Examination of 2-DE in the Human Proteome Organisation Brain Proteome Project pilot studies with the new RAIN gel matching technique

The Human Proteome Organisation (HUPO) Brain Proteome Project (BPP) pilot studies have generated over 200 2-D gels from eight participating laboratories. This data includes 67 single-channel and 60 DIGE gels comparing 30 whole frozen C57/BL6 female mouse brains, ten each at embryonic day 16, postnatal day 7 (juvenile) and postnatal day 54-56 (adult); and ten single-channel and three DIGE gels comparing human epilepsy surgery of the temporal front lobe with a corresponding post-mortem specimen. The samples were generated centrally and distributed to the participating laboratories, but otherwise no restrictions were placed on sample preparation, running and staining protocols, nor on the 2-D gel analysis packages used. Spots were characterised by MS and the annotated gel images published on a ProteinScape web server. In order to examine the resultant differential expression and protein identifications, we have reprocessed a large subset of the gels using the newly developed RAIN (Robust Automated Image Normalisation) 2-D gel matching algorithm. Traditional approaches use symbolic representation of spots at the very early stages of the analysis, which introduces persistent errors due to inaccuracies in spot modelling and matching. With RAIN, image intensity distributions, rather than selected features, are used, where smooth geometric deformation and expression bias are modelled using multi-resolution image registration and bias-field correction. The method includes a new approach of volume-invariant warping which ensures the volume of protein expression under transformation is preserved. An image-based statistical expression analysis phase is then proposed, where small insignificant expression changes over one gel pair can be revealed when reinforced by the same consistent changes in others. Results of the proposed method as applied to the HUPO BPP data show significant intra-laboratory improvements in matching accuracy over a previous state-of-the-art technique, Multi-resolution Image Registration (MIR), and the commercial Progenesis PG240 package.     

Prevalence of Escherichia coli O157:H7 in white-tailed deer from Louisiana

Escherichia coli O157:H7 (EC O157) is an important zoonosis. White-tailed deer (Odocoileus virginianus) have been implicated in transmission of this bacterium to humans and have been suggested as reservoirs that might affect carriage in cattle populations. Our study objectives were to estimate prevalence of EC O157 in feces of hunter-harvested deer and to describe fecal shedding patterns in a captive herd sampled over 1 yr. Prevalence of EC O157 in hunter-harvested deer was 0.3% (n = 338). In August 2001, EC O157 was detected in one of 55 deer (1.8%) from the captive herd. Prevalence over the 1-yr period was 0.4% (n = 226). Escherichia coli O157:H7 was rarely isolated from hunter-harvested deer during the winter. We could not describe a seasonal shedding pattern based on one positive sample in the captive herd. These data do not support a prominent role of deer as a reservoir for EC O157 for cattle or humans.     

Trifluoperazine inhibition of electron transport and adenosine triphosphatase in plant mitochondria

Trifluoperazine inhibits ADP-stimulated respiration in mung bean (Phaseolus aureus) mitochondria when either NADH, malate, or succinate serve as substrates (IC50 values of 56, 59, and 55 microM, respectively). Succinate:ferricyanide oxidoreductase activity of these mitochondria was inhibited to a similar extent. The oxidation of ascorbate/TMPD was also sensitive to the phenothiazine (IC50 = 65 microM). Oxidation of exogenous NADH was inhibited by trifluoperazine even in the presence of excess EGTA [ethylene glycol bis(beta-aminoethyl ether)-N,N'-tetraacetic acid] (IC50 = 60 microM), indicating an interaction with the electron transport chain rather than with the dehydrogenase itself. In contrast, substrate oxidation in Voodoo lily (Sauromatum guttatum) mitochondria was relatively insensitive to the phenothiazine. The results suggest the bc1 complex to be a major site of inhibition. The membrane potential of energized mung bean mitochondria was depressed by micromolar concentrations of trifluoperazine, suggesting an effect on the proton-pumping capability of these mitochondria. Membrane-bound and soluble ATPases were equally sensitive to trifluoperazine (IC50 of 28 microM for both), implying the site of inhibition to be on the F1. Inhibition of the soluble ATPase was not affected by EGTA, CaCl2, or exogenous calmodulin. Trifluoperazine inhibition of electron transport and phosphorylation in plant mitochondria appears to be due to an interaction with a protein of the organelle that is not calmodulin.     

Cloning Vectors for Lactococci Based on a Plasmid Encoding Resistance to Cadmium

An 8.8-kb plasmid (pND302) was identified in Lactococcus lactis spp lactis M71 which encodes cadmium resistance (Cd^R). Most of the commercial lactococcal strains tested were sensitive to cadmium. Therefore, Cd^R should provide a useful selectable marker for constructing cloning vectors in lactococci. pND302 was mapped with a number of restriction enzymes and found to contain a unique EcoRI site suitable for cloning. Two E. coli/L. lactis shuttle cloning vectors, pND304 and pND624, were constructed by subcloning of the E. coli plasmids pBR322 and pGEM-7Zf(+) containing a 1.6-kb gene encoding nisin resistance (Nis^R) of lactococcal origin into the EcoRI site of pND302, separately. The E. coli DNA component of pND624 was removed and the resulting plasmid, pND625, consisted of only lactococcal DNA, expressing Nis^R and Cd^R, with two synthetic polylinkers that contain multiple restriction sites for versatile cloning. Both pND302 and pND625 can be transformed by electroporation into L. lactis LMO230 at 10³/μg DNA and maintained stably in LMO230. The results indicated that pND302 and pND625 are potential food-grade cloning vectors for lactococci. Received: 27 November 1995 / Accepted: 29 December 1995     

Effect of pH and monovalent cations on the formation of quinonoid intermediates of the tryptophan synthase alpha(2)beta(2) complex in solution and in the crystal

Quinonoid intermediates play a key role in the catalytic mechanism of pyridoxal 5'-phosphate-dependent enzymes. Whereas the structures of other pyridoxal 5'-phosphate-bound intermediates have been determined, the structure of a quinonoid species has not yet been reported. Here, we investigate factors controlling the accumulation and stability of quinonoids formed at the beta-active site of tryptophan synthase both in solution and the crystal. The quinonoids were obtained by reacting the alpha-aminoacrylate Schiff base with different nucleophiles, focusing mainly on the substrate analogs indoline and beta-mercaptoethanol. In solution, both monovalent cations (Cs(+) or Na(+)) and alkaline pH increase the apparent affinity of indoline and favor accumulation of the indoline quinonoid. A similar pH dependence is observed when beta-mercaptoethanol is used. As indoline and beta-mercaptoethanol exhibit very distinct ionization properties, this finding suggests that nucleophile binding and quinonoid stability are controlled by some ionizable protein residue(s). In the crystal, alkaline pH favors formation of the indoline quinonoid as in solution, but the effect of cations is markedly different. In the absence of monovalent metal ions the quinonoid species accumulates substantially, whereas in the presence of sodium ions the accumulation is modest, unless alpha-subunit ligands are also present. Alpha-subunit ligands not only favor the formation of the intermediate, but also reduce significantly its decay rate. These findings define experimental conditions suitable for the stabilization of the quinonoid species in the crystal, a critical prerequisite for the determination of the three-dimensional structure of this intermediate.     

Acceptance of neonatal genetic screening for hereditary hemochromatosis by informed parents

The aim of this study was to assess attitudes to neonatal genetic screening for hereditary hemochromatosis. A total of 135 consecutive, pregnant women and their partners attending a hospital antenatal clinic in the Australian Capital Territory were given detailed written and verbal information about potential risks and benefits of neonatal genetic screening. Issues such as uncertainty of disease expression, confidentiality, genetic discrimination, and storage of genetic data were addressed. Attitudes were assessed by interview and questionnaire. There was a high level of acceptance for neonatal genetic screening in general (99%) and for hemochromatosis in particular (91.5%). There was no association of prior knowledge of hemochromatosis, family history of hemochromatosis, ethnicity, age, education, or occupation class with nonacceptance. Of the subjects, 39.5% reported feeling "a little anxious" about the prospect of screening their infants, although only 5.4% reported feeling "very anxious." Reasons given for nonacceptance of screening included inability of the child to give informed consent, insufficient evidence that diagnosis of hemochromatosis in childhood is beneficial, risk of discrimination on genetic grounds, lack of agreement between partners, and privacy issues. These data suggest that an Australian neonatal genetic screening program for hemochromatosis is likely to be accepted by this and similar groups of subjects, but there should be an opportunity for parents who object to screening to opt out of any such program.     

Improved peptide function from random mutagenesis over short 'windows'

We have applied random mutagenesis over short contiguous residue tracts ('windows') within an active peptide (the alpha-peptide of beta-galactosidase) such that all window residues are replaced simultaneously. A novel technique using mixed synthetic oligonucleotides and selection against an EcoK restriction site has allowed the construction of libraries of mutants for two separate windows, sites A and B. Mutant phenotypes can be easily assessed in vivo by a complementation test, and panels of mutants have been quantitatively tested in vitro. This allowed the rapid probing of structural requirements for each site. The two windows yielded markedly disparate results. Site B was much less stringent in its sequence requirements for significant function than Site A, and mutants with improved function were isolated at Site B alone. In addition, one Site B mutant with wild-type levels of activity showed enhanced stability to heat or a protein denaturant. We propose that short tracts with the characteristics of Site B constitute 'secondary' interaction sites which are more tolerant of sequence diversity. Random manipulation of such secondary sites is thus more likely to yield upmutations for standard or altered environments. Window mutagenesis can in principle be applied to any protein--protein or protein--ligand interaction.     

Nitrogen limitation induces expression of the avirulence gene avr9 in the tomato pathogen Cladosporium fulvum

The avirulence gene avr9 of the fungal tomato pathogen Cladosporium fulvum encodes a race-specific peptide elicitor that induces the hypersensitive response in tomato plants carrying the complementary resistance gene Cf9. The avr9 gene is not expressed under optimal growth conditions in vitro, but is highly expressed when the fungus grows inside the tomato leaf. In this paper we present evidence for the induction of avr9 gene expression in C. fulvum grown in vitro under conditions of nitrogen limitation. Only growth medium with very low amounts of nitrogen (nitrate, ammonium, glutamate or glutamine) induced the expression of avr9. Limitation of other macronutrients or the addition of plant factors did not induce the expression of avr9. The induced expression of avr9 is possibly mediated by a positive-acting nitrogen regulatory protein, homologous to the Neurospora crassa NIT2 protein, which induces the expression of many genes under conditions of nitrogen limitation. The avr9 promoter contains several putative NIT2 binding sites. The expression of avr9 during the infection process was explored cytologically using transformants of C. fulvum carrying an avr9 promoter-β-glucuronidase reporter gene fusion. The possibility that expression of avr9 in C. fulvum growing in planta is caused by nitrogen limitation in the apoplast of the tomato leaf is discussed.