such as "Introduction", "Conclusion"..etc
Table 1. Ninety-two (92) P. falciparum Protease Homologs Predicted From Comparative Genomic Analysis
The cut-off criteria of E-score 1e-04 was employed to define protease homologs. The nomenclature of the protease family is: A1 (pepsin), C1 (papain), C2 (calpain), C12 (ubiquitin carboxyl-terminal hydrolase, family 1, UCH1), C13 (hemoglobinase), C14 (caspase), C19 (ubiquitin C-terminal hydrolase family 2, UCH2), C48 (Ubiquitin-like protease, Ulp), C56 (DJ-1 peptidase), M1 (alanyl aminopeptidase, AMPN), M3 (thimet oligopeptidase), M16 (pitrilysin and mitochondrial processing peptidase, MPP), M17 (leucyl aminopeptidase, AMPL), M18 (aspartyl aminopeptidase, DNPE), M22 (O-sialoglycoprotein endopeptidase, GCP), M24A (methionyl aminopeptidase, AMPM), M24B (X-Pro dipeptidase, AMPP), M41 (FtsH endopeptidase), S1 (trypsin), S8 (subtilsin), S9 (acylaminoacyl-peptidase, ACPH), S14 (clp), S16 (Lon protease, La), S26A (prokarytotic signal peptidase I, SP1), S26B (signalase), S54 (rhomboid), and T1 (threonine endopeptidase).
Abbreviations for proteases include: PM, plasmepsin; DPPI, dipeptidyl-peptidase I; UBP, ubiquitin-specific protease; IMP, mitochondrial inner membrane peptidase; SPC21, microsomal signal peptide 21 kDa subunit.
Previously characterized proteases with proteolytic activity are highlighted in bold. The 23 proteases predicted by the official annotation published in PlasmoDB are highlighted in italic.
Potential candidate proteases Calpain, Metacaspase, and Signal peptidase I (SP1) are highlighted in bold italic.
a ± indicate the gene is predicted to contain/not contain an apicoplast transit peptide.
Table 2. Expression Profiles of Putative Plasmodial Proteases
a Expression profile of asynchronous culture using Oligo Microarrays. The microarray slide was printed with 6239 70-mers mapped to 4407 predicted open reading frames. Probes were labeled with fluorescent dyes using mRNAs purified from an asynchronous culture as a template (http://derisilab.ucsf.edu/). Briefly, messenger RNAs were purified using oligo T cellulose and reverse transcription was conducted to incorporate aminoallyl dUTP into the cDNAs. The Cy3 and Cy5 NHS esters were then coupled to amine groups of the cDNA, and dye-labeled probes were hybridized with the microarray slides under standard condition (3X SSC, 50% formamide, 0.1% SDS, 10 mg/ml salmon sperm DNA, 68°C). The slide was scanned with a GenePix 4000B (Axon Instrument) at default PMT settings, 100% power. The array data were analyzed initially with GenePixPro software (Axon Instrument), then with global normalization. The expression level is indicated by the mean signal intensity of all corresponding oligomers in triplicates on the microarray slides (MRA-452) obtained from Malaria Research and Reference Resource Center (http://www.malaria.mr4.org/). Ten predicted proteases without corresponding oligomers are highlighted in bold. Two sets of negative controls were included in the DeRisi design: (1) 20 oligomers from yeast intergenic region with the mean intensity 529; (2) 33 P. falciparum genes cloned in the plasmid, including 16 ribosomal proteins, 17 tRNA genes, LSU, Clp, and tufA. Their mean intensity was 598. The percentiles of expression level over all the spots are 297 (30%), 394 (35%), 512 (40%), 646 (45%), and 795 (50%), respectively. The genes that showed signal intensity below the mean of negative controls are highlighted in italic. An asterisk (*) indicates the gene was reported to be expressed in the parasitic life cycle from proteomics data (Florens et al. 2002).
b Expression profile in the erythrocytic stage using cDNA microarray chip containing 944 elements (317 genes of identiable homology; Ben Mamoun et al. 2001). The average intensities were extracted from PlasmoDB. R, ring. A minus sign (–) indicates signal not detected or below the cut-off (35% percentile over all the spots on the array).
c Expression profile in the parasite life cycle using MUDPIT proteomics technology (Florens et al. 2002), extracted from PlasmoDB. A plus sign (+) indicates at least one peptide of the protein was detected by Mass Spectrum. T, trophozoites; M, merozoites; G, gametocytes; S, sporozoites.
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