Phosphoproteome of Pristionchus pacificus provides insights into architecture of signaling networks in nematode models.

Pristionchus pacificus is a nematode that is increasingly used as a model organism in evolutionary biology. The genome of P. pacificus differs markedly from that of C. elegans, with a high number of orphan genes that are restricted to P. pacificus and have no homologs in other species. To gain insight into the architecture of signal transduction networks in model nematodes, we performed a large-scale qualitative phosphoproteome analysis of P. pacificus. Using two-stage enrichment of phosphopeptides from a digest of P. pacificus proteins and their subsequent analysis via high accuracy MS, we detected and localized 6,809 phosphorylation events on 2,508 proteins. We compared the detected P. pacificus phosphoproteome to the recently published phosphoproteome of C. elegans. The overall numbers and functional classes of phosphoproteins were similar between the two organisms. Interestingly, the products of orphan genes were significantly underrepresented among the detected P. pacificus phosphoproteins. We defined the theoretical kinome of P. pacificus and compared it to that of C. elegans. While tyrosine kinases were slightly underrepresented in the kinome of P. pacificus, all major classes of kinases were present in both organisms. Application of our kinome annotation to a recent transcriptomic study of dauer and mixed stage populations showed that Ser/Thr and Tyr kinases show similar expression levels in P. pacificus but not in C. elegans. This study presents the first systematic comparison of phosphoproteomes and kinomes of two model nematodes and, as such, will be a useful resource for comparative studies of their signal transduction networks.

Proteogenomics of Pristionchus pacificus reveals distinct proteome structure of nematode models.

Pristionchus pacificus is a nematode model organism whose genome has recently been sequenced. To refine the genome annotation we performed transcriptome and proteome analysis and gathered comprehensive experimental information on gene expression. Transcriptome analysis on a 454 Life Sciences (Roche) FLX platform generated >700,000 expressed sequence tags (ESTs) from two normalized EST libraries, whereas proteome analysis on an LTQ-Orbitrap mass spectrometer detected >27,000 nonredundant peptide sequences from more than 4000 proteins at sub-parts-per-million (ppm) mass accuracy and a false discovery rate of <1%. Retraining of the SNAP gene prediction algorithm using the gene expression data led to a decrease in the number of previously predicted protein-coding genes from 29,000 to 24,000 and refinement of numerous gene models. The P. pacificus proteome contains a high proportion of small proteins with no known homologs in other species ("pioneer" proteins). Some of these proteins appear to be products of highly homologous genes, pointing to their common origin. We show that >50% of all pioneer genes are transcribed under standard culture conditions and that pioneer proteins significantly contribute to a unimodal distribution of predicted protein sizes in P. pacificus, which has an unusually low median size of 240 amino acids (26.8 kDa). In contrast, the predicted proteome of Caenorhabditis elegans follows a distinct bimodal protein size distribution, with significant functional differences between small and large protein populations. Combined, these results provide the first catalog of the expressed genome of P. pacificus, refinement of its genome annotation, and the first comparison of related nematode models at the proteome level.

Identification and characterization of onchoastacin, an astacin-like metalloproteinase from the filaria Onchocerca volvulus.

The tissue-invasive nematode Onchocerca volvulus causes skin and eye pathology in human onchocerciasis. While the adult females reside sessile in subcutaneous nodules, the microfilariae are abundantly released from the nodules, males and juvenile worms migrate through the host tissue. Matrix-degrading metallo- and serine proteinases have been detected in excretory-secretory worm products that may be essential for migration of the mobile stages. In this study, a 1713bp long cDNA encoding for a putative proteinase of O. volvulus has been isolated. The predicted protein sequence includes a signal peptide indicating secretion to the extracellular space, a propeptide, an astacin-like protease domain, an EGF-like and a CUB-domain, thereby identifying the protein as a member of the astacin family of zinc endopeptidases. Onchoastacin, Ov-AST-1, is most closely related to a subfamily comprising nematode astacins including Caenorhabditis and Ancylostoma. Ov-AST-1 was expressed as a recombinant protein in baculovirus-infected insect cells and exhibited enzymatic activity. The exposure of onchoastacin to the host immune system is indicated by demonstration of IgG reacting with the recombinant Ov-AST-1 and with two peptides of the protein. Since a homologous metalloproteinase is part of a promising hookworm vaccine, Ov-AST-1 may be a candidate for intervention strategies in filarial infections.

[Quality of the bristle-end rounding in ten brands of children's toothbrushes]. / Die Qualität der Borstenendabrundung von zehn Kinderzahnbürstenmarken.

Animal and clinical studies have shown that sharp, unpolished toothbrush bristles may injure gingival tissue, and their contribution to cervical abrasion is widely discussed. The aim of the present study was to compare the end-roundness and smoothness of the bristle tips of ten commercially available children's toothbrushes (Elmex Lernzahnbürste, Aronal Oko Dent Kinder, Signal Kids, Dr. Best Milchzahn, Dr. Best Best Friends, Colgate Grip'Ems, Colgate My First, Oral B Mickey for Kids, Oral B Disneys' Mickey Mouse, Blend-a-med Blendi). From forty brushes five tufts each were selected randomly and subjected to scanning electron microscopy (45 degrees) at a viewing angle of 45 degrees. On micrographs six bristles located in the first three rows that could clearly be evaluated were analyzed visually for end rounding and evaluated by shape factor (SF) analysis by a blinded single examiner. Mean SF was reported highest for Aronal Oko Dent Kinder at 0.278 (+/- 0.004) followed by Dr. Best Milchzahn (0.277 [+/- 0.005]) and Elmex Lernzahnbürste (0.277 [+/- 0.005]). These values were significantly different from those found for Colgate My First (0.258 [+/- 0.023]) and Colgate Grip'Ems (0.267 [+/- 0.012]) (p<0.001; ANOVA, Bonferroni). More than half of the surfaces of the bristle tips examined were rated as non-acceptable for Signal Kids (75%) and Dr. Best Best Friends (100%). For all the other brands more than 50% of the bristle surfaces were judged as being acceptable. Despite of being flattened during usage, rounded bristle tips with a smooth surface are desirable. A good quality of bristle tips could only be observed in half of the brands examined.