Rapid impedance detection of salmonellas in confectionery using modified LICNR broth

A commercially available broth, with the addition of inhibitors, was used for the rapid impediometric detection of salmonellas in confectionery. Pre-enrichment in skimmed milk was followed by lysine-iron-cystine-neutral red broth in a Bactometer 123 system. Results were obtained 3d earlier than is possible with conventional microbiological tests. Some false positives were obtained predominantly with Citrobacter freundii but this problem is also frequently encountered with traditional methods. Organisms responsible for false positives may be isolated and identified more rapidly than is possible by conventional methods.     

Evaluation of an automated fluorescent antibody procedure for detection of Salmonella in foods and feeds.

A prototype automated system using fluorescent antibody (FA) was evaluated for rapid detection of salmonellae in foods. Samples were enriched in selenite cystine and tetrathionate broths. After incubation, both were transferred into fresh selenite cystine for a 4-h "post-enrichment" to dilute possible background fluorescence from product. These cultures were then analyzed automatically, and results were compared with those obtained by the methods of the Association of Official Analytical Chemists (AOAC). Initially, 167 samples of milk powder, dried yeast, and imported frog legs were examined. The AOAC and automated FA methods correlated well with all samples but frog legs. Difficulty with the latter was caused by procedural and mechanical problems coupled with high numbers of competing microorganisms in post-enrichment cultures. Modification of procedure and partial redesign of equipment corrected these difficulties, and excellent correlation was obtained with another 116 frog leg samples. All 89 AOAC-confirmed positives were also detected by the automated FA method, and there were only 4% false FA positives. The system shows potential for screening products for salmonellae; however, all positives should be confirmed by manual biochemical and serological methods.     

大规模酵母双杂交技术研究蛋白质相互作用的应用

简介了酵母双杂交技术原理, 总结了酵母双杂交技术大规模筛选蛋白质相互作用的基础、应用及存在的问题。因为大规模酵母双杂交技术结果有大量假阳性及假阴性问题, 因此, 有条件情况下有必要同时开展其他方法的大规模蛋白相互作用研究, 以构建规模更大可信度更高的蛋白质相互作用网络图。     

An improved protocol for the detection and rapid confirmation within 48 h of Salmonellas in confectionery products

A modified ornithine decarboxylase broth and a selenite cystine trimethlyamine oxide ribose medium were developed to improve selection and detection of Salmonellas. They were used with a third medium, lysine iron cystine neutral red broth (incubated conventionally) in a screen of 80 Salmonellas and 32 non-salmonellas which showed the combination of media to be specific and sensitive. Subsequent evaluation with 90 product samples (spiked and naturally contaminated) resulted in complete agreement by rapid and conventional methods. The detected wells in these experiments were also used to evaluate a latex slide agglutination test for Salmonellas. Carried out directly on the well contents, this was found to be a rapid, specific and sensitive test for confirmation of Salmonella presence. Further tests with 106 routine production samples gave complete agreement by both methods. Presumptive positives were obtained in <1.0–3·8% of the sample wells and subsequent modification to the Bactometer software has greatly reduced these figures in routine use. The method is recommended for Salmonella testing of foodstuffs with low background flora and high fat/low moisture content.     

Immunofluorescent Identification of Salmonella typhi During a Typhoid Outbreak

Immunofluorescence and conventional bacteriological methods were compared for their ability to detect Salmonella typhi in 134 fecal specimens from 105 individuals associated with an outbreak of typhoid fever. Smears prepared from untreated fecal material (direct method) and after a preliminary incubation in selenite F broth (delayed method) were tested with an anti-Vi serum conjugated with fluorescein isothiocyanate. The delayed method was more sensitive than the direct method in detecting S. typhi. The delayed method was positive in 40 of 41 patients positive by culture methods, but gave positive or questionable reactions in 11 presumably uninfected individuals. The fluorescent-antibody test employing a Vi conjugate is a satisfactory screening procedure for detecting S. typhi, but all positives must be confirmed bacteriologically.     

Isolation of Shigellae: VIII. Comparison of Xylose Lysine Deoxycholate Agar, Hektoen Enteric Agar, Salmonella-Shigella Agar, and Eosin Methylene Blue Agar with Stool Specimens

Two enrichment broths and four plating media were compared for efficiency of detection of enteric pathogens from 1,597 stool specimens. Of 170 salmonellae isolated from the composite of all methods, direct streaking yielded but 54%, whereas enrichment in gram-negative broth found 87% and Selenite-F broth 97%. By contrast, gram-negative broth produced 100% of the 17 shigellae, Selenite-F broth but 77%, and direct streaking only 59%. Thus, enrichment methods produced almost twice the number of both pathogens as direct streaking. Comparison of the plating media revealed xylose lysine deoxycholate agar (XLD) and Hektoen enteric agar to be equal in their abilities to find both pathogens. Both were moderately better than Salmonella-Shigella agar and markedly superior to eosin methylene blue agar. XLD fround 83% of salmonellae produced by the composite of four media and 90% of the shigellae. Hektoen enteric agar found 80% of both. Salmonella-Shigella agar detected 74 and 68%, respectively, and eosin methylene blue agar only 42 and 63%. The numbers of false positives accruing to each medium, however, showed Hektoen enteric and Salmonella-Shigella agars to produce more than twice as many false-positive plates as XLD. Similarly, Selenite-F broth resulted in many more false-positives for all plating media than did gram-negative broth. Consequently, the index of validity, which equates successful isolation of pathogens with total pickings, favored XLD and gram-negative broth as the media of choice, with direct streaking the poorest method by all counts.     

Fluorescent-Antibody Technique in Detection of Salmonellae in Animal Feed and Feed Ingredients

Comparative studies of fluorescent antibody procedure and a cultural method for the detection of Salmonella were made on 1,013 feed and feed-ingredient samples. The agreement between the two methods was 92.1%. There were more false positives (5.7%) than false negatives (2.2%). Of the 22 false negatives, 15 (68%) were obtained on meat meal. Of the total number of samples, 37% were meat meal. An additional study of 73 samples of meat meal indicated that correlation between methods was better than correlation between samples.     

Accurate decisions in an uncertain world: collective cognition increases true positives while decreasing false positives

In a wide range of contexts, including predator avoidance, medical decision-making and security screening, decision accuracy is fundamentally constrained by the trade-off between true and false positives. Increased true positives are possible only at the cost of increased false positives; conversely, decreased false positives are associated with decreased true positives. We use an integrated theoretical and experimental approach to show that a group of decision-makers can overcome this basic limitation. Using a mathematical model, we show that a simple quorum decision rule enables individuals in groups to simultaneously increase true positives and decrease false positives. The results from a predator-detection experiment that we performed with humans are in line with these predictions: (i) after observing the choices of the other group members, individuals both increase true positives and decrease false positives, (ii) this effect gets stronger as group size increases, (iii) individuals use a quorum threshold set between the average true- and false-positive rates of the other group members, and (iv) individuals adjust their quorum adaptively to the performance of the group. Our results have broad implications for our understanding of the ecology and evolution of group-living animals and lend themselves for applications in the human domain such as the design of improved screening methods in medical, forensic, security and business applications.     

Comparison of the Recovery of Escherichia coli from Frozen Foods and Nutmeats by Confirmatory Incubation in EC Medium at 44.5 and 45.5 C

The productivity of confirmatory EC broth for the isolation of fecal Escherichia coli was determined at 44.5 and 45.5 C. A variety of frozen pre-cooked foods and an assortment of nutmeats were examined after primary incubation in Lauryl Sulfate Tryptose (LST) broth. In 85.3% of the cases, the parallel tubes of EC broth incubated for 24 hr at 44.5 and 45.5 C gave rise to identical E. coli responses of positive, false positive, and negative. The remaining 14.7% of the reactions represent the qualitative difference between the two temperatures. The EC test at 45.5 C was more specific for E. coli, since two- to threefold fewer false positives were produced at this temperature than at 44.5 C. However, fecal E. coli recoveries were slightly higher (4%) at the lower temperature. Incubating the EC tubes from the interval of 24 to 48 hr gave rise to an additional 4.3% of E. coli recovery, but this was accompanied by an excessive production of false positives (75.9%), representing a 3.5-fold decrease in specificity. It is recommended that, in the confirmatory use of EC broth in the examination of frozen foods and nutmeats for the recovery of fecal E. coli, the test be made at 45.5 C in a water bath and limited to 24 hr of incubation only, to insure optimal specificity. During the study, a “fixed” productivity ratio was noted; E. coli⁺/LST⁺ equaled approximately one-fourth or 25%. The significance of this ratio is discussed.     

Comparing three different methods to detect selective loci using dominant markers

We carried out a simulation study to compare the efficiency of three alternative programs (dfdist , detseld and bayescan ) to detect loci under directional selection from genome‐wide scans using dominant markers. We also evaluated the efficiency of correcting for multiple testing those methods that use a classical probability approach. Under a wide range of scenarios, we conclude that bayescan appears to be more efficient than the other methods, detecting a usually high percentage of true selective loci as well as less than 1% of outliers (false positives) under a fully neutral model. In addition, the percentage of outliers detected by this software is always correlated with the true percentage of selective loci in the genome. Our results show, nevertheless, that false positives are common even with a combination of methods and multitest correction, suggesting that conclusions obtained from this approach should be taken with extreme caution.     

Immunomagnetic separation as an alternative to enrichment broths for Salmonella detection

One hundred and twenty foodstuffs were tested for the enrichment of Salmonella species by immunoseparation. The foodstuffs covered six groups: raw chicken, prawns, skimmed milk powder, herbs and spices, cocoa powder and animal feed. Half of the food samples were spiked with one Salmonella species: Salm. ealing, Salm. enteritidis, Salm. give, Salm. typhimurium or Salm. virchow . Comparison of Salmonella recovery with standard methods (selenite cystine broth, tetrathionate broth and Rappaport-Vassiliadis broth) was carried out. Immunoseparation gave similar numbers of true positives to the standard enrichment methods in a short time period. Only immunoseparation isolated Salmonella species from spiked garlic granules demonstrating the possible recovery of sublethally injured cells.     

A complete protocol using conductance for rapid detection of salmonellas in confectionery materials

Increased confidence in conductimetric detection of salmonellas was achieved by combining a bacteriophage-based test with use of a selenite cystine trimethylamine oxide dulcitol medium and a modified lysine decarboxylase broth. All 81 Salmonella isolates tested were detected and few of the 39 non-salmonellas gave false positives. Results from the screening of 43 inoculated product samples further support the use of this simple, rapid method for routine salmonella testing in the food industry.     

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity,Prioritization and Specificity

Identification of functional sets of genes associated with conditions of interest from omics data was first reported in 1999, and since, a plethora of enrichment methods were published for systematic analysis of gene sets collections including Gene Ontology and biological pathways. Despite their widespread usage in reducing the complexity of omics experiment results, their performance is poorly understood. Leveraging the existence of disease specific gene sets in KEGG and Metacore® databases, we compared the performance of sixteen methods under relaxed assumptions while using 42 real datasets (over 1,400 samples). Most of the methods ranked high the gene sets designed for specific diseases whenever samples from affected individuals were compared against controls via microarrays. The top methods for gene set prioritization were different from the top ones in terms of sensitivity, and four of the sixteen methods had large false positives rates assessed by permuting the phenotype of the samples. The best overall methods among those that generated reasonably low false positive rates, when permuting phenotypes, were PLAGE, GLOBALTEST, and PADOG. The best method in the category that generated higher than expected false positives was MRGSE.     

Minimizing false positives in kinase virtual screens

In spite of recent improvements in docking and scoring methods, high false-positive rates remain a common issue in structure-based virtual screening. In this study, the distinctive features of false positives in kinase virtual screens were investigated. A series of retrospective virtual screens on kinase targets was performed on specifically designed test sets, each combining true ligands and experimentally confirmed inactive compounds. A systematic analysis of the docking poses generated for the top-ranking compounds highlighted key aspects differentiating true hits from false positives. The most recurring feature in the poses of false positives was the absence of certain key interactions known to be required for kinase binding. A systematic analysis of 444 crystal structures of ligand-bound kinases showed that at least two hydrogen bonds between the ligand and the backbone protein atoms in the kinase hinge region are present in 90% of the complexes, with very little variability across targets. Closer inspection showed that when the two hydrogen bonds are present, one of three preferred hinge-binding motifs is involved in 96.5% of the cases. Less than 10% of the false positives satisfied these two criteria in the minimized docking poses generated by our standard protocol. Ligand conformational artifacts were also shown to contribute to the occurrence of false positives in a number of cases. Application of this knowledge in the form of docking constraints and post-processing filters provided consistent improvements in virtual screening performance on all systems. The false-positive rates were significantly reduced and the enrichment factors increased by an average of twofold. On the basis of these results, a generalized two-step protocol for virtual screening on kinase targets is suggested.     

Isolation of vero cytotoxin-producing Escherichia coli O157 from wild birds

In a survey of wild birds (mainly gulls), 0.9% of the bacterial isolates from faecal samples at an urban landfill site and 2.9% of bacterial isolates from faecal samples on intertidal sediments in Morecambe Bay were Vero cytotoxin-producing Escherichia coli O157. Isolation procedures employing commonly used cultural methods were hindered by the selection of a large number of false positives. The only procedure which resulted in the isolation of E. coli O157 from bird faecal samples was: enrichment (18 h) in a selective tryptone soya broth followed by filtration using hydrophobic grid membranes and growth on Chromagar O157. The majority of isolates selected as potential E. coli O157 by characteristic growth on Chromagar O157 could be eliminated by subsequent growth on CT-SMAC or CR-SMAC. This second identification (characterization) stage reduced the number of potential E. coli O157 requiring further confirmation by typing methods (serotype and Vero cytotoxin) by more than 70%.     

What are the baselines for protein fold recognition?

MOTIVATION: What constitutes a baseline level of success for protein fold recognition methods? As fold recognition benchmarks are often presented without any thought to the results that might be expected from a purely random set of predictions, an analysis of fold recognition baselines is long overdue. Given varying amounts of basic information about a protein-ranging from the length of the sequence to a knowledge of its secondary structure-to what extent can the fold be determined by intelligent guesswork? Can simple methods that make use of secondary structure information assign folds more accurately than purely random methods and could these methods be used to construct viable hierarchical classifications? EXPERIMENTS PERFORMED: A number of rapid automatic methods which score similarities between protein domains were devised and tested. These methods ranged from those that incorporated no secondary structure information, such as measuring absolute differences in sequence lengths, to more complex alignments of secondary structure elements. Each method was assessed for accuracy by comparison with the Class Architecture Topology Homology (CATH) classification. Methods were rated against both a random baseline fold assignment method as a lower control and FSSP as an upper control. Similarity trees were constructed in order to evaluate the accuracy of optimum methods at producing a classification of structure. RESULTS: Using a rigorous comparison of methods with CATH, the random fold assignment method set a lower baseline of 11% true positives allowing for 3% false positives and FSSP set an upper benchmark of 47% true positives at 3% false positives. The optimum secondary structure alignment method used here achieved 27% true positives at 3% false positives. Using a less rigorous Critical Assessment of Structure Prediction (CASP)-like sensitivity measurement the random assignment achieved 6%, FSSP-59% and the optimum secondary structure alignment method-32%. Similarity trees produced by the optimum method illustrate that these methods cannot be used alone to produce a viable protein structural classification system. CONCLUSIONS: Simple methods that use perfect secondary structure information to assign folds cannot produce an accurate protein taxonomy, however they do provide useful baselines for fold recognition. In terms of a typical CASP assessment our results suggest that approximately 6% of targets with folds in the databases could be assigned correctly by randomly guessing, and as many as 32% could be recognised by trivial secondary structure comparison methods, given knowledge of their correct secondary structures.     

Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites.

The reliabilities of parsimony-based and likelihood-based methods for inferring positive selection at single amino acid sites were studied using the nucleotide sequences of human leukocyte antigen (HLA) genes, in which positive selection is known to be operating at the antigen recognition site. The results indicate that the inference by parsimony-based methods is robust to the use of different evolutionary models and generally more reliable than that by likelihood-based methods. In contrast, the results obtained by likelihood-based methods depend on the models and on the initial parameter values used. It is sometimes difficult to obtain the maximum likelihood estimates of parameters for a given model, and the results obtained may be false negatives or false positives depending on the initial parameter values. It is therefore preferable to use parsimony-based methods as long as the number of sequences is relatively large and the branch lengths of the phylogenetic tree are relatively small.     

Using Gaussian process with test rejection to detect T-cell epitopes in pathogen genomes

A major challenge in the development of peptide-based vaccines is finding the right immunogenic element, with efficient and long-lasting immunization effects, from large potential targets encoded by pathogen genomes. Computer models are convenient tools for scanning pathogen genomes to preselect candidate immunogenic peptides for experimental validation. Current methods predict many false positives resulting from a low prevalence of true positives. We develop a test reject method based on the prediction uncertainty estimates determined by Gaussian process regression. This method filters false positives among predicted epitopes from a pathogen genome. The performance of stand-alone Gaussian process regression is compared to other state-of-the-art methods using cross validation on 11 benchmark data sets. The results show that the Gaussian process method has the same accuracy as the top performing algorithms. The combination of Gaussian process regression with the proposed test reject method is used to detect true epitopes from the Vaccinia virus genome. The test rejection increases the prediction accuracy by reducing the number of false positives without sacrificing the method's sensitivity. We show that the Gaussian process in combination with test rejection is an effective method for prediction of T-cell epitopes in large and diverse pathogen genomes, where false positives are of concern.     

"Patchy-tachy" leads to false positives for recombination

Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one such example, which we call "patchy-tachy" (PT), where different partitions of sequences evolve at different rates, that leads to an excess of false positives for recombination inferred by indirect tests. To explore this phenomena, we characterized the false positive rates of six widely used indirect tests for recombination using simulations of general models for mtDNA evolution with PT but without recombination. All tests produced 30-99% false positives for recombination, although the conditions that produced the maximal level of false positives differed between the tests. To evaluate the degree to which conditions that exacerbate false positives are found in published sequence data, we turned to 20 animal mtDNA data sets in which recombination is suggested by indirect tests. Using a model where different regions of the sequences were free to evolve at different rates in different lineages, we demonstrated that PT is prevalent in many data sets in which recombination was previously inferred using indirect tests. Taken together, our results argue that PT without recombination is a viable alternative explanation for detection of widespread recombination in animal mtDNA using indirect tests.     

THE INCIDENCE OF BACTERIUM COLI IN FARM WATER SUPPLIES

SUMMARY: Farm water supplies giving 37° positives in MacConkey's broth within 24 hr. had a much higher incidence of presumptive Bact. coli type I than those which gave 37° positives during the second day of incubation only; presumptive Bact. coli reactions were obtained with 85% of the 7,522 tubes positive in 24 hr. compared with 23% for the 7,593 tubes showing positive reactions during the second day at 37°.