Metabolomic and Lipidomic Profiling of Bacillus Using Two-Dimensional Tandem Mass Spectrometry.

Lipidomic and metabolomic profiles of sporulated and vegetative Bacillus subtilis and Bacillus thuringiensis from irradiated lysates were recorded using a quadrupole ion trap mass spectrometer modified to perform two-dimensional tandem mass spectrometry (2D MS/MS). The 2D MS/MS data domains, acquired using a 1.2 s scan of negative ions generated by nanoelectrospray ionization of microwave irradiated spores, showed the presence of dipicolinic acid (DPA) as well as various lipids. Aside from microwave radiation to extract DPA and lipids from spores, sample preparation was minimal. Characteristic lipid and metabolic profiles were observed using 107─108 cells of the two Bacillus species. Major features of the lipid profiles observed for the vegetative states included sets of phosphatidylglycerol (PG) lipids. Product ion spectra were extracted from the 2D MS/MS data, and they provided structural information on the fatty acid components of the PG lipids. The study demonstrates the flexibility, speed, and informative power of metabolomic and lipidomic fingerprinting for identifying the presence of spore-forming biological agents using 2D MS/MS as a rapid profiling screening method.

In vivo demonstration of Pseudomonas aeruginosa biofilms as independent pharmacological microcompartments.

BACKGROUND: Pseudomonas aeruginosa is difficult to eradicate from the lungs of cystic fibrosis (CF) patients due to biofilm formation. Organs and blood are independent pharmacokinetic (PK) compartments. Previously, we showed in vitro biofilms behave as independent compartments impacting the pharmacodynamics. The present study investigated this phenomenon in vivo. METHODS: Seaweed alginate beads with P. aeruginosa resembling biofilms, either freshly produced (D0) or incubated for 5 days (D5) were installed s.c in BALB/c mice. Mice (n = 64) received tobramycin 40 mg/kg s.c. and were sacrificed at 0.5, 3, 6, 8, 16 or 24 h after treatment. Untreated controls (n = 14) were sacrificed, correspondingly. Tobramycin concentrations were determined in serum, muscle tissue, lung tissue and beads. Quantitative bacteriology was determined. RESULTS: The tobramycin peak concentrations in serum was 58.3 (±9.2) mg/L, in lungs 7.1 mg/L (±2.3), muscle tissue 2.8 mg/L (±0.5) all after 0.5 h and in D0 beads 19.8 mg/L (±3.5) and in D5 beads 24.8 mg/L (±4.1) (both 3 h). A 1-log killing of P. aeruginosa in beads was obtained at 8h, after which the bacterial level remained stable at 16 h and even increased in D0 beads at 24 h. Using the established diffusion retardation model the free tobramycin concentration inside the beads showed a delayed buildup of 3 h but remained lower than the MIC throughout the 24 h. CONCLUSIONS: The present in vivo study based on tobramycin exposure supports that biofilms behave as independent pharmacological microcompartments. The study indicates, reducing the biofilm matrix would increase free tobramycin concentrations and improve therapeutic effects.

Three-Dimensional Super-Resolution Imaging Using a Row-Column Array.

A 3-D super-resolution (SR) pipeline based on data from a row-column (RC) array is presented. The 3-MHz RC array contains 62 rows and 62 columns with a half wavelength pitch. A synthetic aperture (SA) pulse inversion sequence with 32 positive and 32 negative row emissions is used for acquiring volumetric data using the SARUS research ultrasound scanner. Data received on the 62 columns are beamformed on a GPU for a maximum volume rate of 156 Hz when the pulse repetition frequency is 10 kHz. Simulated and 3-D printed point and flow microphantoms are used for investigating the approach. The flow microphantom contains a 100- [Formula: see text] radius tube injected with the contrast agent SonoVue. The 3-D processing pipeline uses the volumetric envelope data to find the bubble's positions from their interpolated maximum signal and yields a high resolution in all three coordinates. For the point microphantom, the standard deviation on the position is (20.7, 19.8, 9.1) [Formula: see text]. The precision estimated for the flow phantom is below [Formula: see text] in all three coordinates, making it possible to locate structures on the order of a capillary in all three dimensions. The RC imaging sequence's point spread function has a size of 0.58 × 1.05 × 0.31 mm3 ( 1.17λ×2.12λ×0.63λ ), so the possible volume resolution is 28900 times smaller than for SA RC B-mode imaging.

Formation of Pseudomonas aeruginosa inhibition zone during tobramycin disk diffusion is due to transition from planktonic to biofilm mode of growth.

Pseudomonas aeruginosa PAO1 (tobramycin MIC = 0.064 µg/mL) was used to perform agar diffusion tests employing tobramycin-containing tablets. Bacterial growth and formation of inhibition zones were studied by stereomicroscopy and by blotting with microscope slides and staining with methylene blue, Alcian blue and a fluorescent lectin for the P. aeruginosa PSL, which was studied by confocal laser scanning microscopy. Diffusion of tobramycin from the deposit was modelled using a 3D geometric version of Fick's second law of diffusion. The time-dependent gradual increase in the minimum biofilm eradication concentration (MBEC) was studied using a Calgary Biofilm Device. The early inhibition zone was visible after 5 h of incubation. The corresponding calculated tobramycin concentration at the border was 1.9 µg/mL, which increased to 3.2 µg/mL and 6.3 µg/mL after 7 h and 24 h, respectively. The inhibition zone increased to the stable final zone after 7 h of incubation. Bacterial growth and small aggregate formation (young biofilms) took place inside the inhibition zone until the small aggregates contained less than ca. 64 cells and production of polysaccharide matrix including PSL had begun; thereafter, the small bacterial aggregates were killed by tobramycin. Bacteria at the border of the stable inhibition zone and beyond continued to grow to a mature biofilm and produced large amount of polysaccharide-containing matrix. Formation of the inhibition zone during agar diffusion antimicrobial susceptibility testing is due to a switch from a planktonic to biofilm mode of growth and gives clinically important information about the increased antimicrobial tolerance of biofilms.

Modelling of ciprofloxacin killing enhanced by hyperbaric oxygen treatment in Pseudomonas aeruginosa PAO1 biofilms.

OUTLINE: In chronic lung infections by Pseudomonas aeruginosa (PA) the bacteria thrive in biofilm structures protected from the immune system of the host and from antibiotic treatment. Increasing evidence suggests that the susceptibility of the bacteria to antibiotic treatment can be significantly enhanced by hyperbaric oxygen treatment. The aim of this study is to simulate the effect of ciprofloxacin treatment in a PAO1 biofilm model with aggregates in agarose when combined with hyperbaric oxygen treatment. This is achieved in a reaction-diffusion model that describes the combined effect of ciprofloxacin diffusion, oxygen diffusion and depletion, bacterial growth and killing, and adaptation of the bacteria to ciprofloxacin. In the model, the oxygen diffusion and depletion use a set of parameters derived from experimental results presented in this work. The part of the model describing ciprofloxacin killing uses parameter values from the literature in combination with our estimates (Jacobs, et al., 2016; Grillon, et al., 2016). Micro-respirometry experiments were conducted to determine the oxygen consumption in the P. aeruginosa strain PAO1. The parameters were validated against existing data from an HBOT experiment by Kolpen et al. (2017). The complete oxygen model comprises a reaction-diffusion equation describing the oxygen consumption by using a Michaelis-Menten reaction term. The oxygen model performed well in predicting oxygen concentrations in both time and depth into the biofilm. At 2.8 bar pure oxygen pressure, HBOT increases the penetration depth of oxygen into the biofilm almost by a of factor 4 in agreement with the scaling that follows from the stationary balance between the consumption term and diffusion term. CONCLUSION: In the full reaction-diffusion model we see that hyperbaric oxygen treatment significantly increases the killing by ciprofloxacin in a PAO1 biofilm in alignment with the experimental results from Kolpen et al. (Kolpen, et al., 2017; Kolpen, et al. 2016). The enhanced killing, in turn, lowers the oxygen consumption in the outer layers of the biofilm, and leads to even deeper penetration of oxygen into the biofilm.

Reconstructing Dynamic Promoter Activity Profiles from Reporter Gene Data.

Accurate characterization of promoter activity is important when designing expression systems for systems biology and metabolic engineering applications. Promoters that respond to changes in the environment enable the dynamic control of gene expression without the necessity of inducer compounds, for example. However, the dynamic nature of these processes poses challenges for estimating promoter activity. Most experimental approaches utilize reporter gene expression to estimate promoter activity. Typically the reporter gene encodes a fluorescent protein that is used to infer a constant promoter activity despite the fact that the observed output may be dynamic and is a number of steps away from the transcription process. In fact, some promoters that are often thought of as constitutive can show changes in activity when growth conditions change. For these reasons, we have developed a system of ordinary differential equations for estimating dynamic promoter activity for promoters that change their activity in response to the environment that is robust to noise and changes in growth rate. Our approach, inference of dynamic promoter activity (PromAct), improves on existing methods by more accurately inferring known promoter activity profiles. This method is also capable of estimating the correct scale of promoter activity and can be applied to quantitative data sets to estimate quantitative rates.

Hyperbaric Oxygen Sensitizes Anoxic Pseudomonas aeruginosa Biofilm to Ciprofloxacin.

Chronic Pseudomonas aeruginosa lung infection is characterized by the presence of endobronchial antibiotic-tolerant biofilm, which is subject to strong oxygen (O2) depletion due to the activity of surrounding polymorphonuclear leukocytes. The exact mechanisms affecting the antibiotic susceptibility of biofilms remain unclear, but accumulating evidence suggests that the efficacy of several bactericidal antibiotics is enhanced by stimulation of aerobic respiration of pathogens, while lack of O2 increases their tolerance. In fact, the bactericidal effect of several antibiotics depends on active aerobic metabolism activity and the endogenous formation of reactive O2 radicals (ROS). In this study, we aimed to apply hyperbaric oxygen treatment (HBOT) to sensitize anoxic P. aeruginosa agarose biofilms established to mimic situations with intense O2 consumption by the host response in the cystic fibrosis (CF) lung. Application of HBOT resulted in enhanced bactericidal activity of ciprofloxacin at clinically relevant durations and was accompanied by indications of restored aerobic respiration, involvement of endogenous lethal oxidative stress, and increased bacterial growth. The findings highlight that oxygenation by HBOT improves the bactericidal activity of ciprofloxacin on P. aeruginosa biofilm and suggest that bacterial biofilms are sensitized to antibiotics by supplying hyperbaric O2.

How fast is a collective bacterial state established?

Bacteria in a biofilm colony have the capacity to monitor the size and growth conditions for the colony and modify their phenotypical behaviour to optimise attacks, defence, migration, etc. The quorum sensing systems controlling this involve production and sensing of diffusive signal molecules. Frequently, quorum sensing systems carry a positive feedback loop which produces a switch at a threshold size of the colony. This all-or-none switch can be beneficial to create a sudden attack, leaving a host little time to establish a defence. The reaction-diffusion system describing a basal quorum sensing loop involves production of signal molecules, diffusion of signal molecules, and detection of signal molecules. We study the ignition process in a numerical solution for a basal quorum sensor and demonstrate that even in a large colony the ignition travels through the whole colony in a less than a minute. The ignition of the positive feedback loop was examined in different approximations. As expected, in the exact calculation the ignition was found to be delayed compared to a calculation where the binding of signal molecules was quasistatic. The buffering of signal molecules is found to have little effect on the ignition process. Contrary to expectation, we find that the ignition does not start when the threshold is reached at the center-instead it allows for the threshold to be approached in the whole colony followed by an almost simultaneous ignition of the whole biofilm aggregate.

High-resolution kinetics and modeling of hydrogen peroxide degradation in live cells.

Although the role of oxidative stress factors and their regulation is well studied, the temporal dynamics of stress recovery is still poorly understood. In particular, measuring the kinetics of stress recovery in the first minutes after acute exposure provides a powerful technique for assessing the role of regulatory proteins or enzymes through the use of mutant backgrounds. This project endeavors to screen the temporal dynamics of intracellular oxidant levels in live cells as a function of gene deletion in the budding yeast, Saccharomyces cerevisiae. Using the detailed time dynamics of extra- and intra-cellular peroxide we have developed a mathematical model that describes two distinct kinetic processes, an initial rapid degradation in the first 10-20min followed by a slower process. Using this model, a qualitative comparison allowed us to assign the dependence of temporal events to genetic factors. Surprisingly, we found that the deletion of transcription factors Yap1p or Skn7p was sufficient to disrupt the establishment of the second degradation phase but not the initial phase. A better fundamental understanding of the role protective factors play in the recovery from oxidative stress may lead to strategies for protecting or sensitizing cell to this stress.

Diffusion Retardation by Binding of Tobramycin in an Alginate Biofilm Model.

Microbial cells embedded in a self-produced extracellular biofilm matrix cause chronic infections, e. g. by Pseudomonas aeruginosa in the lungs of cystic fibrosis patients. The antibiotic killing of bacteria in biofilms is generally known to be reduced by 100-1000 times relative to planktonic bacteria. This makes such infections difficult to treat. We have therefore proposed that biofilms can be regarded as an independent compartment with distinct pharmacokinetics. To elucidate this pharmacokinetics we have measured the penetration of the tobramycin into seaweed alginate beads which serve as a model of the extracellular polysaccharide matrix in P. aeruginosa biofilm. We find that, rather than a normal first order saturation curve, the concentration of tobramycin in the alginate beads follows a power-law as a function of the external concentration. Further, the tobramycin is observed to be uniformly distributed throughout the volume of the alginate bead. The power-law appears to be a consequence of binding to a multitude of different binding sites. In a diffusion model these results are shown to produce pronounced retardation of the penetration of tobramycin into the biofilm. This filtering of the free tobramycin concentration inside biofilm beads is expected to aid in augmenting the survival probability of bacteria residing in the biofilm.

Reinforcement of the bactericidal effect of ciprofloxacin on Pseudomonas aeruginosa biofilm by hyperbaric oxygen treatment.

Chronic Pseudomonas aeruginosa lung infection is the most severe complication in cystic fibrosis patients. It is characterised by antibiotic-tolerant biofilms in the endobronchial mucus with zones of oxygen (O2) depletion mainly due to polymorphonuclear leucocyte activity. Whilst the exact mechanisms affecting antibiotic effectiveness on biofilms remain unclear, accumulating evidence suggests that the efficacy of several bactericidal antibiotics such as ciprofloxacin is enhanced by stimulation of the aerobic respiration of pathogens, and that lack of O2 increases their tolerance. Reoxygenation of O2-depleted biofilms may thus improve susceptibility to ciprofloxacin possibly by restoring aerobic respiration. We tested such a strategy using reoxygenation of O2-depleted P. aeruginosa strain PAO1 agarose-embedded biofilms by hyperbaric oxygen treatment (HBOT) (100% O2, 2.8bar), enhancing the diffusive supply for aerobic respiration during ciprofloxacin treatment. This proof-of-principle study demonstrates that biofilm reoxygenation by HBOT can significantly enhance the bactericidal activity of ciprofloxacin on P. aeruginosa. Combining ciprofloxacin treatment with HBOT thus clearly has potential to improve the treatment of P. aeruginosa biofilm infections.

Microbial biofilm as a smart material.

Microbial biofilm colonies will in many cases form a smart material capable of responding to external threats dependent on their size and internal state. The microbial community accordingly switches between passive, protective, or attack modes of action. In order to decide which strategy to employ, it is essential for the biofilm community to be able to sense its own size. The sensor designed to perform this task is termed a quorum sensor, since it only permits collective behaviour once a sufficiently large assembly of microbes have been established. The generic quorum sensor construct involves two genes, one coding for the production of a diffusible signal molecule and one coding for a regulator protein dedicated to sensing the signal molecules. A positive feedback in the signal molecule production sets a well-defined condition for switching into the collective mode. The activation of the regulator involves a slow dimerization, which allows low-pass filtering of the activation of the collective mode. Here, we review and combine the model components that form the basic quorum sensor in a number of Gram-negative bacteria, e.g., Pseudomonas aeruginosa.

Size of quorum sensing communities.

Ensembles of bacteria are able to coordinate their phenotypic behavior in accordance with the size, density, and growth state of the ensemble. This is achieved through production and exchange of diffusible signal molecules in a cell-cell regulatory system termed quorum sensing. In the generic quorum sensor a positive feedback in the production of signal molecules defines the conditions at which the collective behavior switches on. In spite of its conceptual simplicity, a proper measure of biofilm colony "size" appears to be lacking. We establish that the cell density multiplied by a geometric factor which incorporates the boundary conditions constitutes an appropriate size measure. The geometric factor is the square of the radius for a spherical colony or a hemisphere attached to a reflecting surface. If surrounded by a rapidly exchanged medium, the geometric factor is divided by three. For a disk-shaped biofilm the geometric factor is the horizontal dimension multiplied by the height, and the square of the height of the biofilm if there is significant flow above the biofilm. A remarkably simple factorized expression for the size is obtained, which separates the all-or-none ignition caused by the positive feedback from the smoother activation outside the switching region.

Video surveillance of epilepsy patients using color image processing.

This paper introduces a method for tracking patients under video surveillance based on a color marker system. The patients are not restricted in their movements, which requires a tracking system that can overcome non-ideal scenes e.g. occlusions, very fast movements, lighting issues and other moving objects. The suggested marker system consists of twelve unique markers that are located at each joint. By using a color marker system, each marker (if visible) can be found in every frame disregarding the possibility that it was occluded in the previous frame, compared to other tracking systems.

Kinetic model for signal binding to the Quorum sensing regulator LasR.

We propose a kinetic model for the activation of the las regulon in the opportunistic pathogen Pseudomonas aeruginosa. The model is based on in vitro data and accounts for the LasR dimerization and consecutive activation by binding of two OdDHL signal molecules. Experimentally, the production of the active LasR quorum-sensing regulator was studied in an Escherichia coli background as a function of signal molecule concentration. The functional activity of the regulator was monitored via a GFP reporter fusion to lasB expressed from the native lasB promoter. The new data shows that the active form of the LasR dimer binds two signal molecules cooperatively and that the timescale for reaching saturation is independent of the signal molecule concentration. This favors a picture where the dimerized regulator is protected against proteases and remains protected as it is activated through binding of two successive signal molecules. In absence of signal molecules, the dimerized regulator can dissociate and degrade through proteolytic turnover of the monomer. This resolves the apparent contradiction between our data and recent reports that the fully protected dimer is able to "degrade" when the induction of LasR ceases.

Ligand binding kinetics of the quorum sensing regulator PqsR.

The Pseudomonas aeruginosa quinolone signal (PQS) is a quorum sensing molecule that plays an important role in regulating the virulence of this organism. We have purified the ligand binding domain of the receptor PqsRLBD for PQS and have used Förster resonance energy transfer fluorimetry and kinetic modeling to characterize the ligand binding in vitro. The dissociation constant for binding of PQS to a ligand binding site in (PqsRLBD)2 dimers was determined to be 1.2 ± 0.3 µM. We found no cooperativity in the consecutive binding of two ligand molecules to the dimer.

Automatic multi-modal intelligent seizure acquisition (MISA) system for detection of motor seizures from electromyographic data and motion data.

The objective is to develop a non-invasive automatic method for detection of epileptic seizures with motor manifestations. Ten healthy subjects who simulated seizures and one patient participated in the study. Surface electromyography (sEMG) and motion sensor features were extracted as energy measures of reconstructed sub-bands from the discrete wavelet transformation (DWT) and the wavelet packet transformation (WPT). Based on the extracted features all data segments were classified using a support vector machine (SVM) algorithm as simulated seizure or normal activity. A case study of the seizure from the patient showed that the simulated seizures were visually similar to the epileptic one. The multi-modal intelligent seizure acquisition (MISA) system showed high sensitivity, short detection latency and low false detection rate. The results showed superiority of the multi-modal detection system compared to the uni-modal one. The presented system has a promising potential for seizure detection based on multi-modal data.

Patterns of muscle activation during generalized tonic and tonic-clonic epileptic seizures.

PURPOSE: Tonic seizures and the tonic phase of tonic-clonic epileptic seizures are defined as "sustained tonic" muscle contraction lasting a few seconds to minutes. Visual inspection of the surface electromyogram (EMG) during seizures contributed considerably to a better understanding and accurate diagnosis of several seizure types. However, quantitative analysis of the surface EMG during the epileptic seizures has received surprisingly little attention until now. The aim of our study was to elucidate the pathomechanism of the tonic muscle activation during epileptic seizures. METHODS: Surface EMG was recorded from the deltoid muscles, on both sides, during 63 seizures from 20 patients with epilepsy (10 with generalized tonic and 10 with tonic-clonic seizures). Twenty age- and gender-matched normal controls simulated 100 generalized tonic seizures. To characterize the signal properties we calculated the root mean square (RMS) of the amplitudes, the median frequency (MF), and the coherence. Based on the spectrograms of both epileptic and simulated seizures, we chose to determine the relative spectral power (RP) in the higher (100-500 Hz) frequency domain. KEY FINDINGS: During the tonic seizures there was a significant shift toward higher frequencies, expressed by an increase in the MF and the RP (100-500 Hz). The amplitude characteristic of the signal (RMS) was significantly higher during the tonic phase of the tonic-clonic seizures as compared to the simulated ones, whereas the RMS of the tonic seizures was significantly lower than the simulated ones. The EMG-EMG coherence was significantly higher during the epileptic seizures (both types) as compared to the simulated ones. SIGNIFICANCE: Our results indicate that the mechanism of muscle activation during epileptic seizures is different from the physiologic one. Furthermore the sustained muscle activation during the tonic phase of tonic-clonic seizures is different from that during tonic seizures: The tonic phase of tonic-clonic seizures is characterized by increased amplitude of the signal, whereas tonic seizures are produced by a significant increase in the frequency of the signal.

Seizure onset detection based on one sEMG channel.

We present a new method to detect seizure onsets of tonic-clonic epileptic seizures based on surface electromyography (sEMG) data. The proposed method is generic and based on a single channel making it ideal for a small detection or monitoring device. The sEMG signal is high-pass filtered with a Butterworth filter with a cut-off frequency of 150 Hz. The number of zero-crossings with a hysteresis of ± 50 µV is the only feature extracted. The number of counts in a window of 1 second and the number of windows to make a detection is tested with a leave-one-out method. On 6 patients the method performs with a sensitivity of 100%, a median latency of 7.6 seconds and a median false detection rate of 0.04/h.

Seizure onset detection based on a Uni- or multi-modal intelligent seizure acquisition (UISA/MISA) system.

An automatic Uni- or Multi-modal Intelligent Seizure Acquisition (UISA/MISA) system is highly applicable for onset detection of epileptic seizures based on motion data. The modalities used are surface electromyography (sEMG), acceleration (ACC) and angular velocity (ANG). The new proposed automatic algorithm on motion data is extracting features as "log-sum" measures of discrete wavelet components. Classification into the two groups "seizure" versus "non-seizure" is made based on the support vector machine (SVM) algorithm. The algorithm performs with a sensitivity of 91-100%, a median latency of 1 second and a specificity of 100% on multi-modal data from five healthy subjects simulating seizures. The uni-modal algorithm based on sEMG data from the subjects and patients performs satisfactorily in some cases. As expected, our results clearly show superiority of the multi-modal approach, as compared with the uni-modal one.