Transcriptional and functional predictors of potato virus Y-induced tuber necrosis in potato (Solanum tuberosum)

Introduction

Potato (Solanum tuberosum L.), the fourth most important food crop in the world, is affected by several viral pathogens with potato virus Y (PVY) having the greatest economic impact. At least nine biologically distinct variants of PVY are known to infect potato. These include the relatively new recombinant types named PVY-NTN and PVYN-Wi, which induce tuber necrosis in susceptible cultivars. To date, the molecular plant-virus interactions underlying this pathogenicity have not been fully characterized. We hypothesized that this necrotic behavior is supported by transcriptional and functional signatures that are unique to PVY-NTN and PVYN-Wi.

Methods

To test this hypothesis, transcriptional responses of cv. Russet Burbank, a PVY susceptible cultivar, to three PVY strains PVY-O, PVY-NTN, and PVYN-Wi were studied using mRNA-Seq. A haploid-resolved genome assembly for tetraploid potato was used for bioinformatics analysis.

Results

The study revealed 36 GO terms and nine KEGG 24 pathways that overlapped across the three PVY strains, making them generic features of PVY susceptibility in potato. Ten GO terms and three KEGG pathways enriched for PVY-NTN and PVYN-Wi only, which made them candidate functional signatures associated with PVY-induced tuber necrosis in potato. In addition, five other pathways were enriched for PVYNTN or PVYN-Wi. One carbon pool by folate was enriched exclusively in response to PVY-NTN infection; PVYN-Wi infection specifically impacted cutin, suberine and wax biosynthesis, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, and monoterpenoid biosynthesis.

Discussion

Results suggest that PVYN-Wi-induced necrosis may be mechanistically distinguishable from that of PVY-NTN. Our study provides a basis for understanding the mechanism underlying the development of PVY-induced tuber necrosis in potato.

Development of a novel microfluidic biosensing platform integrating micropillar array electrode and acoustic microstreaming techniques

Quantifying biomarkers at the early stage of the disease is challenging due to the low abundance of biomarkers in the sample and the lack of sensitive techniques. This article reports the development of a novel microfluidic electrochemical biosensing platform to address this challenge. The electrochemical sensing is achieved by utilizing a micropillar array electrode (μAE) coated with 3D bimetallic Pt-Pd nanotrees to enhance the sensitivity. A bubble-based acoustic microstreaming technique is integrated with the device to increase the contact of analyte molecules with the surface of electrodes to further enhance the electrochemical performance. The current density of Pt-Pd NTs/μAE with acoustic microstreaming is nearly 22 times that of the bare planar electrode in potassium ferrocyanide solution. The developed biosensor has demonstrated excellent sensing performance. For hydrogen peroxide detection, both the Pt-Pd NTs/μAE and acoustic microstreaming contribute to the sensitivity enhancement. The current density of the Pt-Pd NTs/μAE is approximatively 28 times that of the bare μAE. With acoustic microstreaming, this enhancement is further increased by nearly 1.6 times. The platform has a linear detection range of 5-1000 μM with a LOD of 1.8 μM toward hydrogen peroxide detection, while for sarcosine detection, the linear range is between 5 and 100 μM and LOD is 2.2 μM, respectively. Furthermore, the sarcosine biosensing shows a high sensitivity of 667 μA mM^-1∙cm^-2. Such a sensing platform has the potential as a portable device for high sensitivity detection of biomarkers.

Pathogen-triggered metabolic adjustments to potato virus Y infection in potato

Potato (Solanum tuberosum L) is affected by several viral pathogens with the most economically damaging being potato virus Y (PVY). At least nine biologically distinct variants of PVY are known to attack potato, with necrotic types named PVY^NTN and PVY^N-Wi being the most recent additions to the list. So far, the molecular plant-virus interactions underlying this pathogenicity are not fully understood. In this study, gas chromatography coupled with mass spectroscopy (GC-MS) was used for an untargeted investigation of the changes in leaf metabolomes of PVY-resistant cultivar Premier Russet, and a susceptible cultivar, Russet Burbank, following inoculation with three PVY strains, PVY^NTN, PVY^N-Wi, and PVY^O. Analysis of the resulting GC-MS spectra with the online software Metaboanalyst (version 5.0) uncovered several common and strain-specific metabolites that are induced by PVY inoculation. In Premier Russet, the major overlap in differential accumulation was found between PVY^N-Wi and PVY^O. However, the 14 significant pathways occurred solely due to PVY^N-Wi. In contrast, the main overlap in differential metabolite profiles and pathways in Russet Burbank was between PVY^NTN and PVY^O. Overall, limited overlap was observed between PVY^NTN and PVY^N-Wi. As a result, PVY^N-Wi-induced necrosis may be mechanistically distinguishable from that of PVY^NTN. Furthermore, 10 common and seven cultivar-specific metabolites as potential indicators of PVY infection and susceptibility/resistance were identified by using PLS-DA and ANOVA. In Russet Burbank, glucose-6-phosphate and fructose-6-phosphate were particularly affected by strain-time interaction. This highlights the relevance of the regulation of carbohydrate metabolism for defense against PVY. Some strain- and cultivar-dependent metabolite changes were also observed, reflecting the known genetic resistance-susceptibility dichotomy between the two cultivars. Consequently, engineering broad-spectrum resistance may be the most effective breeding strategy for managing these necrotic strains of PVY.

Analysis of sound pressure levels generated by nozzle-emitted large bubbles

The sound radiated by newly formed bubbles can be used to determine their properties. However, details of the fluid dynamics driving the acoustic emission remain unclear. A neck-collapsing model has been proposed to explain the sound generation at bubble pinch-off. The model uses a forcing function which drives the Rayleigh-Plesset equation and is linked to the bubble acoustic pressure. Here, the model is tested on bubbles of diameter up to 7 mm generated in distilled water, tap water, and alcohol-water solution. The model works well for bubbles less than 2.2 mm radius but the error increases up to 71% for larger diameters.

Extraction of bubble size and number data from an acoustically-excited bubble chain

The passive-acoustic measurement of bubbly flows could potentially deliver data useful to many industrial and environmental applications. However, acoustic interactions between bubbles complicate interpretations of measured frequencies in terms of the bubble sizes that are of practical interest. Experiments were undertaken on the emissions of a bubble chain when a just-formed bubble at one end of the chain created a sound pulse. This is an idealised paradigm for many applications. The chain was a one-dimensional line of bubbles fixed with known bubble sizes and inter-bubble spacings. Frequencies naturally emitted by the chain were measured for various bubble sizes and spacings, including cases such that the bubbles were close to touching. Semi-empirical fits were found relating the bubble size and number to the lowest and highest-measurable peak frequencies. It was found that all data collapsed onto two curves, one for the lowest-peak and one for the highest-peak frequency. This was confirmed by running numerical simulations for wider ranges of parameters than available experimentally. The results suggest that for a bubble chain, measurements of two peak frequencies could be used to determine the bubble size and also the number of interacting bubbles.

Ultrasonically enhanced fractionation of milk fat in a litre-scale prototype vessel

The ultrasonic fractionation of milk fat in whole milk to fractions with distinct particle size distributions was demonstrated using a stage-based ultrasound-enhanced gravity separation protocol. Firstly, a single stage ultrasound gravity separation was characterised after various sonication durations (5-20 min) with a mass balance, where defined volume partitions were removed across the height of the separation vessel to determine the fat content and size distribution of fat droplets. Subsequent trials using ultrasound-enhanced gravity separation were carried out in three consecutive stages. Each stage consisted of 5 min sonication, with single and dual transducer configurations at 1 MHz and 2 MHz, followed by aliquot collection for particle size characterisation of the formed layers located at the bottom and top of the vessel. After each sonication stage, gentle removal of the separated fat layer located at the top was performed. Results indicated that ultrasound promoted the formation of a gradient of vertically increasing fat concentration and particle size across the height of the separation vessel, which became more pronounced with extended sonication time. Ultrasound-enhanced fractionation provided fat enriched fractions located at the top of the vessel of up to 13 ± 1% (w/v) with larger globules present in the particle size distributions. In contrast, semi-skim milk fractions located at the bottom of the vessel as low as 1.2 ± 0.01% (w/v) could be produced, containing proportionally smaller sized fat globules. Particle size differentiation was enhanced at higher ultrasound energy input (up to 347 W/L). In particular, dual transducer after three-stage operation at maximum energy input provided highest mean particle size differentiation with up to 0.9 μm reduction in the semi-skim fractions. Higher frequency ultrasound at 2 MHz was more effective in manipulating smaller sized fat globules retained in the later stages of skimming than 1 MHz. While 2 MHz ultrasound removed 59 ± 2% of the fat contained in the initial sample, only 47 ± 2% was removed with 1 MHz after 3 ultrasound-assisted fractionation stages.

Cavitation and non-cavitation regime for large-scale ultrasonic standing wave particle separation systems--In situ gentle cavitation threshold determination and free radical related oxidation

We here suggest a novel and straightforward approach for liter-scale ultrasound particle manipulation standing wave systems to guide system design in terms of frequency and acoustic power for operating in either cavitation or non-cavitation regimes for ultrasound standing wave systems, using the sonochemiluminescent chemical luminol. We show that this method offers a simple way of in situ determination of the cavitation threshold for selected separation vessel geometry. Since the pressure field is system specific the cavitation threshold is system specific (for the threshold parameter range). In this study we discuss cavitation effects and also measure one implication of cavitation for the application of milk fat separation, the degree of milk fat lipid oxidation by headspace volatile measurements. For the evaluated vessel, 2 MHz as opposed to 1 MHz operation enabled operation in non-cavitation or low cavitation conditions as measured by the luminol intensity threshold method. In all cases the lipid oxidation derived volatiles were below the human sensory detection level. Ultrasound treatment did not significantly influence the oxidative changes in milk for either 1 MHz (dose of 46 kJ/L and 464 kJ/L) or 2 MHz (dose of 37 kJ/L and 373 kJ/L) operation.

Experimental and theoretical analysis of secondary Bjerknes forces between two bubbles in a standing wave

Bubbles in an acoustic field are affected by forces such as primary and secondary Bjerknes forces, which have been shown to be influenced by acoustic pressure, frequency, bubble size and separation distance between bubbles. However, such studies are predominantly theoretical, and are mostly focused on the sign reversal of the secondary Bjerknes force. This study provides experimental data on the effect of a range of bubble sizes (8-30 μm), distances (⩽0.2 mm), acoustic pressures (20-40 kPa) and frequencies (40-100 kHz) on the relative acceleration of two approaching bubbles. Under these conditions, only variations in the magnitude of the attractive force were observed. Using coupled equations of radial and translational motions, the acceleration and secondary Bjerknes force were calculated and compared to the experimental data. The variations in the magnitude of the secondary Bjerknes forces were explained by simulating bubble radius and coupled volume oscillation as a function of time.

Influence of acoustic pressure and bubble sizes on the coalescence of two contacting bubbles in an acoustic field

In this study, the coalescence time between two contacting sub-resonance size bubbles was measured experimentally under an acoustic pressure ranging from 10kPa to 120kPa, driven at a frequency of 22.4kHz. The coalescence time obtained under sonication was much longer compared to that calculated by the film drainage theory for a free bubble surface without surfactants. It was found that under the influence of an acoustic field, the coalescence time could be probabilistic in nature, exhibiting upper and lower limits of coalescence times which are prolonged when both the maximum surface approach velocity and secondary Bjerknes force increases. The size of the two contacting bubbles is also important. For a given acoustic pressure, bubbles having a larger average size and size difference were observed to exhibit longer coalescence times. This could be caused by the phase difference between the volume oscillations of the two bubbles, which in turn affects the minimum film thickness reached between the bubbles and the film drainage time. These results will have important implications for developing film drainage theory to account for the effect of bubble translational and volumetric oscillations, bubble surface fluctuations and microstreaming.

Temperature effects on the ultrasonic separation of fat from natural whole milk

This study showed that temperature influences the rate of separation of fat from natural whole milk during application of ultrasonic standing waves. In this study, natural whole milk was sonicated at 600kHz (583W/L) or 1MHz (311W/L) with a starting bulk temperature of 5, 25, or 40°C. Comparisons on separation efficiency were performed with and without sonication. Sonication using 1MHz for 5min at 25°C was shown to be more effective for fat separation than the other conditions tested with and without ultrasound, resulting in a relative change from 3.5±0.06% (w/v) fat initially, of -52.3±2.3% (reduction to 1.6±0.07% (w/v) fat) in the skimmed milk layer and 184.8±33.2% (increase to 9.9±1.0% (w/v) fat) in the top layer, at an average skimming rate of ∼5g fat/min. A shift in the volume weighted mean diameter (D[4,3]) of the milk samples obtained from the top and bottom of between 8% and 10% relative to an initial sample D[4,3] value of 4.5±0.06μm was also achieved under these conditions. In general, faster fat separation was seen in natural milk when natural creaming occurred at room temperature and this separation trend was enhanced after the application of high frequency ultrasound.

Design parameters for the separation of fat from natural whole milk in an ultrasonic litre-scale vessel

The separation of milk fat from natural whole milk has been achieved by applying ultrasonic standing waves (1 MHz and/or 2 MHz) in a litre-scale (5L capacity) batch system. Various design parameters were tested such as power input level, process time, specific energy, transducer-reflector distance and the use of single and dual transducer set-ups. It was found that the efficacy of the treatment depended on the specific energy density input into the system. In this case, a plateau in fat concentration of ∼20% w/v was achieved in the creamed top layer after applying a minimum specific energy of 200 kJ/kg. In addition, the fat separation was enhanced by reducing the transducer reflector distance in the vessel, operating two transducers in a parallel set-up, or by increasing the duration of insonation, resulting in skimmed milk with a fat concentration as low as 1.7% (w/v) using raw milk after 20 min insonation. Dual mode operation with both transducers in parallel as close as 30 mm apart resulted in the fastest creaming and skimming in this study at ∼1.6 g fat/min.

From mechanical stimulation to biological pathways in the regulation of stem cell fate

Mechanical stimuli are important in directing the fate of stem cells; the effects of mechanical stimuli reported in recent research are reviewed here. Stem cells normally undergo two fundamental processes: proliferation, in which their numbers multiply, and differentiation, in which they transform into the specialized cells needed by the adult organism. Mechanical stimuli are well known to affect both processes of proliferation and differentiation, although the complete pathways relating specific mechanical stimuli to stem cell fate remain to be elucidated. We identified two broad classes of research findings and organized them according to the type of mechanical stress (compressive, tensile or shear) of the stimulus. Firstly, mechanical stress of any type activates stretch-activated channels (SACs) on the cell membrane. Activation of SACs leads to cytoskeletal remodelling and to the expression of genes that regulate the basic growth, survival or apoptosis of the cells and thus regulates proliferation. Secondly, mechanical stress on cells that are physically attached to an extracellular matrix (ECM) initiates remodelling of cell membrane structures called integrins. This second process is highly dependent on the type of mechanical stress applied and result into various biological responses. A further process, the Wnt pathway, is also implicated: crosstalk between the integrin and Wnt pathways regulates the switch from proliferation to differentiation and finally regulates the type of differentiation. Therefore, the stem cell differentiation process involves different signalling molecules and their pathways and most likely depends upon the applied mechanical stimulation.

Effects of coupling, bubble size, and spatial arrangement on chaotic dynamics of microbubble cluster in ultrasonic fields

Microbubble clustering may occur when bubbles become bound to targeted surfaces or are grouped by acoustic radiation forces in medical diagnostic applications. The ability to identify the formation of such clusters from the ultrasound echoes may be of practical use. Nonlinear numerical simulations were performed on clusters of microbubbles modeled by the modified Keller-Miksis equations. Encapsulated bubbles were considered to mimic practical applications but the aim of the study was to examine the effects of inter-bubble spacing and bubble size on the dynamical behavior of the cluster and to see if chaotic or bifurcation characteristics could be helpful in diagnostics. It was found that as microbubbles were clustered closer together, their oscillation amplitude for a given applied ultrasound power was reduced, and for inter-bubble spacing smaller than about ten bubble radii nonlinear subharmonics and ultraharmonics were eliminated. For clustered microbubbles, as for isolated microbubbles, an increase in the applied acoustic power caused bifurcations and transition to chaos. The bifurcations preceding chaotic behavior were identified by Floquet analysis and confirmed to be of the period-doubling type. It was found that as the number of microbubbles in a cluster increased, regularization occurred at lower ultrasound power and more windows of order appeared.

Quantitative guidelines for the prediction of ultrasound contrast agent destruction during injection

Experiments and theory were undertaken on the destruction of ultrasound contrast agent microbubbles on needle injection, with the aim of predicting agent loss during in vivo studies. Agents were expelled through a variety of syringe and needle combinations, subjecting the microbubbles to a range of pressure drops. Imaging of the bubbles identified cases where bubbles were destroyed and the extent of destruction. Fluid-dynamic calculations determined the pressure drop for each syringe and needle combination. It was found that agent destruction occurred at a critical pressure drop that depended only on the type of microbubble. Protein-shelled microbubbles (sonicated bovine serum albumin) were virtually all destroyed above their critical pressure drop of 109 ± 7 kPa Two types of lipid-shelled microbubbles were found to have a pressure drop threshold above which more than 50% of the microbubbles were destroyed. The commercial lipid-shelled agent Definity was found to have a critical pressure drop for destruction of 230 ± 10 kPa; for a previously published lipid-shelled agent, this value was 150 ± 40 kPa. It is recommended that attention to the predictions of a simple formula could preclude unnecessary destruction of microbubble contrast agent during in vivo injections. This approach may also preclude undesirable release of drug or gene payloads in targeted microbubble therapies. Example values of appropriate injection rates for various agents and conditions are given.

A novel mouse model of atherosclerotic plaque instability for drug testing and mechanistic/therapeutic discoveries using gene and microRNA expression profiling

RATIONALE

The high morbidity/mortality of atherosclerosis is typically precipitated by plaque rupture and consequent thrombosis. However, research on underlying mechanisms and therapeutic approaches is limited by the lack of animal models that reproduce plaque instability observed in humans.

OBJECTIVE

Development and use of a mouse model of plaque rupture that reflects the end stage of human atherosclerosis.

METHODS AND RESULTS

On the basis of flow measurements and computational fluid dynamics, we applied a tandem stenosis to the carotid artery of apolipoprotein E-deficient mice on high-fat diet. At 7 weeks postoperatively, we observed intraplaque hemorrhage in ≈50% of mice, as well as disruption of fibrous caps, intraluminal thrombosis, neovascularization, and further characteristics typically seen in human unstable plaques. Administration of atorvastatin was associated with plaque stabilization and downregulation of monocyte chemoattractant protein-1 and ubiquitin. Microarray profiling of mRNA and microRNA (miR) and, in particular, its combined analysis demonstrated major differences in the hierarchical clustering of genes and miRs among nonatherosclerotic arteries, stable, and unstable plaques and allows the identification of distinct genes/miRs, potentially representing novel therapeutic targets for plaque stabilization. The feasibility of the described animal model as a discovery tool was established in a pilot approach, identifying a disintegrin and metalloprotease with thrombospondin motifs 4 (ADAMTS4) and miR-322 as potential pathogenic factors of plaque instability in mice and validated in human plaques.

CONCLUSIONS

The newly described mouse model reflects human atherosclerotic plaque instability and represents a discovery tool toward the development and testing of therapeutic strategies aimed at preventing plaque rupture. Distinctly expressed genes and miRs can be linked to plaque instability.

Nonlinear dynamic behavior of microscopic bubbles near a rigid wall

The nonlinear dynamic behavior of microscopic bubbles near a rigid wall is investigated. Oscillations are driven by the ultrasonic pressure field that arises in various biomedical applications such as ultrasound imaging or targeted drug delivery. It is known that, when bubbles approach a blood-vessel wall, their linear dynamic response is modified. This modification may be very useful for real-time detection of bubbles that have found targets; in future therapeutic technologies, it may be useful for controlled release of medical agents encapsulating microbubbles. In this paper, the nonlinear response of microbubbles near a wall is studied. The Keller-Miksis-Parlitz equation is adopted, but modified to account for the presence of a rigid wall. This base model describes the time evolution of the bubble surface, which is assumed to remain spherical, and accounts for the effect of acoustic radiation losses owing to liquid compressibility in the momentum conservation. Two situations are considered: the base case of an isolated bubble in an unbounded medium, and a bubble near a rigid wall. In the latter case, the wall influence is modeled by including a symmetrically oscillating image bubble. The bubble dynamics is traced using a numerical solution of the model equation. Subsequently, Floquet theory is used to accurately detect the bifurcation point where bubble oscillations stop following the driving ultrasound frequency and undergo period-changing bifurcations. Of particular interest is the detection of the subcritical period-tripling and -quadrupling transition. The parametric bifurcation maps are obtained as functions of nondimensional parameters representing the bubble radius, the frequency and pressure amplitude of the driving ultrasound field, and the distance from the wall. It is shown that the presence of the wall generally stabilises the bubble dynamics, so that much larger values of the pressure amplitude are needed to generate nonlinear responses. Thus, a clinical protocol in which selected nonlinear harmonics are examined under varying insonation amplitudes may be useful in detecting microbubble proximity to walls.

Acoustic microstreaming increases the efficiency of reverse transcription reactions comprising single-cell quantities of RNA

Correlating gene expression with behavior at the single-cell level is difficult, largely because the small amount of available mRNA (<1 pg) degrades before it can be reverse transcribed into a more stable cDNA copy. This study tested the capacity for a novel acoustic microstreaming method ("micromixing"), which stirs fluid at microliter scales, to improve cDNA yields from reverse transcription (RT) reactions comprising single-cell quantities of RNA. Micromixing significantly decreased the number of qPCR cycles to detect cDNA representing mRNA for hypoxanthine phosphoribosyl-transferase (Hprt) and nuclear receptor-related 1 (Nurr1) by ~9 and ~15 cycles, respectively. The improvement was equivalent to performing RT with 10- to 100-fold more cDNA in the absence of micromixing. Micromixing enabled reliable detection of the otherwise undetectable, low-abundance transcript, Nurr1. It was most effective when RNA concentrations were low (0.1-1 pg/µL, a "single-cell equivalent") but had lesser effects at higher RNA concentrations (~1 ng/µL). This was supported by imaging experiments showing that micromixing improved mixing of a low concentration (20 pg/µL) of fluorescence-labeled RNA but not a higher concentration (1 ng/µL). We conclude that micromixing significantly increases RT yields obtainable from single-cell quantities of RNA.

Increasing cDNA yields from single-cell quantities of mRNA in standard laboratory reverse transcriptase reactions using acoustic microstreaming

Correlating gene expression with cell behavior is ideally done at the single-cell level. However, this is not easily achieved because the small amount of labile mRNA present in a single cell (1-5% of 1-50 pg total RNA, or 0.01-2.5 pg mRNA, per cell) mostly degrades before it can be reverse transcribed into a stable cDNA copy. For example, using standard laboratory reagents and hardware, only a small number of genes can be qualitatively assessed per cell. One way to increase the efficiency of standard laboratory reverse transcriptase (RT) reactions (i.e. standard reagents in microliter volumes) comprising single-cell amounts of mRNA would be to more rapidly mix the reagents so the mRNA can be converted to cDNA before it degrades. However this is not trivial because at microliter scales liquid flow is laminar, i.e. currently available methods of mixing (i.e. shaking, vortexing and trituration) fail to produce sufficient chaotic motion to effectively mix reagents. To solve this problem, micro-scale mixing techniques have to be used. A number of microfluidic-based mixing technologies have been developed which successfully increase RT reaction yields. However, microfluidics technologies require specialized hardware that is relatively expensive and not yet widely available. A cheaper, more convenient solution is desirable. The main objective of this study is to demonstrate how application of a novel "micromixing" technique to standard laboratory RT reactions comprising single-cell quantities of mRNA significantly increases their cDNA yields. We find cDNA yields increase by approximately 10-100-fold, which enables: greater numbers of genes to be analyzed per cell; more quantitative analysis of gene expression; and better detection of low-abundance genes in single cells. The micromixing is based on acoustic microstreaming, a phenomenon where sound waves propagating around a small obstacle create a mean flow near the obstacle. We have developed an acoustic microstreaming-based device ("micromixer") with a key simplification; acoustic microstreaming can be achieved at audio frequencies by ensuring the system has a liquid-air interface with a small radius of curvature. The meniscus of a microliter volume of solution in a tube provides an appropriately small radius of curvature. The use of audio frequencies means that the hardware can be inexpensive and versatile, and nucleic acids and other biochemical reagents are not damaged like they can be with standard laboratory sonicators.

Development of optimized vascular fractal tree models using level set distance function

Using the concepts of fractal scaling and constrained constructive optimization (CCO), a branching tree model, which has physiologically meaningful geometric properties, can be constructed. A vascular branching tree model created in this way, although statistically correct in representing the vascular physiology, still does not possess a physiological correct arrangement of the major arteries. A distance-function based technique for "staged growth" of vascular models has been developed in this work to address this issue. Time-dependent constraints based on a signed-distance level set function have been added, so that the tree models will first be grown near the designated surface(s) and, then, gradually allowed to penetrate into the enclosed volume. The proposed technique has been applied to construct a model of the human cerebral vasculature, which is characterized by the above-mentioned distribution of the arteries.

Cavitation microstreaming and stress fields created by microbubbles

Cavitation microstreaming plays a role in the therapeutic action of microbubbles driven by ultrasound, such as the sonoporative and sonothrombolytic phenomena. Microscopic particle-image velocimetry experiments are presented. Results show that many different microstreaming patterns are possible around a microbubble when it is on a surface, albeit for microbubbles much larger than used in clinical practice. Each pattern is associated with a particular oscillation mode of the bubble, and changing between patterns is achieved by changing the sound frequency. Each microstreaming pattern also generates different shear stress and stretch/compression distributions in the vicinity of a bubble on a wall. Analysis of the micro-PIV results also shows that ultrasound-driven microstreaming flows around bubbles are feasible mechanisms for mixing therapeutic agents into the surrounding blood, as well as assisting sonoporative delivery of molecules across cell membranes. Patterns show significant variations around the bubble, suggesting sonoporation may be either enhanced or inhibited in different zones across a cellular surface. Thus, alternating the patterns may result in improved sonoporation and sonothrombolysis. The clear and reproducible delineation of microstreaming patterns based on driving frequency makes frequency-based pattern alternation a feasible alternative to the clinically less desirable practice of increasing sound pressure for equivalent sonoporative or sonothrombolytic effect. Surface divergence is proposed as a measure relevant to sonoporation.

Eigenmodal resonances of polydisperse bubble systems on a rigid boundary

This paper presents theory and experimental data on the resonance frequency of systems consisting of different-sized air bubbles attached to a rigid wall. Effects of the change in resonant frequency with bubble size and distance between the bubbles were studied. It was found that the symmetric mode resonance frequency of the bubble system decreased with increasing r=R(02)/R(01), where R(01) and R(02) are the equilibrium radii of bubbles in the system. Both the symmetric and antisymmetric modes of oscillation were detected in the experiments, with the resonant frequency of the symmetric mode dominant at small bubble separation and the frequency of the antisymmetric mode dominant when the bubbles were farther apart. A linear coupled-oscillator theoretical model was used to describe the oscillations of the bubble system, in which the method of images was used to approximate the effects of the wall. It was found that there was fair to good agreement between the predictions of the coupled-oscillator model with the experimental data.

Dynamics of pulsatile flow in fractal models of vascular branching networks

Efficient regulation of blood flow is critically important to the normal function of many organs, especially the brain. To investigate the circulation of blood in complex, multi-branching vascular networks, a computer model consisting of a virtual fractal model of the vasculature and a mathematical model describing the transport of blood has been developed. Although limited by some constraints, in particular, the use of simplistic, uniformly distributed model for cerebral vasculature and the omission of anastomosis, the proposed computer model was found to provide insights into blood circulation in the cerebral vascular branching network plus the physiological and pathological factors which may affect its functionality. The numerical study conducted on a model of the middle cerebral artery region signified the important effects of vessel compliance, blood viscosity variation as a function of the blood hematocrit, and flow velocity profile on the distributions of flow and pressure in the vascular network.

Analysis of time delay effects on a linear bubble chain system

A chain of vertically rising discrete air bubbles represents a transition phenomenon from individual to continuum behavior in a bubbly liquid. Previous studies have reported that there is a preference for acoustic energy to propagate along the bubble chain and that this behavior could be explained by a coupled-oscillator model. However, it has recently been demonstrated that quantitative results from the coupled-oscillator model do not match experimental data. In this paper, it is shown how adding time delays to the coupled-oscillator model can produce results that are in better agreement with experimental data. In addition, the effects of time delays on the natural frequencies and damping of individual eigenmodes of the vertical bubble chain are also investigated. It was found that adding time delays can dramatically change the damping of the different modes of the system while having less dramatic impact on the natural frequencies of the individual eigenmodes. Counterintuitively, it is found that the effects of time delays appear to be more important when the bubbles are closer together than when they are farther apart.