Optical sensing of microbial life on surfaces

The label-free detection of microbial cells attached to a surface is an active field of research. The field is driven by the need to understand and control the growth of biofilms in a number of applications, including basic research in natural environments, industrial facilities, and clinical devices, to name a few. Despite significant progress in the ability to monitor the growth of biofilms and related living cells, the sensitivity and selectivity of such sensors are still a challenge. We believe that among the many different technologies available for monitoring biofilm growth, optical techniques are the most promising, as they afford direct imaging and offer high sensitivity and specificity. Furthermore, as each technique offers different insights into the biofilm growth mechanism, our analysis allows us to provide an overview of the biological processes at play. In addition, we use a set of key parameters to compare state-of-the-art techniques in the field, including a critical assessment of each method, to identify the most promising types of sensors. We highlight the challenges that need to be overcome to improve the characteristics of current biofilm sensor technologies and indicate where further developments are required. In addition, we provide guidelines for selecting a suitable sensor for detecting microbial cells on a surface

The theory of a "staphylococcus superantigen" in chronic rhinosinusitis with nasal polyps: myth or reality?

OBJECTIVE: The aim of our study was to search for evidence of a "staphylococcus superantigen" in chronic rhinosinusitis with nasal polyps. PATIENTS AND METHODS: Sixty-nine patients with chronic rhinosinusitis with nasal polyps and 45 healthy controls were included in the study. All patients in the study and control groups underwent bacteriological and immunological examination on nasal smear samples. Total IgE and the following cytokines were tested in all patients: tumor necrosis factor (TNF), interleukin-1 (IL1), interleukin-6 (IL6), interleukin-8 (IL8). RESULTS: The concentration of bacteria in the nasal cavity was much higher in patients in the study group compared to those in the control group, mainly due to staphylococci. In species identification of staphylococci, bacteria most represented were S. aureus and S. epidermidis. The greater the concentration of S. aureus, the lower the level of IgE. Proinflam-matory cytokines were uniformly increased in patients with nasal polyps. The level of IgE was maximal in patients with chronic rhinosinusitis with nasal polyps with a poor growth of culture and minimal in patients with abundant growth, suggesting that in the latter the effect of eosinophilic inflammation on the disease was reduced, and conversely, the activity of eosinophilic inflammation was maximal with a poor seeding of the nasal cavity. CONCLUSIONS: Although this study has some limits, our findings do not support the theory of a staphylococcus superantigen in which the IgE level and eosinophilic inflammation should increase with increasing activity of Staphylococcus aureus. Further research supported by a larger sample of patients is required to better delineate the role of a staphylococcus superantigen in the pathogenesis of patients with chronic rhinosinusitis with nasal polyps

Measuring Pain Withdrawal Threshold using a Novel Device in Pseudo-continuous Mode

The study of pain and analgesia is an important area of biomedical research that has led to a significant number of advances in the treatment of acute and chronic pain. This study introduces a novel approach to mechanical testing of pain withdrawal of a rat hind paw to a stimulus. This systematic method involves a modified electronic esthesiometer controlled by an IDEA drive that allows for consistency in experiments. The device gives the experimenter computer control of the step size and velocity of approach of the probe stimulus. We discuss here some of the limitations in the current techniques used and illustrate how this device will result in reduced errors during an experiment. The standard method primarily involves manually raising the probe towards the animal. The data presented herein shows how the computer controlled pseudo-continuous mode of operation is effective in determining the pain threshold with a lesser deviation from the mean

Living on the edge: Biofilms developing in oscillating environmental conditions

For the first time, the densities and diversity of microorganisms developed on ocean gliders were investigated using flow cytometry and Illumina MiSeq sequencing of 16S and 18S rRNA genes. Ocean gliders are autonomous buoyancy-driven underwater vehicles, equipped with sensors continuously recording physical, chemical, and biological parameters. Microbial biofilms were investigated on unprotected parts of the glider and surfaces coated with base, biocidal and chitosan paints. Biofilms on the glider were exposed to periodical oscillations of salinity, oxygen, temperature, pressure, depth and light, due to periodic ascending and descending of the vehicle. Among the unprotected surfaces, the highest microbial abundance was observed on the bottom of the glider’s body, while the lowest density was recorded on the glider’s nose. Antifouling paints had the lowest densities of microorganisms. Multidimensional analysis showed that the microbial communities formed on unprotected parts of the glider were significantly different from those on biocidal paint and in seawater

Gramella portivictoriae sp nov, a novel member of the family Flavobacteriaceae isolated from marine sediment (vol 55, pg 2497, 2005)

A yellow-pigmented, Gram-negative, slowly gliding, rod-shaped, strictly aerobic bacterium (UST040801-001T) was isolated from marine sediment. The DNA G+C content was 39?9 mol%. The predominant fatty acids were a15 : 0, i15 : 0, i15 : 0 3-OH, i17 : 1v9c, i17 : 0 3-OH and summed feature 3, comprising i15 : 0 2-OH and/or 16 : 1v7c (altogether representing 76?2% of the total). MK-6 was the only respiratory quinone. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences indicated that Gramella echinicola KMM 6050T (the only species in the genus) was the closest relative of UST040801-001T, sharing 98?0% sequence similarity. The DNA–DNA relatedness between UST040801-001T and Gramella echinicola KMM 6050T was 13 %. Strain UST040801-001T can be distinguished from G. echinicola by means of 11 phenotypic traits. The results of molecular and phenotypic analyses suggested that UST040801-001T represents a novel species of Gramella. The name Gramella portivictoriae sp. nov. is proposed for this bacterium, with UST040801-001T (=NRRL 41137T=JCM 13192T) as the type strain

Description of Fabibacter halotolerans gen. nov., and reclassification of [Marinicola] seohaensis as Roseivirga seahaensis comb. nov.

Bacterial strains UST030701-097T and UST030701-084T were isolated from a marine sponge in the Bahamas. Both strains were pink-pigmented, Gram-negative, strictly aerobic and chemo-organotrophic. Cells of strain UST030701-097T were short, curved rods with fast-gliding motility, whereas those of strain UST030701-084T were straight rods with a less rapid gliding motion. The two strains had MK-7 as the major respiratory quinone and did not produce flexirubin-type pigments. The DNA G+C contents of strains UST030701-097T and UST030701-084T were 42.5 and 43.7 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two strains belonged to the family 'Flexibacteraceae' of the phylum Bacteroidetes. 16S rRNA gene sequence similarity between strains UST030701-097T and UST030701-084T was 95.0 %; their closest relative was [Marinicola] seohaensis, with 93.3 % and 96.0 % sequence similarity, respectively. Phylogenetic tree topology indicated that the two strains belonged to the same lineage, but were on separate branches. Whilst strain UST030701-084T and [Marinicola] seohaensis were found on one branch, strain UST030701-097T was in another branch that had no species with validly published names. Based on the polyphasic taxonomic data obtained in the present study, we propose that strain UST030701-097T represents a novel genus and that strain UST030701-084T represents a novel species in the phylum Bacteroidetes. The genus Fabibacter gen. nov. is proposed, with strain UST030701-097T (=NRRL B-41220T=JCM 13334T) as the type strain of the type species, Fabibacter halotolerans sp. nov. Strain UST030701-084T (=NRRL B-41219T=JCM 13337T) is proposed as the type strain of Roseivirga spongicola sp. nov. In an earlier study, it was suggested that the genus Marinicola is a later heterotypic synonym of the genus Roseivirga. However, a formal proposal to reclassify [Marinicola] seohaensis, the only member of the genus Marinicola, has not yet been made. The results of phylogenetic analyses in this study support the reclassification of [Marinicola] seohaensis as Roseivirga seohaensis comb. nov

Stenothermobacter spongiae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from a marine sponge in the Bahamas, and emended description of Nonlabens tegetincola

A bacterial strain, UST030701-156T, was isolated from a marine sponge in the Bahamas. Strain UST030701-156T was orange-pigmented, Gram-negative, rod-shaped with tapered ends, slowly motile by gliding and strictly aerobic. The predominant fatty acids were a15 : 0, i15 : 0, i15 : 0 3-OH, i17 : 0 3-OH, i17 : 1ω9c and summed feature 3, comprising i15 : 0 2-OH and/or 16 : 1ω7c. MK-6 was the only respiratory quinone. Flexirubin-type pigments were not produced. Phylogenetic analysis based on 16S rRNA gene sequences placed UST030701-156T within a distinct lineage in the family Flavobacteriaceae, with 93·3 % sequence similarity to the nearest neighbour, Nonlabens tegetincola. The DNA G+C content of UST030701-156T was 41·0 mol% and was much higher than that of N. tegetincola (33·6 mol%). Strain UST030701-156T can be distinguished from other members of the Flavobacteriaceae by means of a number of chemotaxonomic and phenotypic characteristics. It is proposed, therefore, that UST030701-156T represents a novel taxon designated Stenothermobacter spongiae gen. nov., sp. nov. The type strain is UST030701-156T (=NRRL B-41138T=JCM 13191T). Carbon-source utilization by N. tegetincola was re-examined and an emended description is therefore included

Secretion of DNases by Marine Bacteria: A Culture Based and Bioinformatics Approach

The vast majority of bacteria present in the natural environment are present in the form of aggregates and/or biofilms. Microbial aggregates are ubiquitous in the marine environment and are inhabited by diverse microbial communities which often express intense extracellular enzymatic activities. However, the secretion of an important group of enzymes, DNases, by bacteria from marine aggregates has not been studied, despite the importance of these aggregates in biogeochemical cycling of nutrients in the oceans. In this work, we therefore, employed both culture-based and bioinformatics approaches to understand the diversity of bacterial DNases in marine bacterioplankton. We found that 34% of 345 strains of attached and non-attached marine bacteria showed extracellular DNase activity. Most of these isolates belong to Proteobacteria (53%) and Firmicutes (34%). Secretion of DNases by bacteria isolated from marine gel particles (MGP) is reported here for the first time. Then, to further understand the wider diversity of the potential to produce DNases, sequences were compared using 2316 whole genome and 42 metagenome datasets. Thirty-nine different taxonomic groups corresponding to 10 bacterial phyla were found to encode genes responsible for DNase secretion. This study highlights the unexpected and widespread presence of DNase secretion in bacteria in general and in MGP more specifically. This has important implications for understanding the dynamics and fate of marine microbial aggregates in the oceans

Studies of concentration and temperature dependencies of precipitation kinetics in iron-copper alloys using kinetic monte carlo and stochastic statistical simulations

The earlier-developed ab initio model and the kinetic Monte Carlo method (KMCM) are used to simulate precipitation in a number of iron-copper alloys with different copper concentrations x and temperatures T. The same simulations are also made using the improved version of the earlier-suggested stochastic statistical method (SSM). The results obtained enable us to make a number of general conclusions about the dependencies of the decomposition kinetics in Fe-Cu alloys on x and T. We also show that the SSM describes the precipitation kinetics in a fair agreement with the KMCM, and employing the SSM in conjunction with the KMCM enables us to extend the KMC simulations to the longer evolution times. The results of simulations seem to agree with available experimental data for Fe-Cu alloys within statistical errors of simulations and the scatter of experimental results. Comparison of results of simulations to experiments for some multicomponent Fe-Cu-based alloys enables us to make certain conclusions about the influence of alloying elements in these alloys on the precipitation kinetics at different stages of evolution.Comment: 18 pages, 17 postscript figures, LaTe