Current concepts of the biology of bacteria in genus Campylobacter and their role in human pathology

An analytical review of literature on the problem of biological properties of campylobacteria is presented. Taxonomic characteristics of campylobacteriosis agents are given. Morphological and cultural peculiarities of campylobacteria are considered, their ability to form coccal forms is emphasized. Peculiar attention is paid to serotype and biotype characteristics of bacteria of the Campylobacter genus. It is shown expedient to develop the home schemes of sero- and biotypization. Data on biological properties of "new" agents of human campylobacteriosis (Campylobacter cinaedi, C. hypointestinalis, C. upsaliensis) are generalized for the first time in home literature. A conclusion is made that the study of biological properties of campylobacteria strains circulating in the Ukrainian territory as well as the development of efficient prophylactic and antiepidemic measures on this basis are urgent now.     

Two-laboratory collaborative study on identification of mycobacteria: molecular versus phenotypic methods

Previous studies have indicated that the conventional tests used for the identification of mycobacteria may (i) frequently result in erroneous identification and (ii) underestimate the diversity within the genus Mycobacterium. To address this issue in a more systematic fashion, a study comparing phenotypic and molecular methods for the identification of mycobacteria was initiated. Focus was given to isolates which were difficult to identify to species level and which yielded inconclusive results by conventional tests performed under day-to-day routine laboratory conditions. Traditional methods included growth rate, colonial morphology, pigmentation, biochemical profiles, and gas-liquid chromatography of short-chain fatty acids. Molecular identification was done by PCR-mediated partial sequence analysis of the gene encoding the 16S rRNA. A total of 34 isolates was included in this study; 13 of the isolates corresponded to established species, and 21 isolates corresponded to previously uncharacterized taxa. For five isolates, phenotypic and molecular analyses gave identical results. For five isolates, minor discrepancies were present; four isolates remained unidentified after biochemical testing. For 20 isolates, major discrepancies between traditional and molecular typing methods were observed. Retrospective analysis of the data revealed that the discrepant results were without exception due to erroneous biochemical test results or interpretations. In particular, phenotypic identification schemes were compromised with regard to the recognition of previously undescribed taxa. We conclude that molecular typing by 16S rRNA sequence determination is not only more rapid (12 to 36 h versus 4 to 8 weeks) but also more accurate than traditional typing.     

Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data

Evolutionary biologists have long sought a way to determine whether a phenotypic difference between two taxa was caused by natural selection or random genetic drift. Here I argue that data from quantitative trait locus (QTL) analyses can be used to test the null hypothesis of neutral phenotypic evolution. I propose a sign test that compares the observed number of plus and minus alleles in the "high line" with that expected under neutrality, conditioning on the known phenotypic difference between the taxa. Rejection of the null hypothesis implies a role for directional natural selection. This test is applicable to any character in any organism in which QTL analysis can be performed.     

The effect of differentiation inducers on the integrin expression of K562 erythroleukemia cells

The DNA sequences of the recA gene from 25 strains of bacteria are known. The evolution of these recA gene sequences, and of the derived RecA protein sequences, is examined, with special reference to the effect of variations in genomic G + C content. From the aligned RecA protein sequences, phylogenetic trees have been drawn using both distance matrix and maximum parsimony methods. There is a broad concordance between these trees and those derived from other data (largely 16S ribosomal RNA sequences). There is a fair degree of certainty in the relationships among the "Purple" or Proteobacteria, but the branching pattern between higher taxa within the eubacteria cannot be reliably resolved with these data.     

Occurrence of multiple genomovars of Burkholderia cepacia in cystic fibrosis patients and proposal of Burkholderia multivorans sp. nov

We performed an integrated genotypic and phenotypic analysis of 128 strains of the genera Burkholderia, Ralstonia, and Pseudomonas in order to study the taxonomic structure of Burkholderia cepacia and its relationships with other Burkholderia species. Our data show that presumed B. cepacia strains isolated from cystic fibrosis patients belong to at least five distinct genomic species, one of which was identified as Burkholderia vietnamiensis. This group of five phenotypically similar species is referred to as the B. cepacia complex. The name Burkholderia multivorans is proposed for one of these genomic species, which was formerly referred to as B. cepacia genomovar II; the remaining B. cepacia groups are referred to as genomovars I, III, and IV, pending additional differential phenotypic tests. The role and pathogenic potential of each of these taxa, particularly in view of the potentially fatal infections in cystic fibrosis patients, need further evaluation. The data presented also demonstrate that Pseudomonas glathei and Pseudomonas pyrrocinia should be reclassified as Burkholderia species.     

A functional role for osteopontin in experimental crescentic glomerulonephritis in the rat

Fifty two isolates of atypical Aeromonas salmonicida, recovered from a wide range of hosts and geographical locations, were heterogeneous in terms of molecular and phenotypic characteristics, and represented taxa which could not be accommodated by the current classification of four subspecies. Generally, there was incongruence between the molecular (PCR, RAPD and ribotyping) and phenotypic methods in terms of cluster membership. By PCR, 6 groups were described of which Group 1 encompassed 12 isolates including the type strain of A. salmonicida subsp. smithia. Group 2 accommodated 23 isolates including the reference cultures of subspecies achromogenes and masoucida. The named culture of Haemophilus piscium was recovered in Group 6. By ribotyping and RAPD, the reference cultures were recovered in separate groups. All methods pointed to the uniqueness of subspecies smithia. Most isolates contained 2-6 plasmids, of 2.3 to 150 kb in length. Nevertheless, all isolates possessed certain key characteristics, including Gram-negativity, and the absence of motility.     

A comparison of power to detect a QTL in sib-pair data using multivariate phenotypes, mean phenotypes, and factor scores

The power to detect a quantitative trait locus (QTL) in sib-pair data is investigated. We assume that we have at our disposal 3 or 4 related phenotypic measures in a sample of sib-pairs. Individual differences in these phenotypes are due to a common QTL and specific (i.e., unique to each phenotype) nonshared environmental and specific polygenic additive effects. In addition, models are considered that include common nonshared environmental effects and/or common polygenic additive effects. We calculate the power to detect the QTL in a genetic covariance structure analysis of the multivariate data, of the mean phenotypic data, and of factor scores. The use of factor scores is shown to be universally more powerful than the use of multivariate or mean phenotypic data. We also investigate the effect of using a single sample of sib-pairs to both calculate the factor score regression matrix and to carry out the QTL analysis. The use of a single sample to both these ends results in a loss of power compared to the theoretical, expected power. The gain in power attributable to the use of factor scores, however, outweighs this observed loss in power. The advantages of using factor scores in selecting sib-pairs are discussed.     

Diversity and prevalence of Arcobacter spp. in broiler chickens

Ninety-nine strains of Arcobacter spp., isolated from 10 chicken carcasses purchased from a supermarket and 15 chicken carcasses collected from a poultry abattoir, were speciated using a variety of phenotypic identification methods. All were tested using API Campy test strips and the 16-test (Preston) identification scheme developed for campylobacters. Fifty strains were selected for examination using a more comprehensive probabilistic identification scheme, and the identity of representative strains confirmed by protein profiling using SDS-PAGE. All 25 carcasses yielded Arcobacter butzleri. Three supermarket and 10 abattoir carcasses also carried A. cryaerophilus, and two abattoir carcasses carried A. skirrowii. The API Campy scheme proved unsatisfactory for identifying these strains: only 20 of 99 strains were accurately identified, all of which were A. cryaerophilus, the only Arcobacter sp. included in the database. Moreover, 76 of 99 strains were misidentified. The 16-test scheme identified all the arcobacter strains as A. cryaerophilus, since neither A. butzleri nor A. skirrowii had been described when the scheme was developed. The computer-assisted probabilistic scheme succeeded in identifying all but one strain, the identity of which was clarified by the use of SDS-PAGE. To our knowledge this is the first time that arcobacters other than A. butzleri have been reported in poultry meat or any other food of animal origin. Their high prevalence in poultry products may be of significance to public health.     

Uncertain Dynamical Systems in the Medium-Frequency Range

This paper presents a novel probabilistic model of random uncertainties for dynamical system in the medium-frequency (MF) range. This approach combines a nonparametric probabilistic model of random uncertainties for the reduced matrix models in structural dynamics with a reduced matrix model adapted to the MF range. The theory is presented and the random energy matrix relating to a given MF band, its random trace, and its random eigenvalues are studied. A numerical example is presented allowing convergence properties and stability of random responses with respect to the bandwidth to be analyzed.     

Unified Approach to Probabilistic and Possibilistic Analysis of Uncertain Systems

Various methods exist for assessing the safety of a structural or mechanical system that has uncertain parameters. These methods are either statistical (probabilistic), in which case the probability of failure is sought, or deterministic (possibilistic), in which case bounds on the response are sought. Well-known statistical methods include the first-order reliability method (FORM) and the second-order reliability method (SORM), while deterministic methods include interval analysis, convex modeling, and fuzzy set theory (although the categorization of the latter approach as a deterministic method is debatable). The development of probabilistic and possibilistic methods has tended to occur independently, with specialized algorithms being developed for the implementation of each technique. It is shown here that a wide range of probabilistic and possibilistic methods can be encompassed by a single mathematical algorithm, so that, for example, existing codes for FORM and SORM can potentially be employed for other methods, thus allowing the designer to readily choose the method most suited to the available data. A second common algorithm is also derived, and the analysis is illustrated by application to a simple system composed of N structural components in series.     

Probabilistic Estimating: Mathematics and Applications

In response to the increased risk levels found in today's projects, project participants are attempting to quantify project cost risk. Various detailed and conceptual estimating formats are reviewed and a number of probabilistic estimating methods are introduced. Particular attention is given to the process of matching a suitable probabilistic estimating technique to a specific estimating format. To select an appropriate probabilistic method, an estimator must consider data availability, existing correlations, output data requirements, the form of the, estimating model, and the number of cost elements contained in the model. Existing obstacles to more realistic probabilistic cost estimates are reviewed.     

Genetic tagging of humpback whales

The ability to recognize individual animals has substantially increased our knowledge of the biology and behaviour of many taxa. However, not all species lend themselves to this approach, either because of insufficient phenotypic variation or because tag attachment is not feasible. The use of genetic markers ('tags') represents a viable alternative to traditional methods of individual recognition, as they are permanent and exist in all individuals. We tested the use of genetic markers as the primary means of identifying individuals in a study of humpback whales in the North Atlantic Ocean. Analysis of six microsatellite loci among 3,060 skin samples collected throughout this ocean allowed the unequivocal identification of individuals. Analysis of 692 'recaptures', identified by their genotype, revealed individual local and migratory movements of up to 10,000 km, limited exchange among summer feeding grounds, and mixing in winter breeding areas, and also allowed the first estimates of animal abundance based solely on genotypic data. Our study demonstrates that genetic tagging is not only feasible, but generates data (for example, on sex) that can be valuable when interpreting the results of tagging experiments.     

Validation and Application of Empirical Liquefaction Models

Empirical liquefaction models (ELMs) are the standard approach for predicting the occurrence of soil liquefaction. These models are typically based on in situ index tests, such as the standard penetration test (SPT) and cone penetration test (CPT), and are broadly classified as deterministic and probabilistic models. No objective and quantitative comparison of these models have been published. Similarly, no rigorous procedure has been published for choosing the threshold required for probabilistic models. This paper provides (1) a quantitative comparison of the predictive performance of ELMs; (2) a reproducible method for choosing the threshold that is needed to apply the probabilistic ELMs; and (3) an alternative deterministic and probabilistic ELM based on the machine learning algorithm, known as support vector machine (SVM). Deterministic and probabilistic ELMs have been developed for SPT and CPT data. For deterministic ELMs, we compare the “simplified procedure,” the Bayesian updating method, and the SVM models for both SPT and CPT data. For probabilistic ELMs, we compare the Bayesian updating method with the SVM models. We compare these different approaches within a quantitative validation framework. This framework includes validation metrics developed within the statistics and artificial intelligence fields that are not common in the geotechnical literature. We incorporate estimated costs associated with risk as well as with risk mitigation. We conclude that (1) the best performing ELM depends on the associated costs; (2) the unique costs associated with an individual project directly determine the optimal threshold for the probabilistic ELMs; and (3) the more recent ELMs only marginally improve prediction accuracy; thus, efforts should focus on improving data collection.     

Advances in statistical methods to map quantitative trait loci in outbred populations

Statistical methods to map quantitative trait loci (QTL) in outbred populations are reviewed, extensions and applications to human and plant genetic data are indicated, and areas for further research are identified. Simple and computationally inexpensive methods include (multiple) linear regression of phenotype on marker genotypes and regression of squared phenotypic differences among relative pairs on estimated proportions of identity-by-descent at a locus. These methods are less suited for genetic parameter estimation in outbred populations but allow the determination of test statistic distributions via simulation or data permutation; however, further inferences including confidence intervals of QTL location require the use of Monte Carlo or bootstrap sampling techniques. A method which is intermediate in computational requirements is residual maximum likelihood (REML) with a covariance matrix of random QTL effects conditional on information from multiple linked markers. Testing for the number of QTLs on a chromosome is difficult in a classical framework. The computationally most demanding methods are maximum likelihood and Bayesian analysis, which take account of the distribution of multilocus marker-QTL genotypes on a pedigree and permit investigators to fit different models of variation at the QTL. The Bayesian analysis includes the number of QTLs on a chromosome as an unknown.     

Isolation and identification of Helicobacter spp. from canine and feline gastric mucosa

It is known that virtually all healthy adult dogs and cats harbor spiral helicobacters in their gastric mucosa. Three species, Helicobacter felis, Helicobacter bizzozeronii, and Helicobacter salomonis have been isolated in vitro from the gastric mucosa of these animals. The aims of this study were to evaluate the efficacy of an isolation method for canine and feline gastric helicobacters that has been developed at the University of Helsinki; to estimate the prevalence and distribution of these taxa in the samples examined; and to assess the efficacy and validity of an extensive set of standardized conventional phenotypic tests, whole-cell protein profiling, and ultrastructural analysis in identifying the different species isolated from canine and feline gastric mucosa. We cultured 95 and 22 gastric mucosal biopsies from dogs and cats, respectively. Twenty-one H. bizzozeronii strains, 8 H. felis strains, 8 H. salomonis strains, 3 mixed cultures, 2 "Flexispira rappini"-like organisms, and 3 as yet uncharacterized strains were isolated from the dogs, and 3 H. felis strains were isolated from the cats. The methods used here yielded Helicobacter isolation rates of 51% from dogs and 13.6% from cats, which exceed those reported previously. The main difficulties were primary isolation, mixed cultures, and identification to the species level. In the species identification, a detailed morphological examination was found to yield important phenotypic characteristics. A large panel of biochemical and tolerance tests did not clearly differentiate the closely related species H. bizzozeronii, H. felis, and H. salomonis. Highly standardized whole-cell protein profiling was shown to be an excellent method for species identification. Improvements in culture conditions for these bacteria are still needed, especially for cats. A genetic identification method not requiring culture is needed for future studies of these very fastidious helicobacters, as the clinical significance and ecology of these species within the gastric mucosa of the domestic carnivores remain largely unknown.     

CPT-Based Probabilistic and Deterministic Assessment of In Situ Seismic Soil Liquefaction Potential

This paper presents a complete methodology for both probabilistic and deterministic assessment of seismic soil liquefaction triggering potential based on the cone penetration test (CPT). A comprehensive worldwide set of CPT-based liquefaction field case histories were compiled and back analyzed, and the data then used to develop probabilistic triggering correlations. Issues investigated in this study include improved normalization of CPT resistance measurements for the influence of effective overburden stress, and adjustment to CPT tip resistance for the potential influence of “thin” liquefiable layers. The effects of soil type and soil character (i.e., “fines” adjustment) for the new correlations are based on a combination of CPT tip and sleeve resistance. To quantify probability for performance-based engineering applications, Bayesian “regression” methods were used, and the uncertainties of all variables comprising both the seismic demand and the liquefaction resistance were estimated and included in the analysis. The resulting correlations were developed using a Bayesian framework and are presented in both probabilistic and deterministic formats. The results are compared to previous probabilistic and deterministic correlations.     

The prevalence of campylobacters and arcobacters in broiler chickens

Chicken carcasses from a supermarket and from a poultry abattoir were examined using methods designed to isolate as many strains of campylobacters and related organisms as possible. Strains of arcobacter, but no campylobacters, were isolated from every carcass after enrichment. Campylobacter jejuni subsp. jejuni was isolated from all carcasses examined by direct plating and other Campylobacter-like strains were isolated from nine out of 15 abattoir carcasses by direct plating but not after enrichment. Only the Camp. jejuni subsp. jejuni strains could be identified to species level using a readily available identification scheme and/or a commercial identification kit. Examination of caecal contents from the 15 abattoir poultry yielded Camp. jejuni subsp. jejuni and Campylobacter-like strains from 15 and eight by direct plating, and from six and nine after enrichment, respectively. Four sites in the intestine of the abattoir birds (60 samples) were examined for arcobacters and only one strain was isolated. This indicates that arcobacters are probably not normal inhabitants of the poultry intestine. Poultry is a rich source of other campylobacteria besides the thermophilic Campylobacter spp.     

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by replacing both taxa by this node. Moreover, BIONJ uses a simple first-order model of the variances and covariances of evolutionary distance estimates. This model is well adapted when these estimates are obtained from aligned sequences. At each step it permits the selection, from the class of admissible reductions, of the reduction which minimizes the variance of the new distance matrix. In this way, we obtain better estimates to choose the pair of taxa to be agglomerated during the next steps. Moreover, in comparison with NJ's estimates, these estimates become better and better as the algorithm proceeds. BIONJ retains the good properties of NJ--especially its low run time. Computer simulations have been performed with 12-taxon model trees to determine BIONJ's efficiency. When the substitution rates are low (maximum pairwise divergence approximately 0.1 substitutions per site) or when they are constant among lineages, BIONJ is only slightly better than NJ. When the substitution rates are higher and vary among lineages,BIONJ clearly has better topological accuracy. In the latter case, for the model trees and the conditions of evolution tested, the topological error reduction is on the average around 20%. With highly-varying-rate trees and with high substitution rates (maximum pairwise divergence approximately 1.0 substitutions per site), the error reduction may even rise above 50%, while the probability of finding the correct tree may be augmented by as much as 15%.