Proteomic profile of culture filtrate from the Brazilian vaccine strain <Emphasis Type="Italic">Mycobacterium bovis</Emphasis> BCG Moreau compared to <Emphasis Type="Italic">M. bovis</Emphasis> BCG Pasteur

Background  

Bacille Calmette-Guerin (BCG) is currently the only available vaccine against tuberculosis (TB) and comprises a heterogeneous family of sub-strains with genotypic and phenotypic differences. The World Health Organization (WHO) affirms that the characterization of BCG sub-strains, both on genomic and proteomic levels, is crucial for a better comprehension of the vaccine. In addition, these studies can contribute in the development of a more efficient vaccine against TB. Here, we combine two-dimensional electrophoresis (2DE) and mass spectrometry to analyse the proteomic profile of culture filtrate proteins (CFPs) from M. bovis BCG Moreau, the Brazilian vaccine strain, comparing it to that of BCG Pasteur. CFPs are considered of great importance given their dominant immunogenicity and role in pathogenesis, being available for interaction with host cells since early infection.     

A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase

Tetrachlorohydroquinone (TCHQ) dehalogenase is profoundly inhibited by its aromatic substrates, TCHQ and trichlorohydroquinone (TriCHQ). Surprisingly, mutations that change Ile12 to either Ser or Ala give an enzyme that shows no substrate inhibition. We have previously shown that TriCHQ is a noncompetitive inhibitor of the thiol-disulfide exchange reaction between glutathione and ESSG, a covalent adduct between Cys13 and glutathione formed during dehalogenation of the substrate. Substrate inhibition of the thiol-disulfide exchange reaction is less severe in the I12S and I12A mutant enzymes, primarily due to weaker binding of TriCHQ to ESSG. These mutations also result in a decrease in the rate of dehalogenation. Because the rate-limiting step in the I12S and I12A enzymes is dehalogenation, rather than the thiol-disulfide exchange reaction, the relatively modest inhibition of the thiol-disulfide exchange reaction does not affect the overall rate of turnover.     

MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs

MotifCluster finds related motifs in a set of sequences, and clusters the sequences into families using the motifs they contain. MotifCluster, at , lets users test whether proteins are related, cluster sequences by shared conserved motifs, and visualize motifs mapped onto trees, sequences and three-dimensional structures. We demonstrate MotifCluster's accuracy using gold-standard protein superfamilies; using recommended settings, families were assigned to the correct superfamilies with 0.17% false positive and no false negative assignments.     

Randomised controlled trial of gabapentin in Complex Regional Pain Syndrome type 1 [ISRCTN84121379]

Background  

Complex Regional Pain Syndrome type one (CRPS I) or formerly Reflex Sympathetic Dystrophy (RSD) is a disabling syndrome, in which a painful limb is accompanied by varying symptoms. Neuropathic pain is a prominent feature of CRPS I, and is often refractory to treatment. Since gabapentin is an anticonvulsant with a proven analgesic effect in various neuropathic pain syndromes, we sought to study the efficacy of the anticonvulsant gabapentin as treatment for pain in patients with CRPS I.     

Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes

Background  

Glutathione is found primarily in eukaryotes and in Gram-negative bacteria. It has been proposed that eukaryotes acquired the genes for glutathione biosynthesis from the alpha-proteobacterial progenitor of mitochondria. To evaluate this, we have used bioinformatics to analyze sequences of the biosynthetic enzymes γ-glutamylcysteine ligase and glutathione synthetase.     

HSPG modification by the secreted enzyme Notum shapes the Wingless morphogen gradient

The secreted signaling protein Wingless acts as a morphogen to pattern the imaginal discs of Drosophila. Here we report identification of a secreted repressor of Wingless activity, which we call Notum. Loss of Notum function leads to increased Wingless activity by altering the shape of the Wingless protein gradient. When overexpressed, Notum blocks Wingless activity. Notum encodes a member of the alpha/beta-hydrolase superfamily, with similarity to pectin acetylesterases. We present evidence that Notum influences Wingless protein distribution by modifying the heparan sulfate proteoglycans Dally-like and Dally. High levels of Wingless signaling induce Notum expression. Thus, Wingless contributes to shaping its own gradient by regulating expression of a protein that modifies its interaction with cell surface proteoglycans.     

Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways

We provide statistically reliable sequence evidence indicating that at least 12 of 23 SCOP (betaalpha)(8) (TIM) barrel superfamilies share a common origin. This includes all but one of the known and predicted TIM barrels found in central metabolism. The statistical evidence is complemented by an examination of the details of protein structure, with certain structural locations favouring catalytic residues even though the nature of their molecular function may change. The combined analysis of sequence, structure and function also enables us to propose a phylogeny of TIM barrels. Based on these data, we are able to examine differing theories of pathway and enzyme evolution, by mapping known TIM barrel folds to the pathways of central metabolism. The results favour widespread recruitment of enzymes between pathways, rather than a "backwards evolution" model, and support the idea that modern proteins may have arisen from common ancestors that bound key metabolites.     

Biomechanical evaluation of fetal calf skull as a model for testing halo-pin designs for use in children

Rigid immobilization of the cervical spine in children is normally accomplished with a halo ring attached to the skull with pins. Concern exists about the risk of halo pin complications in small children due to their diminished skull thickness. More data are needed on biomechanical properties of the immature skull and on safe levels for halo pin penetration forces. The study included halo pin penetration tests on 43 skull samples obtained from eight fetal calves, radial compression tests of 11 skull samples, and histology. Compressive composite elastic modulus (15-139MPa), yield stress (1-5MPa) and composite consolidation modulus (188-479MPa) were measured in the skull's radial direction. Pin penetration force (F) in Newtons at a pin-penetration depth equal to the original skull thickness (T) in mm, was related to T as: F=100+4.3e(T) (R(2)=0.76, p<0.0001). However, the 95% confidence limits on individual predictions were wide, e.g., 0-475MPa for T=1.5mm and 0-700MPa for T=4mm. These results suggest that skull thickness cannot be reliably used to predict halo pin penetration loads in a skull with similar structural and mechanical properties to that of the fetal calf. Due to the lack of available human data for comparison, the relevance of using the fetal calf skull as a model for human infants and young children remains inconclusive. Clinical recommendations regarding pediatric halo pin penetration loads cannot be made without further study of children's skull structure and biomechanical properties.     

Design of a novel quantitative PCR (QPCR)-based protocol for genotyping mice carrying the neuroprotective Wallerian degeneration slow (Wld s ) gene

Background

The strain of MeCP2^tm1.1Bird mice is a broadly used model for Rett syndrome. Because males carrying the invalidated MeCP2 locus are sterile, this strain has to be maintained in a heterozygous state. All animals therefore have to be genotyped at every generation to discriminate those carrying the invalidated allele (+/- females and y/- males) from those that do not. This is conveniently carried out by PCR on tail genomic DNA but because the primer pairs described initially for this purpose yield very similar size DNA bands on the WT and the KO alleles, this requires to carry out two independent PCR reactions on tail DNA preparations from all animals.

Results

After cloning and sequencing the PCR fragment amplified on the KO allele, we tested several sets of primers that were designed to yield PCR fragments of different sizes on the KO and WT alleles.

Conclusion

We have thus identified a set of three primers that allows for efficient genotyping of the animals by a single PCR reaction. Furthermore, using of this set of primers also resolves a recurrent problem related to the tendency of one of the initial primers to give rise to a non specific band because of its capacity to anneal at both ends of a repeated genomic element which we have identified as MurvyLTR.