Exploration of multivariate analysis in microbial coding sequence modeling

ABSTRACT: BACKGROUND: Gene finding is a complicated procedure that encapsulates algorithms for coding sequence modeling, identification of promoter regions, issues concerning overlapping genes and more. In the present study we focus on coding sequence modeling algorithms; that is, algorithms for identification and prediction of the actual coding sequences from genomic DNA. In this respect, we promote a novel multivariate method known as Canonical Powered Partial Least Squares (CPPLS) as an alternative to the commonly used Interpolated Markov model (IMM). Comparisons between the methods were performed on DNA, codon and protein sequences with highly conserved genes taken from several species with different genomic properties. RESULTS: The multivariate CPPLS approach classified coding sequence substantially better than the commonly used IMM on the same set of sequences. We also found that the use of CPPLS with codon representation gave significantly better classification results than both IMM with protein (p < 0.001) and with DNA (p < 0.001). Further, although the mean performance was similar, the variation of CPPLS performance on codon representation was significantly smaller than for IMM (p < 0.001). CONCLUSIONS: The performance of coding sequence modeling can be substantially improved by using an algorithm based on the multivariate CPPLS method applied to codon or DNA frequencies.     

Influence on motility of Escherichia coli and Salmonella typhimurium by a naturally occurring conjugative plasmid.

In a collection of 45 R-plasmids, one was found to be associated with loss of motility of its Escherichia coli K-12 and Salmonella typhimurium host bacteria when tested in conventional motility agar. Genetic experiments, as well as analyses of deoxyribonucleic acid, showed that inhibition of motility was caused by a conjugative plasmid that was separate from the R-plasmid. This second plasmid, named pUM5, was fi- and mediated the same type of sex pilus (F-like) as the accompanying R-plasmid but lacked resistance determinants. Preliminary studies indicated that bacterial cells carrying the motility inhibition plasmid pUM5 were still equipped with flagella. The mechanism by which flagellar action is disturbed by the plasmid is presently not known.     

Date of smolt migration depends on body-size but not age in wild sea-run brown trout

Wild, one- and two-summers-old sea-trout parr in a small stream, were tagged with PIT-tags in late autumn and recaptured in a smolt trap during the following spring. One-summer-old smolts migrated later than older ones and were smaller at migration. ANCOVA indicated that migration date was negatively related to body length at tagging, but we found no significant effect of age or condition factor at tagging on this relation. The difference in timing between the age-classes was thus an effect of body size rather than age.     

Dissecting Antibodies with Regards to Linear and Conformational Epitopes

An important issue for the performance and specificity of an antibody is the nature of the binding to its protein target, including if the recognition involves linear or conformational epitopes. Here, we dissect polyclonal sera by creating epitope-specific antibody fractions using a combination of epitope mapping and an affinity capture approach involving both synthesized peptides and recombinant protein fragments. This allowed us to study the relative amounts of antibodies to linear and conformational epitopes in the polyclonal sera as well as the ability of each antibody-fraction to detect its target protein in Western blot assays. The majority of the analyzed polyclonal sera were found to have most of the target-specific antibodies directed towards linear epitopes and these were in many cases giving Western blot bands of correct molecular weight. In contrast, many of the antibodies towards conformational epitopes did not bind their target proteins in the Western blot assays. The results from this work have given us insights regarding the nature of the antibody response generated by immunization with recombinant protein fragments and has demonstrated the advantage of using antibodies recognizing linear epitopes for immunoassay involving wholly or partially denatured protein targets.     

Product profiles in enzymic and non-enzymic oxidations of the lignin model compound erythro-1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1,3-propanediol

The erythro form of the lignin model compound 1-(3,4-dimethoxyphenyl)-2-(2-methoxyphenoxy)-1,3-propanediol (1) was oxidized with laccase/ABTS, lead(IV) tetraacetate (LTA), lignin peroxidase/H₂O₂, cerium(IV) ammonium nitrate (CAN) and Fenton's reagent. The product profiles obtained with the different oxidants were compared after separation, identification and quantification of the products using HPLC, UV-diode array detector and electrospray ionization mass spectrometry in positive ionization mode. The oxidants generated different product profiles that reflected their different properties. Oxidation with laccase/ABTS resulted almost exclusively in formation of 1-(3,4-dimethoxyphenyl)-3-hydroxy-2-(2-methoxyphenoxy)-1-propanone (2). Oxidation with LTA resulted in more 3,4-dimethoxybenzaldehyde (3) than ketone 2. Lignin peroxidase and CAN gave similar product profiles and aldehyde 3 was the predominant product (only small amounts of ketone 2 were formed). Oxidation with Fenton's reagent resulted in the formation of more aldehyde 3 than ketone 2 but the yields were very low. CAN served as an excellent model for the lignin peroxidase-catalyzed oxidation, while the laccase-mediator system, LTA and Fenton's reagent provided distinctly different product profiles. Erythro-1-(3,4-dimethoxyphenyl)-1,2,3-propanetriol was present among the products obtained on oxidation with LTA, lignin peroxidase, CAN and Fenton's reagent. The differences in redox potential between the oxidants afford an explanation of the diverse product patterns but other factors may also be of importance. The reactions leading to cleavage of the β-ether bond with formation of 1-(3,4-dimethoxyphenyl)-1,2,3-propanetriol (veratrylglycerol) were found to proceed without affecting the configuration at the β-carbon atom.     

Feeding on Profitable and Unprofitable Prey: Comparing Behaviour of Growth-Enhanced Transgenic and Normal Coho Salmon (Oncorhynchus kisutch)

We compared the performance of normal and growth hormone‐transgenic coho salmon feeding on surface drifting edible and inedible novel prey items in various social environments. With an inherently higher appetite, we predicted that transgenic fish would be more willing to feed on novel prey, and that visual company with another fish would enhance this difference further. Transgenic and normal fish, of similar size and age, were equally willing to attack both the edible (live insects) and inedible (artificial angling lure flies) prey, but transgenic fish did so faster and were more likely to make repeated attacks. Transgenic fish managed to seize and consume the edible prey after fewer attacks than did normal fish. However, swallowing of prey took longer than for normal fish. More transgenic individuals interacted with the inedible prey compared with normal salmon, and initially, transgenic fish in visual company with another fish also interacted more with the prey than single transgenic or any constellation of normal focal fish. With repeated exposures, the number of individuals attacking and the number of interactions with the prey decreased. These responses were stronger in transgenic fish, partly explained by the initially low response in normal fish. The observed differences are most likely the consequences of elevated levels of growth hormone in transgenic fish generating enhanced feeding motivation and reinforcement capacity. In a natural environment, the performance of a growth hormone‐transgenic fish may therefore depend on the relative abundance of profitable vs. unprofitable prey, as well as the presence of other transgenic individuals.     

An evolutionary analysis of genome expansion and pathogenicity in Escherichia coli

Background

There are several studies describing loss of genes through reductive evolution in microbes, but how selective forces are associated with genome expansion due to horizontal gene transfer (HGT) has not received similar attention. The aim of this study was therefore to examine how selective pressures influence genome expansion in 53 fully sequenced and assembled Escherichia coli strains. We also explored potential connections between genome expansion and the attainment of virulence factors. This was performed using estimations of several genomic parameters such as AT content, genomic drift (measured using relative entropy), genome size and estimated HGT size, which were subsequently compared to analogous parameters computed from the core genome consisting of 1729 genes common to the 53 E. coli strains. Moreover, we analyzed how selective pressures (quantified using relative entropy and dN/dS), acting on the E. coli core genome, influenced lineage and phylogroup formation.

Results

Hierarchical clustering of dS and dN estimations from the E. coli core genome resulted in phylogenetic trees with topologies in agreement with known E. coli taxonomy and phylogroups. High values of dS, compared to dN, indicate that the E. coli core genome has been subjected to substantial purifying selection over time; significantly more than the non-core part of the genome (p<0.001). This is further supported by a linear association between strain-wise dS and dN values (β = 26.94 ± 0.44, R²~0.98, p<0.001). The non-core part of the genome was also significantly more AT-rich (p<0.001) than the core genome and E. coli genome size correlated with estimated HGT size (p<0.001). In addition, genome size (p<0.001), AT content (p<0.001) as well as estimated HGT size (p<0.005) were all associated with the presence of virulence factors, suggesting that pathogenicity traits in E. coli are largely attained through HGT. No associations were found between selective pressures operating on the E. coli core genome, as estimated using relative entropy, and genome size (p~0.98).

Conclusions

On a larger time frame, genome expansion in E. coli, which is significantly associated with the acquisition of virulence factors, appears to be independent of selective forces operating on the core genome.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-882) contains supplementary material, which is available to authorized users.     

RETRACTED ARTICLE: Interspecific competition among ants in the boreal forest: Testing predictions from a linear hierarchical competition model

Competitive interactions often play an important role in local community structure, and particularly so in ant communities. We test predictions derived from a competition model proposed for Scandinavian ant communities by comparing ant nest densities inside and outside fifty randomly-selected territories of competitively dominant wood ants within 30 km of Ume?, northern Sweden. As predicted by the model, competitively-intermediate encounter species, as well as other territorial species, showed complementary occurrences with both studied wood ants, Formica aquilonia Yarrow and F. lugubris Zett.. In contrast, complementary abundances, i.e. lower density of competitively-inferior submissive species in the presence of wood ants, as predicted by the model, was not supported for all submissive species. Of the two studied wood ant species, the nest density of submissive species was negatively correlated only with F. aquilonia. Submissives as a group, as well as Myrmica-species, showed complementary abundances with F. aquilonia, but one Leptothorax and two Serviformica species had higher nest densities in the presence of this competitively-dominant species. We propose that, for Leptothorax, these deviations from the model predictions may be because of limited niche overlap with dominant wood ants, a small worker force and a timid behaviour which does not elicit aggression in wood ants. For the two Serviformica species, we propose a combination of protection against social parasites, inter-specific social control performed by F. aquilonia, and dominance relationships between competitively-inferior submissive species as reasons for the higher nest density inside F. aquilonia territories. Monogyny, and thereby smaller nests, lower worker force, smaller territory (as shown by this study) in F. lugubris, as compared to the polygyny in F. aquilonia, may also help explain the differences in their effects on subordinate species. Our analyses indicate that the linear competition hierarchy model proposed for Scandinavian ants accurately predicts the outcome of interaction between and community composition for dominant territorial and encounter species, but that it needs refinement with respect to the relationship between territorial and submissive species and the resulting community composition. Further studies are needed, especially addressing the complex relationships between these latter groups, and the effects of different competitively-dominant wood ants, to determine the mechanisms determining the outcome of these relationships and to more accurately predict community composition. Received 11 June 2007; revised 11 September 2007; accepted 17 September 2007.     

Investigations of oligonucleotide usage variance within and between prokaryotes

Oligonucleotide usage in archaeal and bacterial genomes can be linked to a number of properties, including codon usage (trinucleotides), DNA base-stacking energy (dinucleotides), and DNA structural conformation (di- to tetranucleotides). We wanted to assess the statistical information potential of different DNA ‘word-sizes’ and explore how oligonucleotide frequencies differ in coding and non-coding regions. In addition, we used oligonucleotide frequencies to investigate DNA composition and how DNA sequence patterns change within and between prokaryotic organisms. Among the results found was that prokaryotic chromosomes can be described by hexanucleotide frequencies, suggesting that prokaryotic DNA is predominantly short range correlated, i.e., information in prokaryotic genomes is encoded in short oligonucleotides. Oligonucleotide usage varied more within AT-rich and host-associated genomes than in GC-rich and free-living genomes, and this variation was mainly located in non-coding regions. Bias (selectional pressure) in tetranucleotide usage correlated with GC content, and coding regions were more biased than non-coding regions. Non-coding regions were also found to be approximately 5.5% more AT-rich than coding regions, on average, in the 402 chromosomes examined. Pronounced DNA compositional differences were found both within and between AT-rich and GC-rich genomes. GC-rich genomes were more similar and biased in terms of tetranucleotide usage in non-coding regions than AT-rich genomes. The differences found between AT-rich and GC-rich genomes may possibly be attributed to lifestyle, since tetranucleotide usage within host-associated bacteria was, on average, more dissimilar and less biased than free-living archaea and bacteria.