Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions

Initial environmental pyrosequencing studies suggested highly complex protistan communities with phylotype richness decisively higher than previously estimated. However, recent studies on individual bacteria or artificial bacterial communities evidenced that pyrosequencing errors may skew our view of the true complexity of microbial communities. We pyrosequenced two diversity markers (hypervariable regions V4 and V9 of the small-subunit rDNA) of an intertidal protistan model community, using the Roche GS-FLX and the most recent GS-FLX Titanium sequencing systems. After pyrosequencing 24 reference sequences we obtained up to 2039 unique tags (from 3879 V4 GS-FLX Titanium reads), 77% of which were singletons. Even binning sequences that share 97% similarity still emulated a pseudodiversity exceeding the true complexity of the model community up to three times (V9 GS-FLX). Pyrosequencing error rates were higher for V4 fragments compared with the V9 domain and for the GS-FLX Titanium compared with the GS-FLX system. Furthermore, this experiment revealed that error rates are taxon-specific. As an outcome of this study we suggest a fast and efficient strategy to discriminate pyrosequencing signals from noise in order to more realistically depict the structure of protistan communities using simple tools that are implemented in standard tag data-processing pipelines.     

Density-dependent effects on the survival and growth of the rodent stomach worm Protospirura muricola in laboratory mice

The spirurid nematode, Protospirura muricola, is of intrinsic interest as a rodent model of gastric nematode infections. Since worm burdens can be very heavy in nature, density dependent processes may constrain parasite growth. Laboratory mice (BKW) were exposed to varying doses of infective larvae of P. muricola in the range 5 to 40 third-stage larvae (L3), in four separate experiments in which progressively higher doses were utilized. All mice were culled 60 days after infection and a total of 518 worms (226 male and 292 female worms) was recovered, measured and weighed. Overall survival was 58.9%, but survival declined significantly with increasing dose by approximately 21% (from 66% at 5 L3 per mouse to 52% at 40 L3 per mouse). The length and weight of worms correlated positively in both sexes. Total worm biomass increased linearly with increasing numbers of worms. However, whilst the length and weight of male worms declined with increasing worm burden (8.4 and 24.6% respectively), female worms were less affected, only length showing a significant reduction with increasing parasite burden (16.0%). Therefore, increasing worm burdens impeded growth of P. muricola, but reduction in length and weight were relatively small in relation to the overall size of this nematode. Increasing worm burdens were associated with loss of host weight and reduction in stomach weight and worm burdens in excess of 20 exerted a measurable cost to the host, which in the field, may be associated with loss of overall host fitness.     

Thermodynamic characterization of cytosolic phospholipase A2 alpha inhibitors

Cytosolic phospholipase A₂ alpha (cPLA₂α, type IVA phospholipase) acts at the membrane surface to release free arachidonic acid, which is metabolized into inflammatory mediators, including leukotrienes and prostaglandins. Thus, specific cPLA₂α inhibitors are predicted to have antiinflammatory properties. However, a key criterion in the identification and development of such inhibitors is to distinguish between compounds that bind stoichiometrically to cPLA₂α and nonspecific membrane perturbants. In the current study, we developed a method employing isothermal titration calorimetry (ITC) to characterize the binding of several distinct classes of cPLA₂α inhibitors. Thermodynamic parameters and the binding constants were obtained following titration of the inhibitor to the protein at 30 °C and pH 7.4. The compounds tested bound cPLA₂α with a 1:1 stoichiometry, and the dissociation constant K_d of the inhibitors calculated from the ITC experiments correlated well with the IC₅₀ values obtained from enzymatic assays. Interestingly, binding was observed only in the presence of a micellar surface, even for soluble compounds. The site of binding of these inhibitors within cPLA₂α was analyzed by testing for binding in the presence of methyl arachidonyl fluorophosphonate (MAFP), an irreversible active site inhibitor of cPLA₂α. Lack of binding of inhibitors in the presence of MAFP suggested that the compounds tested bound specifically at or near the active site of the protein. Furthermore, the effect of various detergents on the binding of certain inhibitors to cPLA₂α was also tested. The results are discussed with reference to thermodynamic parameters such as changes in enthalpy (ΔH), entropy (ΔS), and free energy (ΔG). The data obtained from these studies provide not only structure-activity relationships for compounds but also important information regarding mechanism of binding. This is the first example of ITC used for studying inhibitors of enzymes with interfacial kinetics.     

Signal-peptide-peptidase-like 2a (SPPL2a) is targeted to lysosomes/late endosomes by a tyrosine motif in its C-terminal tail

Signal-peptide-peptidase-like 2A (SPPL2a), an aspartyl intramembrane protease, has been implicated in the proteolysis of TNF-alpha, Fas Ligand and Bri2. Here, we show that endogenous SPPL2a - in agreement with overexpression studies - is localised in membranes of lysosomes/late endosomes. Furthermore, we have analysed the molecular determinants for lysosomal sorting of SPPL2a by creating chimaeric constructs between SPPL2a and its plasma membrane localised homologue SPPL2b. Lysosomal transport of SPPL2a critically depends on its cytosolic carboxyterminal tail. A canonical tyrosine-based sorting motif of the YXX? type at position 498 is sufficient to direct SPPL2a to lysosomal/late endosomal compartments. This motif accounts for the differential localisation of the homologous proteases SPPL2a and SPPL2b and thereby influences the access to substrates and biological function of SPPL2a.     

Arsanilazoprocarboxypeptidase activation

Modification of procarboxypeptidase A with diazotized arsanilic acid under mild conditions generates extrinsic Cotton effects attributed to the 1.7 tyrosyl residues substituted. The C.D. spectrum exhibits extrema at 305, 400 and 500 nm. Activation shifts the band at 400 to 438 nm, almost doubling its molecular rotation. The 500 nm band shifts to 525 nm. The time course of the spectral changes correlate directly with that of the induction of activity. The arsanilazochromophore is thus a suitable probe of conformational changes accompanying the activation process of this trimeric zymogen.     

The suppression of homologous immunity by soluble adult antigens of Nematospiroides dubius

An established adult infection of Nematospiroides dubius was unaffected by the administration of immune lymphocytes and immune sera whereas an incoming larval infection was expelled. Past experiments have shown that the immune inoculum at least had the ability to recognize adult stages, leading to the hypothesis that adult stages secrete or excrete an immunomodulatory shield around themselves in the gastrointestinal tract. This hypothesis was given further credence by the demonstration that soluble antigens derived from adults abolished the generation of homologous immunity to this parasite. Modulation of immunity was reflected by increased fecundity, increased worm size, and increased survival time in the gut.     

Expression and subcellular location of native and mutant hTNF alpha proteins in Escherichia coli.

Several mutant hTNF alpha genes were constructed by deletion and stepwise reconstitution of regions coding for C-terminal sequences. The mutant hTNF alpha proteins behaved differently from native hTNF alpha when expressed in Escherichia coli. They were either sensitive to proteolytic degradation or formed insoluble aggregates depending on the strains and conditions used for expression. By contrast, native hTNF alpha was always present in a soluble form and had a tendency to associate with the cytoplasmic membrane. It was even transported to the periplasmic space in E. coli as shown by both cell fractionation and immunoelectron microscopy. The different behaviour of mutant hTNF alpha proteins probably results from a disturbance of protein folding.     

Marker rescue allows direct selection for recombinant plasmids in streptococci

Summary Resident deletion derivatives (Em^s or Cm^s) of the streptococcal plasmid vector pGB301 rescue antibiotic resistance genes from linearized pGB301 (Em^r, Cm^r) DNA with high frequency. Insertion of passenger DNA next to an antibiotic resistance determinant of pGB301, which is missing on the resident plasmid, forces corescue of these two plasmid domains, thus allowing direct selection for recombinant plasmids.