Albert E. Parker

Retinal motion estimation in adaptive optics scanning laser ophthalmoscopy

We apply a novel computational technique known as the map-seeking circuit algorithm to estimate the motion of the retina of eye from a sequence of frames of data from a scanning laser ophthalmoscope. We also present a scheme to dewarp and co-add frames of retinal image data, given the estimated motion. The motion estimation and dewarping techniques are applied to data collected from an adaptive optics scanning laser ophthalmoscopy.

Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis

BackgroundTranscriptome analysis was applied to characterize the physiological activities of Pseudomonas aeruginosa grown for three days in drip-flow biofilm reactors. Conventional applications of transcriptional profiling often compare two paired data sets that differ in a single experimentally controlled variable. In contrast this study obtained the transcriptome of a single biofilm state, ranked transcript signals to make the priorities of the population manifest, and compared ranki ngs for a priori identified physiological marker genes between the biofilm and published data sets.ResultsBiofilms tolerated exposure to antibiotics, harbored steep oxygen concentration gradients, and exhibited stratified and heterogeneous spatial patterns of protein synthetic activity. Transcriptional profiling was performed and the signal intensity of each transcript was ranked to gain insight into the physiological state of the biofilm population. Similar rankings were obtained from data sets published in the GEO database http://www.ncbi.nlm.nih.gov/geo. By comparing the rank of genes selected as markers for particular physiological activities between the biofilm and comparator data sets, it was possible to infer qualitative features of the physiological state of the biofilm bacteria. These biofilms appeared, from their transcriptome, to be glucose nourished, iron replete, oxygen limited, and growing slowly or exhibiting stationary phase character. Genes associated with elaboration of type IV pili were strongly expressed in the biofilm. The biofilm population did not indicate oxidative stress, homoserine lactone mediated quorum sensing, or activation of efflux pumps. Using correlations with transcript ranks, the average specific growth rate of biofilm cells was estimated to be 0.08 h-1.ConclusionsCollectively these data underscore the oxygen-limited, slow-growing nature of the biofilm population and are consistent with antimicrobial tolerance due to low metabolic activity.

Antimicrobial Penetration and Efficacy in an In Vitro Oral Biofilm Model

ABSTRACT The penetration and overall efficacy of six mouthrinse actives was evaluated by using an in vitro flow cell oral biofilm model. The technique involved preloading biofilm cells with a green fluorescent dye that leaked out as the cells were permeabilized by a treatment. The loss of green color, and of biomass, was observed by time-lapse microscopy during 60 min of treatment under continuous flow conditions. The six actives analyzed were ethanol, sodium lauryl sulfate, triclosan, chlorhexidine digluconate (CHX), cetylpyridinium chloride, and nisin. Each of these agents effected loss of green fluorescence throughout biofilm cell clusters, with faster action at the edge of a cell cluster and slower action in the cluster center. The time to reach half of the initial fluorescent intensity at the center of a cell cluster, which can be viewed as a combined penetration and biological action time, ranged from 0.6 to 19 min for the various agents. These times are much longer than the predicted penetration time based on diffusion alone, suggesting that anti-biofilm action was controlled more by the biological action time than by the penetration time of the active. None of the agents tested caused any removal of the biofilm. The extent of fluorescence loss after 1 h of exposure to an active ranged from 87 to 99.5%, with CHX being the most effective. The extent of fluorescence loss in vitro, but not penetration and action time, correlated well with the relative efficacy data from published clinical trials.

Comparing the Chlorine Disinfection of Detached Biofilm Clusters with Those of Sessile Biofilms and Planktonic Cells in Single- and Dual-Species Cultures

ABSTRACT Although the detachment of cells from biofilms is of fundamental importance to the dissemination of organisms in both public health and clinical settings, the disinfection efficacies of commonly used biocides on detached biofilm particles have not been investigated. Therefore, the question arises whether cells in detached aggregates can be killed with disinfectant concentrations sufficient to inactivate planktonic cells. Burkholderia cepacia and Pseudomonas aeruginosa were grown in standardized laboratory reactors as single species and in coculture. Cluster size distributions in chemostats and biofilm reactor effluent were measured. Chlorine susceptibility was assessed for planktonic cultures, attached biofilm, and particles and cells detached from the biofilm. Disinfection tolerance generally increased with a higher percentage of larger cell clusters in the chemostat and detached biofilm. Samples with a lower percentage of large clusters were more easily disinfected. Thus, disinfection tolerance depended on the cluster size distribution rather than sample type for chemostat and detached biofilm. Intact biofilms were more tolerant to chlorine independent of species. Homogenization of samples led to significantly increased susceptibility in all biofilm samples as well as detached clusters for single-species B. cepacia, B. cepacia in coculture, and P. aeruginosa in coculture. The disinfection efficacy was also dependent on species composition; coculture was advantageous to the survival of both species when grown as a biofilm or as clusters detached from biofilm but, surprisingly, resulted in a lower disinfection tolerance when they were grown as a mixed planktonic culture.

Influence of Season and Plant Species on the Abundance and Diversity of Sulfate Reducing Bacteria and Ammonia Oxidizing Bacteria in Constructed Wetland Microcosms

Constructed wetlands offer an effective means for treatment of wastewater from a variety of sources. An understanding of the microbial ecology controlling nitrogen, carbon and sulfur cycles in constructed wetlands has been identified as the greatest gap for optimizing performance of these promising treatment systems. It is suspected that operational factors such as plant types and hydraulic operation influence the subsurface wetland environment, especially redox, and that the observed variation in effluent quality is due to shifts in the microbial populations and/or their activity. This study investigated the biofilm associated sulfate reducing bacteria and ammonia oxidizing bacteria (using the dsrB and amoA genes, respectively) by examining a variety of surfaces within a model wetland (gravel, thick roots, fine roots, effluent), and the changes in activity (gene abundance) of these functional groups as influenced by plant species and season. Molecular techniques were used including quantitative PCR and denaturing gradient gel electrophoresis (DGGE), both with and without propidium monoazide (PMA) treatment. PMA treatment is a method for excluding from further analysis those cells with compromised membranes. Rigorous statistical analysis showed an interaction between the abundance of these two functional groups with the type of plant and season (p < 0.05). The richness of the sulfate reducing bacterial community, as indicated by DGGE profiles, increased in planted vs. unplanted microcosms. For ammonia oxidizing bacteria, season had the greatest impact on gene abundance and diversity (higher in summer than in winter). Overall, the primary influence of plant presence is believed to be related to root oxygen loss and its effect on rhizosphere redox.

A Modified CDC Biofilm Reactor to Produce Mature Biofilms on the Surface of PEEK Membranes for an In Vivo Animal Model Application

Biofilm-related infections have become a major clinical concern. Typically, animal models that involve inoculation with planktonic bacteria have been used to create positive infection signals and examine antimicrobial strategies for eradicating or preventing biofilm-related infection. However, it is estimated that 99.9% of bacteria in nature dwell in established biofilms. As such, open wounds have significant potential to become contaminated with bacteria that reside in a well-established biofilm. In this study, a modified CDC biofilm reactor was developed to repeatably grow mature biofilms of Staphylococcus aureus on the surface of polyetheretherketone (PEEK) membranes for inoculation in a future animal model of orthopaedic implant biofilm-related infection. Results indicated that uniform, mature biofilms repeatably grew on the surface of the PEEK membranes.

Direct Electric Current Treatment under Physiologic Saline Conditions Kills Staphylococcus epidermidis Biofilms via Electrolytic Generation of Hypochlorous Acid

The purpose of this study was to investigate the mechanism by which a direct electrical current reduced the viability of Staphylococcus epidermidis biofilms in conjunction with ciprofloxacin at physiologic saline conditions meant to approximate those in an infected artificial joint. Biofilms grown in CDC biofilm reactors were exposed to current for 24 hours in 1/10th strength tryptic soy broth containing 9 g/L total NaCl. Dose-dependent log reductions up to 6.7 log10 CFU/cm2 were observed with the application of direct current at all four levels (0.7 to 1.8 mA/cm2) both in the presence and absence of ciprofloxacin. There were no significant differences in log reductions for wells with ciprofloxacin compared to those without at the same current levels. When current exposures were repeated without biofilm or organics in the medium, significant generation of free chlorine was measured. Free chlorine doses equivalent to the 24 hour endpoint concentration for each current level were shown to mimic killing achieved by current application. Current exposure (1.8 mA/cm2) in medium lacking chloride and amended with sulfate, nitrate, or phosphate as alternative electrolytes produced diminished kills of 3, 2, and 0 log reduction, respectively. Direct current also killed Pseudomonas aeruginosa biofilms when NaCl was present. Together these results indicate that electrolysis reactions generating hypochlorous acid from chloride are likely a main contributor to the efficacy of direct current application. A physiologically relevant NaCl concentration is thus a critical parameter in experimental design if direct current is to be investigated for in vivo medical applications.

An in vitro model for the growth and analysis of chronic wound MRSA biofilms

Aims:  To develop an in vitro model (Colony/drip‐flow reactor – C/DFR) for the growth and analysis of methicillin‐resistant Staphylococcus aureus (MRSA) biofilms.

Sampling Gaussian Distributions in Krylov Spaces with Conjugate Gradients

This paper introduces a conjugate gradient sampler that is a simple extension of the method of conjugate gradients (CG) for solving linear systems. The CG sampler iteratively generates samples from a Gaussian probability density, using either a symmetric positive definite covariance or precision matrix, whichever is more convenient to model. Similar to how the Lanczos method solves an eigenvalue problem, the CG sampler approximates the covariance or precision matrix in a small dimensional Krylov space. As with any iterative method, the CG sampler is efficient for high dimensional problems where forming the covariance or precision matrix is impractical, but operating by the matrix is feasible. In exact arithmetic, the sampler generates Gaussian samples with a realized covariance that converges to the covariance of interest. In finite precision, the sampler produces a Gaussian sample with a realized covariance that is the best approximation to the desired covariance in the smaller dimensional Krylov space. ...

Whole cell kinetics of ureolysis by Sporosarcina pasteurii

Ureolysis drives microbially induced calcium carbonate precipitation (MICP). MICP models typically employ simplified urea hydrolysis kinetics that do not account for cell density, pH effect or product inhibition. Here, ureolysis rate studies with whole cells of Sporosarcina pasteurii aimed to determine the relationship between ureolysis rate and concentrations of (i) urea, (ii) cells, (iii) NH4+ and (iv) pH (H+ activity).