dataesr/scientific-paragraphs-categorization huggingface dataset:
Muller et al. had  shown that secretion of GAP50 acid phosphatase provides a possible mechanism to acquire host nutrients by P. falciparum  [65]. PF3D7_1464600 shows elaborate structural similarity to PF3D7_0918000. STRING database analysis shows its interaction with GAP50 acid phosphatase on the basis of binding evidences. VPS29: VPS29 superfamily protein PF3D7_1406700 is characterized by a vacuolar sorting protein 29 domain, also known as vacuolar membrane protein Pep11, a subunit of the retromer complex which is responsible for the retrieval of mannose-6-phosphate receptors (MPRs) from the endosomes for retrograde transport back to the Golgi  [67] [68] [69]. VPS29 consist of a phosphoestrase fold which acts as a protein interaction scaffold for retromer complex assembly as well as a phosphatase with specificity for the cytoplasmic tail of the MPR  [70].
The retromer includes the following 5 subunits: Vps35, Vps26, Vps29, and a dimer of the sorting nexins Vps5 (Snx1), and Vps17 (Snx2). STRING database analysis shows that it interacts with the other vacuolar proteins like Vps35 and Vps26. The protein is also predicted to interact with vacuolar ATP synthase Subunit F, vacuolar ATP synthase Subunit D -beta 3, and proteasome subunit as well as 20S beta-4 proteasome subunit. It is shown in human that Vps29 binds with Vps35 and Vps26 to perform biological functions by participating in the formation of retromer complexes  [71]. MPP_Dbr1: PF3D7_1340600 belongs to MPP_Dbr1 group of metallophosphatases. Dbr1 is an RNA lariat debranching enzyme that hydrolyzes 2′-5′ phosphodiester bonds at the branch points of excised intron lariats  [72]. Severe growth defect occurs in a Schizosaccharomyces pombe mutant defective in intron lariat degradation  [73] , which is also true for human RNA lariat debranching enzyme  [74].
Structure-function analysis of yeast RNA debranching enzyme (Dbr1) shows that it is a manganesedependent phosphodiesterases enzyme  [75]. To the best of our knowledge, there is no published work related to the P. falciparum phosphatase. MPP_PhoD: PF3D7_0912400 consists of MPP_PhoD domain. PhoD phosphatase also known as alkaline phosphatase D/APaseD in Bacillus subtilis, is a secreted phosphodiesterases encoded by PhoD of the Pho regulon in Bacillus subtilis  [76]. Its homologs are found in prokaryotes, eukaryotes and archaea. It contains a twin arginine (RR) motif and transported by the Tat (Twinarginine translocation) translocation pathway machinery (TatAyCy)  [77]. STRING database analysis shows its interaction with GTP cyclohydrolase I and 6-pyruvoyl tetrahydropterin synthase. MPP_Mre: Mre11 (also known as SbcD in E.
PF3D7_0107800 consists of 2 incomplete but catalytically active MPP_Mre11 domains. MPP_CSTP1: PF3D7_1403900 consists of complete S-transactivated protein 1 (CSTP1) domain. CSTP1 domain is similar to H. sapiens protein with a metallophosphatase domain, which is transactivated by the complete S protein of hepatitis B virus. STRING database analysis shows its interaction with other P. falciparum phosphatases.
Genetic characterization of PF3D7_0413500 (PfPGM2) homolog in rodent parasite P. berghei indicates that PF3D7_0413500 may be essential for blood stage asexual growth and zygote ookinetes development  [99]. Their experiments show that PfPGM2 has a prominent phosphatase activity in contrast to weak mutase activity and it acts as an enzyme in phosphate metabolism or regulator of parasite life cycle. STRING database analysis shows the interaction of this phosphatase with the proteins/enzymes involved in glycolysis pathway like enolase, phosphoglycerate kinase, PF3D7_1120100 and others. PF3D7_1430300 consists of an additional domain ATP-grasp_4.
STRING database analysis predicts that PF3D7_1355700 and PF3D7_1012700 are probably involved in the transcription process as they interact with enzymes or proteins involved in transcription mainly RNA polymerase. PF3D7_0726900 contains several disrupted partial DxDx (T/V) motifs, having only DxDx part of the active motif, suggesting it may be inactive and may not possess phosphatase activity. CDD results also show the absence of catalytically active site in PF3D7_0726900. Gene ontology analysis predicts its involvement in protein binding. Other than the four, all the other members of this superfamily are new inclusions to the HAD_like superfamily. PF3D7_1363200, a bifunctional polynucleotide phosphatase/kinases (PNKP) enzyme consists of a proximal 5′-kinase module with an essential P-loop motif, GXGK (S/T) and a distal 3′-phosphatase module with an essential acyl-phosphatase motif, DX-DXT.
Hence PNKP is able to perform phosphorylation as well as dephosphorylation. Siribal et al. characterized PNKP enzyme and detected phosphatase activity  [105]. PF3D7_0817400 also contains two PNKP domains, however only the first containing the active domain region. PF3D7_0715000 is a 4-nitrophenylphosphatase, which probably interacts with many cellular proteins involving Succinate dehydrogenase, cytidine triphosphate synthetase, asparagine synthetase, GTPases, RNA binding Protein, tRNA synthetase, ribosomal proteins and many more involved in transcription regulation and related cellular functions (STRING database analysis).
INPP5c phosphatases are Mg 2+ dependent and hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) as well as inositol phosphatases. PF3D7_0705500, in addition to EEP domain, consists of Syja_N superfamily domain too. PF3D7_0319200 BLAST results showed that sequences similar to it are 2′5 -Phosphodiesterases. PFD7_1238600 is annotated as sphingomyelin phosphodiesterases in PlasmoDB database. STRING database analysis reveals its possible interactions with cAMP-specific 3′,5′-cyclic phosphodiesterases 4D, merozoite surface protein 9, actins (PFL2215w), rhoptry associated protein 2 (RAP2), GAP50 and diacylglycerol kinases based on co-expression profile showing that PF3D7_1238600 may play important role in parasite development and its growth.
STRING results show that apyrase interacts with proteins/enzymes involved in DNA replication, DNA repair as well as in pre-mRNA splicing. Adenosine diphosphatase STRING database analysis shows that it interacts with chromosome condensation protein, peptidase, and cysteine-rich surface protein. Protein expression profile also suggests that it is expressed throughout all the stages of malaria parasite, making it a suitable target for antimalarial drug target.
RHOD group Rhodanese homology domain is an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active form (CX5R) is also present in Cdc25 class of protein phosphatases. Cdc25 plays an important role in cell cycle  [107]. CDD search reported 2 phosphatase sequences; PF3D7_1206400 (two domains) and PF3D7_1305500 (one domain) containing RHOD (an alpha beta fold domain) domain, none of them with CX5R motif. CDD predicts the presence of catalytic active residue in RHOD domain present in both phosphatases. STRING database analysis shows that these phosphatases may be involved in interaction with 6pyruvoyl tetrahydropterin synthase and NLI interacting factor-like phosphatase. Recently PF3D7_1305500 has been shown as a MAPK phosphatase playing an essential role in the life cycle and development of P.
It consist of highly positively charged Nterminus; however this predicted structure could not be verified using ESTs and not found conserved in other Plasmodium species, suggesting it may be a case of incorrect exon prediction (it has been reported that almost ¼ predicted open reading frame in P. falciparum have incorrect exon structure  [114, 59]. STRING database analysis suggests that PTPLA may interact with steroid dehydrogenase kik-i, which in turn is involved in many metabolic pathways.
Syja_N group This Sacl homology domain is found at the amino terminal of inositol-5-phopshatase synaptojanin. These phosphatases are involved in recycling of synaptic vesicles secreted, nerve impulse transmission and predicted to be involved in the coordination of activities of secretary pathway and actin cytoskeleton. We identified three Syja_N domain containing sequences (PF3D7_0705500, PF3D7_0802500, and PF3D7_1354200) belonging to inositol phosphatases, were identified in P. falciparum proteome. This family represents a protein domain, which shows homology to the yeast protein SacI. STRING database analysis shows that PF3D7_1354200 interacts with 2oxoglutarate/malate translocator protein, P-type ATPase, acyl CoA binding protein and beta-hydroxyacyl-acp dehydratase precursor. It is also predicted to interact with the mitochondrial inner membrane translocase.
Additional functional characterizations Since good quality Protein Data Bank (PDB) experimental structures and homology-based models could be used for in-silico screening experiments for finding novel drug leads, we set out to explore available plasmodium phosphatase structures and possibility of generating reliable molecular models of the proteins for which experimental structures are unavailable. A PlasmoDB search identified 12 structures of phosphatases, out of which 3 are experimental structures (PF3D7_0413500, PF3D7_0918000 and PF3D7_1120100). NCBI PDB sequence BLAST helped in identification of 17 phosphatases with more than 40% similarity to suitable templates (threshold value for homology modelling). Homology based modelling could be performed only on 11 malarial phosphatases, with conserved domain region present in the models (Data not shown) while the remaining 7 do not contain conserved domain region in the homology based models, especially in the cases where query sequence similarity with the template is poor.
For few cases our analysis does not show all the orthologs classified by OrthoMCL database due to the fact that we retrieved only the referenced and reviewed non-apicomplexan phosphatase sequences from UNIPROT. Phylogenetic analysis of MPP superfamily shows clustering of phosphatases into distinct groups, according to different metallophosphatase subgroups, namely PP1, PPKL, PP2B, PP5, Shelphs and others. This indicates the conservation of metallophosphatase superfamily during the course of evolution across various lineages. PP2B absent in plants hence, A. thaliana sequence is missing in the PP2B phylogenetic tree. PTPc superfamily phylogenetic shows two dual specific phosphatases, PF3D7_0309000 and PF3D7_1455100 Figure  4  Phosphatase proteins distribution according to their protein expression (using mass spectroscopic evidences).
Selection of protein phosphatase catalytic domains We performed query text search with 'Phosphatase' in PlasmoDB (www. plasmodb. org version 9. 2)  [43]  and EuPathDB (http://eupathdb. org/eupathdb/) [123]  to get phosphatase sequences for apicocomplexan model organisms. We retrieved E. coli, A. thaliana, S. cerevisiae and H. sapiens phosphatase protein sequences from uniprot (www. uniprot. org/) dated November, 2012. Only referenced and reviewed sequences were included to perform further analysis. We performed NCBI Conserved domain database (CDD)  [29]  search for the selected predicted phosphatase sequences. Sequence having phosphatase domain were selected. Text search in PlasmoDB, which resulted in 89 phosphatases after performing CDD analysis and gene ontology analysis for functions, resulted in 67 phosphatases.
Further analysis of P. falciparum phosphatases resulted in its assignment to 13 phosphatase super-families, on the basis of CDD result. We also used PFAM to confirm predicted phosphatases in amongst selected P. falciparum sequences. To crosscheck our results, we also repeated the domain search for complete P. falciparum proteome (5777 P. falciparum proteins) to find phosphatase domain using both CDD and PFAM databases, which finally resulted in same number of predicted phosphatases. Additionally, we performed pBLAST against NCBI non-redundant database, for each predicted phosphatase as query to further validate protein sequence assignment as phosphatases. We used protein expression profile (Mass spectroscopic evidences) of these 67 phosphatase proteins to distribute into different stages of P.
Gene ontology and ortholog group analysis We used PlasmoDB version 9. 2 assigned gene ontologies and orthologs in order to study the molecular and biological function performed by various phosphatase in P. falciparum and orthology with respect to other apicomplexans, host and model organisms. Only annotated gene ontology assigned to protein was selected. PlasmoDB (ver9. 2) and OrthoMCL 5 database (www. OrthoMCL. org) was used to identify phosphatase orthologs of P. falciparum in the model organisms included in our study.
Interacting partner analysis We used STRING 9. 05 database and PlasmoMAP (version 1. 0) to predict the interacting partners of the phosphatases. STRING uses neighbourhood, gene fusion, co expression, co-occurrence, homology, text mining, database information and experiments to list the interacting partners using scoring method. We preformed sequence search in STRING database, as it does not identify new PlasmoDB IDs. PlasmoMAP network is generated using various computational tools and functional genomic data within a Bayesian framework to predict interacting network.
Phylogenetic analysis Multiple sequence alignment P. falciparum sequences and the sequences of other apicomplexan model organisms were retrieved from Plas-moDB and EuPathDB databases, respectively. Protein Sequences for E. coli, A. thaliana, S. cerevisiae and H. sapiens were retrieved from Uniprot database (Dated November, 2012). Pairwise and multiple sequence alignment was performed for different phosphatases group using Clustal X2 and then Muscle software to get better alignment. Default parameters (Additional file 6) were used in both the cases to perform multiple sequence alignment. Phylogenetic tree generation MEGA 5. 2 software was used to generate phylogenetic tree. We used Neighbour Joining method to generate the phylogenetic tree. Jones Taylor Thornton (JTT) model was used for amino acid substitution.
Acknowledgements The authors thank  Department of Biotechnology (DBT, India)  grants for " Bioinformatics Infrastructure Facility " (Grant no. BT/BI/25/001/2006 ) and " Programme Support for Centre of Excellence  (Grant no. BT/01/CEIB/11/V/ 01 )" at  ICGEB, New Delhi. RP acknowledges University Grants Commission  ( UGC, India) for Junior Research Fellowship.
berghei (PBANKA), P. vivax (PVX), P. chabaudi chabaudi (PCHAS), P. cynomolgi (PCYB), P. knowlesi (PKH), T. gondii (TGME49), and E. tenella (ETH), B. bovis (BBOV), T. parva (TP), C. parvam (cgd) is used to perform evolutionary analysis. MEGA software is used to perform Phylogenetic analysis.
Host gene expression and viral load measurement by Real Time RT-PCR Lung tissues from both GX À / À and GX þ / þ mice were collected at 3 and 6 days post infection (pi) and from uninfected controls (four mice per group). RNA was purified from lung tissue using TriPure (Roche, Indianapolis, IN, USA). Purified RNA was then reverse transcribed using ImProm-II Reverse Transcription System (Promega, Madison, WI, USA). Real Time RT-PCR was performed using the ABI-Prism 7900HT Sequence Detection Systems (Applied Biosystems, Foster City, CA, USA). Data was collected with Applied Biosystems Sequence Detection Systems Version 2. 3 software. Each reaction well contained 4 μL of 0. 625 ng/μL cDNA, 0. 5 μL each of forward and reverse primers (final concentration of 200 nM), and 5 μL SYBR Green Master Mix, for a total reaction volume of 10 μL and run in quadruplicate.
Rabbit antimurine GX-sPLA 2  (Degousee et al. , 2008)  was used to assess the tissue distribution of the GX-sPLA 2 protein. Sections were counterstained with hematoxylin and eosin and observed under light microscope (Accu-scope s , Commack, NY, USA). Images were captured using a digital camera and SE Premium software (Micrometrics TM , Londonderry, NH, USA)  (Degousee et al. , 2006). For Mac-3 tissue expression, rat anti-mouse Mac-3 was used (BD Biosciences, Mississauga, ON). For CD3 immunofluorescence, following heat-induced antigen retrieval, lung tissue sections were blocked with donkey serum and stained with primary antibodies rabbit anti-CD3 (Dako, Burlington, ON). Donkey anti-rabbit Cy3 was used as secondary antibodies (Millipore, Billerica, MA) and DAPI (Sigma) for nuclear counterstain.
Microarray analysis Lung tissues from both GX À / À and GX þ / þ mice were collected at 3 and 6 days pi and from uninfected controls (four mice per group) as with the Real Time RT-PCR. RNA was purified from lung tissue using TriPure (Roche, Indianapolis, IN, USA) and amplified with Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX, USA). 1. 5 mg of cRNA was labeled and hybridized to Mouse WG-6 v2. 0 Expression BeadChip (Illumina, San Diego, CA, USA) and scanned on Illumina BeadStation 500GX. Raw data was processed with Illumina GenomeStudio V2010. 3 software. The data sets were subjected to quantile normalization, variance stabilization and log 2 transformation. Genes were considered significantly regulated if the expression levels with respect to the uninfected controls were Z1.
5fold different and the Student t-test's p value was o0. 05. DAVID Bioinformatics Resource v6. 7 (http://david. abcc. ncifcrf. gov/home. jsp) (Hicks et al. , 2007)  was used to perform functional classification of differentially expressed genes. Additionally, interferon regulated genes were selected by using the Interferome (v2) database (http://interfer ome. its. monash. edu. au/interferome/home. jspx)  (Rubin et al. , 2005). Immunoglobulin chains and prostaglandin-related gene categories were defined by searching for relevant keywords in the annotated microarray datasets. MultiExperiment Viewer v4. 7. 2 (http://www. tm4. org/mev/) was used to perform complete Hierarchical clustering and generate heatmap representations of selected genes.
Statistical analysis Data are presented as mean 7SEM. Analyses of data recorded at one time point were performed by 2-tailed, unpaired, Student t-tests. Analyses of data recorded at several time points for two groups (GX þ / þ and GX À / À mice) were performed by 2-way ANOVA (to evaluate the effect of group, time and group-time interactions); if significant, a Bonferroni correction for multiple comparisons was applied for post-hoc analysis between different time points or between different groups at the same time point. Survival after H1N1pdm influenza infection was assessed by a logrank test. A value of p o0. 05 was accepted as statistically significant. The authors had full access to and take full responsibility for the integrity of the data. All authors have read and agree to the manuscript as written.
Acknowledgments A/Mexico/4108/2009 was obtained through the  Influenza Reagent Resource, Influenza Division, WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza, Centers for Disease Control and Prevention, Atlanta, GA, USA. We thank the  Li Ka-Shing Foundation of Canada, Immune Diagnostics & Research, Shantou University Medical College ,  NIH  (Grant  R37 HL36235 ),  NIH   1U01AI11598-01  Subaward no. 0038591 ( 123721-3 ) to the support of this study and the  Canadian Institutes of Health Research (CIHR)  (Grant  MOP 126205  ( Dr. Rubin )) for the support of this study. We thank the staff from the  Animal Resource Center of University Health Network  for their help with the animal experiments.
2005; Rewitz et al. 2009 ). To ask whether Hh signaling might disturb either of these processes, we quantified expression of insulin receptor (InsR) or the PTTH receptor torso by qRT-PCR in brain-ring gland complexes. Neither ptcRNAi nor expression of ptc SSD significantly changed the expression of insR or torso, suggesting that Hh signaling does not act by reducing susceptibility to PTTH or Drosophila insulin-like peptides (Dilps) (Fig. 7H ; Supplemental Fig. 7F ). Thus, high Hh signaling reduces transcription of ecdysteroid biosynthetic enzymes and inhibits production of ecdysone and makisterone A, delaying pupariation. Taken together, these data suggest that the increase in ecdysteroid biosynthesis that precedes and initiates pupariation does not occur if Hh signaling in the prothoracic gland is too high.
Lipids extraction and shotgun MS Lipids were extracted from the fat body and whole larvae and quantified by shotgun MS as described in  Carvalho et al. (2012)  with modifications. Briefly, samples were homogenized in 150 mM ammonium bicarbonate buffer. From each homogenate, a volume containing ;2 nmol of lipid material was removed and extracted using a modified Folch protocol at 4°C (whole larva, n = 3; fat body, n = 4; fed to 12 h of starvation, n = 6 for 24 h of starvation experiment). MS analyses were performed on a Q Exactive instrument (Thermo Fisher Scientific) equipped with a robotic nanoflow ion source TriVersa NanoMate (Advion BioSciences) using chips with 4. 1-mm diameter spraying nozzles. The ion source was controlled by Chipsoft 8. 1 software. Ionization voltage was set at +0. 95 kV and À0.
Lipids were identified by LipidXplorer  (Herzog et al. 2011)  software by matching the m/z of their monoisotopic peaks to the corresponding elemental composition constraints. Molecular Fragmentation Query Language (MFQL) queries compiled for all of the aforementioned lipid classes are available at the LipidXplorer wiki site (https://wiki. mpicbg. de/wiki/lipidx/index. php/Main_Page). Mass tolerance was 5 ppm, and intensity threshold was set according to the noise level reported by Xcalibur software (Thermo Scientific). The content of glycerolipids was normalized per polar lipids and expressed in picomole of lipid x/picomole of polar lipids. Lipid standards were purchased from Avanti Polar Lipids (Alabaster). Solvents were purchased from Sigma-Aldrich.
Acknowledgments We are grateful to  Bruce Edgar ,  Michael O'Connor ,  Isabell Guerrero , and the  Bloomington Stock Center  for fly stocks. We gratefully acknowledge  Robert Holmgren  and the  Developmental Studies Hybridoma Bank  for providing antibodies. We thank  Sven Ssykor  and  Marko Brankatschk  for help with transgenesis. We thank  Andreas Sagner ,  Marko Brankatschk , and  Jochen Rink  for critical comments on the manuscript.
eIF4E1-pvr2 2 allele in the same eifiso4e rtm1 background did not restore susceptibility to TEV HAT in any of the 6 independent lines tested (Figure  5B  and data not shown). To ensure that those phenotypes were not due to differences in transgene expression, the levels of Ca. One T2 line transformed with the 35S:GUS construct was tested and five independent T2 lines transformed with 35S:AteIFiso4E. C, Western blot analysis of eIFiso4E protein levels in total proteins extracted from 1-month-old leaves. Actin protein levels were assessed as a loading control. D, One-month-old Arabidopsis plants were inoculated with TEV-HAT and assayed for viral coat protein accumulation by ELISA at 24 dpi.
Protein accession numbers and phylogeny The following protein sequences were used for the phylogeny analysis with the accession numbers shown in brackets: Pd. eIF4E1 (JX137116) and Pd. eIFiso4E (JX137117) from Prunus domestica; Ps. eIF4E1 (AAR04332) and Ps. eIFiso4E (ABH09880) from Pisum sativum; Ls. eIF4E1 (AAP86602) and Ls. eIFiso4E (AAP86603) from Lactuca sativa; Ca. eIF4E1 (AAN74644) and Ca. eIFiso4E (AAY62607) from Capsicum annuum; At. eIF4E1  (NP_ 193538)  and At. eIFiso4E (NP_198412) from Arabidopsis thaliana; and Sl. eIF4E1 (ABF83563) and Sl. eIFiso4E (ABV23495) from Solanum lycopersicum. The phylogenetic tree was generated using phylogeny. fr [39]. Protein sequences were aligned using MultiAlin (http:// multalin. toulouse. inra. fr) and BoxShade (http://www. ch. embnet. org/software/BOX_form.