EGID: an ensemble algorithm for improved genomic island detection in genomic sequences

Genomic islands (GIs) are genomic regions that are originally transferred from other organisms. The detection of genomic islands in genomes can lead to many applications in industrial, medical and environmental contexts. Existing computational tools for GI detection suffer either low recall or low precision, thus leaving the room for improvement. In this paper, we report the development of our Ensemble algorithm for Genomic Island Detection (EGID). EGID utilizes the prediction results of existing computational tools, filters and generates consensus prediction results. Performance comparisons between our ensemble algorithm and existing programs have shown that our ensemble algorithm is better than any other program. EGID was implemented in Java, and was compiled and executed on Linux operating systems. EGID is freely available at http://www5.esu.edu/cpsc/bioinfo/software/EGID.     

Different microbial biofilm formation on polymethylmethacrylate (PMMA) bone cement loaded with gentamicin and vancomycin

We studied the in vitro effects of gentamicin and vancomycin alone and in combination added to polymethylmethacrylate (PMMA) cement specimens on the bacterial adhesion of multiresistant clinical isolates.The PMMA specimens (discs) loaded with gentamicin (1.9%) or vancomycin (1.9%) or with a combination of the two were placed in Mueller-Hinton Broth inoculated with bacterial strains. After incubation, bacterial growth was determined by optical density (OD₅₄₀) and sub-cultures. The biofilm PMMA-associated dye (crystal violet) was measured. Antibiotic concentrations in broth were determined by fluorescence polarisation immunoassay.All antibiotic-loaded PMMA cement specimens released high, inhibitory concentrations of gentamicin and vancomycin. However, differences in strain growth and adhesion were recorded. The clinical isolates Met-R/Gent-R CoNS showed no adhesion to gentamicin-loaded specimens for 24 h; strains with Gent-Intermediate susceptibility exhibited growth after 48 h but reduced adhesion. Some Gent-R strains exhibited growth and adhesion to antibiotic-loaded specimens similar to controls (plain discs). Only the VRSA strain (Staphylococcus aureus 5/7) and Escherichia coli were able to grow and adhere to vancomycin-loaded specimens after 24 h of incubation. The specimens loaded with the gentamicin + vancomycin combination showed a synergistic inhibitory effect against all tested strains (no bacterial growth). The degree of bacterial adhesion to PMMA cement loaded with gentamicin or vancomycin may be reduced in spite of a normal growth rate and is different for the tested strains.The effect of gentamicin and vancomycin on bacterial growth and adhesion to PMMA bone cement depends on the antibiotic concentrations, on the characteristics of each specific strain and on its ability to produce biofilm and adhere to antibiotic-loaded PMMA bone cement.     

In vitro assay of the antimicrobial activity of kephir against bacterial and fungal strains

Kephir is a fermented carbonated refreshing milk, with a slightly acidic aromatic taste and creamy foam composition which contains lactobacilli, leuconostocci, acetic acid bacteria, lactostreptococci and yeasts. Recent studies have demonstrated its antibacterial, immunostimulating, antitumoral and cholesterol-lowering activities.

Purpose

The purpose of this study was to investigate the antimicrobial activity of kephir against Bacillus subtilis spp. spizizenii ATCC 6633, Staphylococcus aureus ATCC 6538, Enterococcus faecalis ATCC 29212, Escherichia coli ATCC 8739, Salmonella enteritidis ATCC 13076, Pseudomonas aeruginosa ATCC 9027 and Candida albicans ATCC 10231. The kephir fermented for 24 h and 48 h, as well and after 7 days preservation at 4–8 °C was tested by in vitro disk diffusion method. The intensity of the antimicrobial activity was interpreted by comparison with two antibiotics, i.e. ampicillin and neomycin.

Results

The antimicrobial activity of 24 h as well as 48 fermented kephir, fresh or after 7 days preservation at 4–8 °C was similar and observed against B. subtilis, S. aureus, E. coli, E. faecalis and S. enteritidis. For E. coli, E. faecalis and S. enteritidis the antimicrobial activity was superior to both tested antibiotics and for B. subtilis and S. aureus to one antibiotic. The tested products exhibited no activity against P. aeruginosa and C. albicans.

Conclusion

Kephir is exhibiting large spectrum and strong antibacterial activity probably due to the complex viable probiotic strains association producing antimicrobial substances.     

Characterization of composted olive mill wastes to predict potential plant disease suppressiveness

Despite its proven agronomic value, the plant disease suppressive effect of composts from olive waste has not been adequately investigated. In the present study, the disease suppressive potential of two olive waste (OW) composts against soil-borne plant pathogens was investigated. Both OW composts showed sizeable, active microbial populations, which were able to grow actively on chitin and cellulose. In plate inhibition trials, OW compost water extracts (CWEs) exerted a significant inhibitory effect on the growth of the pathogens Fusarium oxysporum f.sp. lycopersici (Fol), Pythium ultimum, Phytophtora infestans, Sclerotina sclerotiorum and Verticillium dahliae; and in pot experiments, the OW composts significantly reduced P. ultimum damping-off and Fol wilt diseases on tomato seedlings. The disease suppressive effect of OW composts seems to be due to the combined effects of suppression phenomena caused by the presence of microorganisms competing for both nutrients and space as well as by the activity of specific antagonistic microorganisms.     

Impacts of climate warming on hybrid zone movement: Geographically diffuse and biologically porous “species borders”

Abstract The ecology and evolutionary biology of insect–plant associations has realized extensive attention, especially during the past 60 years. The classifications (categorical designations) of continuous variation in biodiversity, ranging from global patterns (e.g., latitudinal gradients in species richness/diversity and degree of herbivore feeding specialization) to localized insect–plant associations that span the biospectrum from polyphenisms, polymorphisms, biotypes, demes, host races, to cryptic species, remain academically contentious. Semantic and biosystematic (taxonomical) disagreements sometimes detract from more important ecological and evolutionary processes that drive diversification, the dynamics of gene flow and local extinctions. This review addresses several aspects of insect specialization, host‐associated divergence and ecological (including “hybrid”) speciation, with special reference to the climate warming impacts on species borders of hybridizing swallowtail butterflies (Papilionidae). Interspecific hybrid introgression may result in collapse of multi‐species communities or increase species numbers via homoploid hybrid speciation. We may see diverging, merging, or emerging genotypes across hybrid zones, all part of the ongoing processes of evolution. Molecular analyses of genetic mosaics and genomic dynamics with “divergence hitchhiking”, combined with ecological, ethological and physiological studies of “species porosity”, have already begun to unveil some answers for some important ecological/evolutionary questions. (i) How rapidly can host‐associated divergence lead to new species (and why doesn't it always do so, e.g., resulting in “incomplete” speciation)? (ii) How might “speciation genes” function, and how/where would we find them? (iii) Can oscillations from specialists to generalists and back to specialists help explain global diversity in herbivorous insects? (iv) How could recombinant interspecific hybridization lead to divergence and speciation? From ancient phytochemically defined angiosperm affiliations to recent and very local geographical mosaics, the Papilionidae (swallowtail butterflies) have provided a model for enhanced understanding of ecological patterns and evolutionary processes, including host‐associated genetic divergence, genomic mosaics, genetic hitchhiking and sex‐linked speciation genes. Apparent homoploid hybrid speciation in Papilio appears to have been catalyzed by climate warming‐induced interspecific introgression of some, but not all, species diagnostic traits, reflecting strong divergent selection (discordant), especially on the Z (= X) chromosome. Reproductive isolation of these novel recombinant hybrid genotypes appears to be accomplished via a delayed post‐diapause emergence or temporal isolation, and is perhaps aided by the thermal landscape. Changing thermal landscapes appear to have created (and may destroy) novel recombinant hybrid genotypes and hybrid species.     

Bioprocess monitoring by marker gene analysis

The optimization and the scale up of industrial fermentation processes require an efficient and possibly comprehensive analysis of the physiology of the production system throughout the process development. Furthermore, to ensure a good quality control of established bioprocesses, on-line analysis techniques for the determination of marker gene expression are of interest to monitor the productivity and the safety of bioprocesses. A prerequisite for such analyses is the knowledge of genes, the expression of which is critical either for the productivity or for the performance of the bioprocess. This work reviews marker genes that are specific indicators for stress- and nutrient-limitation conditions or for the physiological status of the bacterial production hosts Bacillus subtilis, Bacillus licheniformis and Escherichia coli. The suitability of existing gene expression analysis techniques for bioprocess monitoring is discussed. Analytical approaches that enable a robust and sensitive determination of selected marker mRNAs or proteins are presented.     

Microbial substrate preference and community dynamics during decomposition of Acer saccharum

The Guild Decomposition Model (GDM) hypothesized that temporal shifts in microbial “guilds,” each with distinct substrate preferences, drive decomposition dynamics and regulate soil carbon (C) losses and sequestration. To test this hypothesis, we established a laboratory incubation of Acer saccharum litter and monitored respiration, microbial biomass and enzyme activities, inorganic nutrients and shifts in functional groups of decomposers using phospholipid fatty acid (PLFA) analysis. Biomass and respiration peaked within the first 2 d of incubation, and the Gram negative PLFA biomarker 18:1ω7c predominated during the first 5 d. Hydrolytic enzyme activities and two fungal biomarkers (18:2ω6,9c and 18:3ω6c) increased by 25 d and lignolytic enzyme activity was detected at 68 d. Our results suggest that decomposers preferentially use labile substrates and that shifts in decomposer groups occur in response to changes in available substrates, which supports the GDM.     

Screening for bacterial-fungal associations in a south-eastern US salt marsh using pre-established fungal monocultures

Both bacteria and fungi play critical roles in decomposition processes in many natural environments, yet only rarely have they been studied as an integrated community. We examined whether physical associations exist between individual bacterial and fungal species that co-occur on decaying smooth cordgrass, Spartina alterniflora, in a south-eastern US salt marsh. Fungal-pervaded decaying Spartina was used as "bait" for potential bacterial associates. The bundles (infiltrated with one of three dominant fungal members of the decomposer assemblage, or an autoclaved control) were placed in a salt marsh and collected biweekly for 6 weeks during the first experiment (late summer 2002), and weekly for 3 weeks during the second experiment (early summer 2003). Terminal-restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes was used to track colonization by bacterial taxa in association with the established fungal species. T-RFLP analysis of 18S-to-28S internal transcribed spacer (ITS) regions was used to monitor changes in fungal communities once bundles had been placed in the field. Results from both years were nearly identical, and showed that invasion by fungi other than the bait species was slow, resulting in a virtual fungal monoculture for several weeks into the experiments. Surprisingly, bacterial communities were unaffected by the identity of the fungal bait. Regardless of the fungal species, and even in the absence of prior fungal colonization, bacterial 16S rRNA profiles were remarkably similar. These results suggest that few species-specific associations, either positive or negative, exist between bacterial and fungal members of the Spartina decomposer community during initial colonization.     

Coating of a surface with 2-methacryloyloxyethyl phosphorylcholine (MPC) co-polymer significantly reduces retention of human pathogenic microorganisms

The present study compares the retention of four species that are often isolated in association with biomedical device-related infections - Staphylococcus aureus, Streptococcus mutans, Pseudomonas aeruginosa, and Candida albicans - to three different surfaces. All four bacterial species were found to bind significantly less well to MPC-coated surfaces than to non-coated surfaces. We attribute this effect to the "superhydrophilicity" of MPC-coated surfaces, whereas hydrophobic surfaces are well known to reduce bacterial retention and thus to inhibit a crucial step in the formation of bacterial biofilms that lead to biomedical device-related infections and complications.