45 mL each) were spiked with four ten-fold dilutions (6 ng -6 μg) of DNA or RNA obtained from the lyophilized S. thermophilus starter culture or with 22 mg of the starter itself. Samples were centrifuged at 9700 ×g for 15 min at 4 °C and supernatants were discarded. The resulting pellets, as well as cells from PM, were subjected to DNA and/or RNA extraction followed by qPCR or RT-qPCR, respectively.
Statistical analysis Two-factor factorial designs were applied to the Ct values obtained from qPCR and RT-qPCR assays. One factor was assigned to the type of cheese produced (two levels: C and F) and the other one to the ripening day sampled (five levels: 7, 20, 40, 57 and 81 days). Differences in mean Ct values were analyzed by two-way analysis of variance (ANOVA) and all-pairwise comparisons were carried out using a Tukey's HSD test. Analyses were performed using InfoStat software (Di  Rienzo et al. , 2015).
Primer specificity To determine primer specificity of the qPCR assays, we compared our primer pair (Stherm) against primers (Tuf) also targeting the tuf gene from S. thermophilus previously reported by  Falentin et al. (2012) , across selected samples containing varying amounts of target DNA (Table  2 ). The microbial diversity of RM used for these experiments was confirmed by denaturing gradient gel electrophoresis (DGGE) analysis (data not shown). In addition, both primer sets were evaluated against DNA obtained from lyophilized L. lactis subsp. lactis and L. lactis subsp. cremoris, which was found in our RM samples by DGGE experiments (data not shown) but was not studied by  Falentin et al. (2012). In all cases, qPCR results showed that the samples analyzed with both primer pairs had similar Ct values.
Acknowledgments This work was funded by the  INTA-PNAIyAV-1130043 project  " Strategies for the development of new food products " and  FONARSEC 0004/2010  project " Design of functional dairy products " involving  INTA, Ministerio de Ciencia, Tecnología e Innovación Productiva (MINCyT)  and  Lácteos Capilla del Señor.
Pregnancy and delivery At approximately gestational week 8, information was collected through household visits on household assets and was compiled into an asset score, in addition to women's health, pregnancy history and attained level of education. Trained personnel took anthropometric measurements at week 8 at the first health clinic visit. Body Mass Index (BMI) was calculated by dividing the weight (kg) by the height squared (m 2 ). Through a birth notification system, anthropometric data of the newborns were collected within 72 h. Maternal use of food supplements was assessed by repeated 4-week recall collected at household visits. Adherence to micronutrient supplementation was monitored by an electronic device, eDEM V R , recording each opening of the capsule bottle and used as an indicator of supplement adherence.
Non-normally distributed biomarkers were transformed to the natural logarithm before analyses. Due to the proportion of cases having a CRP below detection level (0. 20 mg/l), we performed an additional analysis only including children with detectable CRP using log transformation. There was no association between the interventions and CRP levels using this exclusion (data not shown). Differences between categorical variables were assessed by Pearson's chi-square test. Independent two-sample t-tests and analysis of variance (ANOVA) were used in the case of continuous variables to compare group differences (presented as differences of means). According to the original study protocol and study hypotheses, biomarkers of children born into the MMS supplement group were compared with the standard of micronutrient care provided in the Fe60F group.
We performed analyses including the variables of maternal height, maternal BMI at recruitment (around gestational week 9), socioeconomic status of the household (represented by asset score), child age and child sex. The inclusion of any of these variables only caused minor changes to the effect estimates and made no difference to the interpretation of results. We are therefore only presenting the crude effect estimates. Sex differences have been reported previously from this cohort  31  and also suggested in related literature. 37, 38 Thus, regardless of whether any significant interactions between interventions and sex on the different outcomes were found, we present additional analyses stratified for sex of child in supplementary tables (available as Supplementary data at IJE online). Analyses were done using the IBM SPSS Statistics 20.
Results and Discussion Functional complementation of the P. pastoris fep1∆ strain by Fep1. We have already reported the cloning of the region between the two zinc finger motifs (highly conserved in other iron-responsive fungal GATA factors) of P. pastoris Fep1 3. We then cloned the entire coding sequence of Fep1 (337 amino acids) plus 415 bp upstream of the ATG codon and 250 bp downstream of the stop codon (GenBank accession number AM503349) by inverse PCR on genomic DNA. Our sequence is identical to that found as a result of the Pichia genome sequencing project of strain GS115  10  , which was made publicly available after completion of our work. Recombinant Fep1 WT with a C-terminal Flag tag expressed in a fep1∆ strain restored the iron-dependent regulation of two systems under the physiological control of Fep1, namely the ferroxidase Fet3 and the iron-reductase complex.
Size exclusion chromatography suggested that Fep1 (1-208) WT and 4S are both dimeric. SAXS analysis confirmed that Fep1 (1-208) WT and 4S are indeed dimeric, independently of the amount of [2Fe-2S] cluster bound by the protein (Fig. 4 ). The radius of gyration, a measure of the overall molecular size, of Fep1 (1-208) WT and 4S as-purified and after reconstitution was determined from the electron-pair distribution function. The radius of gyration and the shape of the electron-pair distribution function are similar for WT and 4S and do not change significantly after reconstitution (Fig. 4 ). Estimated molecular weights from ab initio calculation with the ATSAS suite  25  are indicative of a dimer.
All spectra were baseline corrected. Protein concentrations were 0. 3-0. 4 mM Fe. Solution small-angle X-ray scattering (SAXS) measurements were performed at the beamline BM29 of the European Synchrotron Radiation Facility (ESRF). The synchrotron was operating in 16-bunch mode giving a beam intensity of between 85 and 90 mA. Data collection was performed at 12 keV with BsxCuBE, exposing each frame for 2 sec, with continuous flow in the capillary; three dilutions of each sample were measured at 293 K. The analyzed spectra were the result of 5-10 averaged single curves (collected taking care to eliminate curves with radiation damage). Data analysis was performed with the ATSAS suite  25.
Acknowledgements We thank  Teodoro Coppola  ( Dept. Earth Sciences, Sapienza University of Rome ) for the ICP-AES metal analysis. This work was supported by Local Italian grants (ex  60% ) (to G. S. and M. C. B. ). The  European Union Seventh Framework Programme  (FP7/2007-2013) under BioStruct-X (grant agreement n. 283570) is gratefully acknowledged for granting SAXS beamtime at BM29 of  ESRF.
In agreement with this, we observed an increased content of filamentous actin in resting Trpm7 fl/fl-Pf4Cre platelets (Supplementary Fig. 15a, b ) and a decreased polymerization of filamentous actin on platelet activation (Fig. 6g ; Supplementary Fig. 15b, c ). Moreover, spread Trpm7 fl/fl-Pf4Cre platelets displayed an increased surface area (Fig. 6h ; Supplementary Fig. 16 ) most likely reflecting the activation-dependent rapid degradation of NMMIIA and consequently the loss of coherent cytoplasmic contractile forces normally generated by activated NMMIIA (refs 31,32). Variants in TRPM7 may cause macrothrombocytopenia. We next hypothesized that some DNA variants of extreme low-frequency affecting TRPM7 channel function might also cause macrothrombocytopenia in humans. Examining the results of genome sequencing of 702 cases with bleeding and platelet disorders of unknown genetic basis in the BRIDGE database of the NIHR BioResource-Rare Diseases revealed three cases with a coding variant unobserved in nearly 81,000 control DNA samples: UCN 0012 with p.
Further subjects with bleeding and platelet disorders (BPD) and with unrelated rare disorders (control data) were enrolled to the BRIDGE-BPD project of the NIHR BioResource-Rare Diseases study (UK REC 13/EE/0325). Here, gene variants were retained in an analysis set if they occur at a frequency of o1:10,000 in the exome aggregation consortium database based on over 60,000 individuals (http://exac. broadinstitute. org/). All cases provided informed written consent at enrolment. The BRIDGE bleeding and platelet disorders collection. We searched for cases with coding variants of extreme low frequency in the TPRM7 gene by analysing data from 702 index cases with BPDs of unknown genetic basis recruited to the BRIDGE study of the NIHR BioResource-Rare Diseases. Gene variants were identified in genome sequencing data by comparison with reference human genome build GRCh37 and consequences were predicted using the Ensembl version 75 TPRM7 transcript ENST00000313478.
Variants predicted to alter the amino acid sequence of the protein were retained in the analysis set if they occurred at frequencies of o1 in 10,000 out of 67,000 individuals of the Exome Aggregation Consortium (ExAC) database, o1 in 1,000 in the 10,000 subjects of UK10K database and o1 in 100 in 3,453 subjects with unrelated rare disorders or unaffected pedigree members recruited to other branches of the NIHR BioResource. We selected cases with extreme low-frequency variants and on the basis of clinical and laboratory characteristics, which were coded using Human Phenotype Ontology (HPO) terms  50  retrieved from the BRIDGE-BPD study database. We then focused our further exploration on the cases with extremely rare variants that were unobserved in the nearly 81,000 control DNA samples. The first step was to contact the families to explain the necessity to control these results by performing co-segregation studies.
Cells were transiently co-transfected with eukaryotic expression vectors encoding WT TRPM7 or the p. C721G and p. R902C variant with 100 ng of an enhanced green fluorescent protein (EGFP) reporter construct (pcDNA3. 1) using Lipofectamine2000 (Invitrogen) according to the manufacturer's instructions and processed for patch clamp measurements or confocal microscopy. Electrophysiology. Patch clamp experiments were performed at a whole-cell configuration. Currents were elicited by a ramp protocol from À 100 to þ 100 mV over 50 ms acquired at 0. 5 Hz and a holding potential of 0 mV. Inward currents were extracted at À 80 mV, outward currents at þ 80 mV and plotted versus time. Data were normalized to cell size as pA pF À 1. Capacitance was measured using the automated capacitance cancellation function of the EPC10 (HEKA).
Acknowledgements We thank the patients and healthy volunteers for donating blood samples;  Jonas Mu ¨ller ,  Stefanie Hartmann  and  Birgit Midloch  for excellent technical assistance. We are thankful to  Prof David E. Clapham  for providing the Trpm7 fl/fl mice. We acknowledge  Prof Willem Ouwehand , the  NIHR BioResource-Rare Diseases  and the associated  BRIDGE-BPD consortium  for performing whole-exome sequencing of the index cases. We thank the microscopy platform of the  Bioimaging Centre (Rudolf Virchow Centre ) for providing technical infrastructure and support. This work was supported by the  Deutsche Forschungsgemeinschaft  ( SFB 688  to H. S. , B. N. and A. B. ). S. S. and J. M. M. v. E. were supported by a grant of the  German Excellence Initiative  to the  Graduate School of Life Sciences, University of Wu ¨rzburg.
Family history was based on patient interviews and questionnaires, and affected maternal relatives supported the clinical diagnosis. Since 1989, mutation analyses have been performed in at least one member from each line. 7 Several members of a single large multigenerational line (line no. 706) participated in a research project with the purpose of assessing heteroplasmy for the pathogenic mutation and the association between the mutational load and the clinical phenotype. Prevalence data were calculated based on individuals with an identified mitochondrial mutation only. Genealogic tracing along the maternal ancestry line back to at least 1800 was conducted in every newly identified person manifesting LHON. Besides the primary mutation, haplogroups and their subclades were included as a guide for the clarification of the matrilineal genealogy.
Acknowledgments Supported by grants from the  Danish Society of the Blind (JS) , the  Portuguese National Research Council (PJM) , and the  Erasmus Student Mobility  Program (DV), respectively, and were involved in LHON mtDNA analyses in 1996, 1991 to 1995, and 1993, respectively. Laboratory equipment was partly obtained through a research grant from the  Toyota Foundation, Denmark. Disclosure:  T. Rosenberg , None; S. Nørby, None;  M. Schwartz , None;  J. Saillard , None;  P. J. Magalha  ˜es, None;  D. Leroy , None;  E. C. Kann , None;  M. Duno , None.
They synthesize ␣-glucans, which vary in terms of size, osidic linkages as well as degree and arrangement of branching. Devoid of polymerase activity, the ␣-(132) branching sucrases are specialized in dextran branching through the formation of ␣-(132) glucosidic linkages from sucrose to dextran acceptor (Fig. 1 )  (9, 10). In the absence of acceptor, these enzymes essentially catalyze sucrose hydrolysis. Glucansucrases are also known to bind dextrans via a carbohydrate-binding domain remote from the active site  (2, 11). This domain is referred to as the glucan-binding domain (GBD) and is not classified in the CAZy database. Carbohydrate-protein interactions often play critical roles in the catalytic activities of carbohydrate active enzymes involved in polysaccharide synthesis, degradation, or decoration.
20). They were also identified at the N-terminal or C-terminal domains of glucansucrases from Leuconostoc spp. and shown to share homology with the cell wall binding repeats of choline-binding proteins or toxins (Pfam CW_binding 1 (PF01473))  (21) (22) (23). In particular, the five repeats found at the C-terminal extremity of the GBD of DsrP glucansucrase are capable of binding the cell surface of Leuconostoc cells  (24). Mutagenesis of conserved aromatic or basic residues of the repeats found in Streptococcus downei GtfI was performed and led to a reduction of the glucan binding capability  (25). The elimination of some repeats by truncation was also shown to influence transglucosylation, modify glucan binding properties, and affect the polymer size  (26 -29). In particular, the GBD was suggested to provide a glucan anchoring platform, which may affect the single-chain elongation in a semi-processive manner  (29).