Richard Manasseh

Refining a Protocol for Faecal Microbiota Engraftment in Animal Models After Successful Antibiotic-Induced Gut Decontamination

Publisher: Frontiers Media SA

Date: 09-02-2022

DOI: 10.3389/FMED.2022.770017

Abstract: There is mounting evidence for the therapeutic use of faecal microbiota transplant (FMT) in numerous chronic inflammatory diseases. Germ free mice are not always accessible for FMT research and hence alternative approaches using antibiotic depletion prior to FMT in animal studies are often used. Hence, there is a need for standardising gut microbiota depletion and FMT methodologies in animal studies. The aim of this study was to refine gut decontamination protocols prior to FMT engraftment and determine efficiency and stability of FMT engraftment over time. Male C57BL/6J mice received an antibiotic cocktail consisting of icillin, vancomycin, neomycin, and metronidazole in drinking water for 21 days ad libitum . After antibiotic treatment, animals received either FMT or saline by weekly oral gavage for 3 weeks (FMT group or Sham group, respectively), and followed up for a further 5 weeks. At multiple timepoints throughout the model, stool s les were collected and subjected to bacterial culture, qPCR of bacterial DNA, and fluorescent in-situ hybridisation (FISH) to determine bacterial presence and load. Additionally, 16S rRNA sequencing of stool was used to confirm gut decontamination and subsequent FMT engraftment. Antibiotic treatment for 7 days was most effective in gut decontamination, as evidenced by absence of bacteria observed in culture, and reduced bacterial concentration, as determined by FISH as well as qPCR. Continued antibiotic administration had no further efficacy on gut decontamination from days 7 to 21. Following gut decontamination, 3 weekly doses of FMT was sufficient for the successful engraftment of donor microbiota in animals. The recolonised animal gut microbiota was similar in composition to the donor s le, and significantly different from the Sham controls as assessed by 16S rRNA sequencing. Importantly, this similarity in composition to the donor s le persisted for 5 weeks following the final FMT dose. Our results showed that 7 days of broad-spectrum antibiotics in drinking water followed by 3 weekly doses of FMT provides a simple, reliable, and cost-effective methodology for FMT in animal research.

Experimental comparison between acoustic and pressure signals from a bubbling flow

Publisher: Elsevier BV

Date: 12-2008

DOI: 10.1016/J.CES.2008.08.032

Eigenmodal resonances of polydisperse bubble systems on a rigid boundary

Publisher: Acoustical Society of America (ASA)

Date: 12-2009

DOI: 10.1121/1.3257581

Abstract: 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=R02∕R01, where R01 and R02 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.

Congregation of particles on a plane boundary due to the flow induced by an oscillating sphere

Publisher: AIP Publishing

Date: 07-2022

DOI: 10.1063/5.0096749

Abstract: The complex flow-field associated with a spherical structure oscillating adjacent to a solid boundary is significant in ocean engineering. The dynamic interaction between the flow induced by an oscillating sphere and the boundary is evident not only in terms of flow-field deformation around the structures but also on the boundary in the form of shear stress modifications. The present study aims to understand the influence of a plane boundary on the shear stress distributions and particle motion near the boundary induced by the flow due to a submerged sphere oscillating in a viscous fluid. Experiments are conducted using a non-intrusive flow visualization technique, and three-dimensional direct numerical simulations are used to link the time-mean results of the experiments to the simulated Lagrangian particle drift on the plane boundary. The dye tracer in the experiments and the Lagrangian particles in the simulation congregate at the same location. This stagnation location coincides with a ring of zero mean shear stress centered on the point on the plane boundary through which the axis of oscillation of the sphere passes. This ring of zero mean stress is termed the congregation zone. The radius of the particle congregation zone is investigated as a function of the sphere oscillating litude, Reynolds number, and the distance between the center of the sphere and the plane boundary. Furthermore, a systematic power scaling law is established for the radius of the congregation zone from the control parameters.

Anisotropy in the sound field generated by a bubble chain

Publisher: Elsevier BV

Date: 12-2004

DOI: 10.1016/J.JSV.2003.10.015

Energy loss and developing length during reciprocating flow in a pipe with a free-end

Publisher: AIP Publishing

Date: 08-2020

DOI: 10.1063/5.0011701

Abstract: Direct numerical simulations of reciprocating pipe flow in a straight pipe with a free-end are presented. The range of litudes and frequencies studied span the laminar regime and the beginning of transition toward a conditionally turbulent flow. Two primary results are reported: the measurement of the flow development length and the loss of energy, both due to the presence of the free-end. Two regimes of flow are identified with distinct length scales. For low frequencies, the development length scales with the pipe diameter D. However, for higher frequencies, the development length scales with the Stokes layer thickness δ=2ν/ω. The energy loss is studied by calculating the viscous dissipation function, indicating where energy is lost, and allowing the energy lost due to the presence of the free-end to be isolated. While strong vortices are formed and convected from the exit, most of the energy they dissipate is lost within a few pipe diameters of the exit. It is shown that these trends continue even as the litude and frequency are increased so that the flow begins to transition from a laminar toward a turbulent state. Two modes of instability are observed in the Stokes layers near the free-end, one short wavelength mode with a wavelength set by the Stokes layer thickness and the other long wavelength mode with a wavelength set by the litude of the oscillatory flow. These modes are related to those observed in the fully developed oscillatory flow.

Analysis of time delay effects on a linear bubble chain system

Publisher: Acoustical Society of America (ASA)

Date: 08-2008

DOI: 10.1121/1.2945156

Abstract: A chain of vertically rising discrete air bubbles represents a transition phenomenon from in idual 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 d ing of in idual eigenmodes of the vertical bubble chain are also investigated. It was found that adding time delays can dramatically change the d ing of the different modes of the system while having less dramatic impact on the natural frequencies of the in idual 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.

Cavitation microstreaming and material transport around microbubbles

Publisher: Elsevier BV

Date: 2010

DOI: 10.1016/J.PHPRO.2010.01.056

Air Entrainment Processes in a Circular Plunging Jet: Void-Fraction and Acoustic Measurements

Publisher: ASME International

Date: 09-2003

DOI: 10.1115/1.1595672

Abstract: Circular plunging jets were studied by both void fraction and acoustic techniques. There were two aims: to measure the structure of the jet flow and its regimes as a function of jet speed and free-jet length and to develop and validate the acoustic measurement technique in the developing flow. Void fractions and bubble count rates were measured in the developing shear layer of a large-size plunging jet d1=25 mm. The data compared well with a solution of an advective diffusion equation and showed an increased air entrainment rate with increasing free-jet length for x1/d1⩽12. The acoustic data were processed by a novel technique to extract both bubble count and bubble size data. Three plunging jet flow regimes were noted. Near inception, acoustic pulses are isolated and indicate in idual bubble entrainment as observable visually. Above a characteristic jet velocity, the number of the bubble pulses increases sharply although bubbles are still produced intermittently. At higher velocities, bubble production becomes quasi-continuous. The study suggests that an acoustic technique calibrated through detailed laboratory measurements can provide useful, absolute data in high-void fraction flows. The robust acoustic sensor can then be used in hostile industrial or environmental flows where more delicate instruments are impractical.

Cavitation microstreaming and stress fields created by microbubbles

Publisher: Elsevier BV

Date: 02-2010

DOI: 10.1016/J.ULTRAS.2009.10.002

Abstract: 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 ergence is proposed as a measure relevant to sonoporation.

Measurement of pressure on a surface using bubble acoustic resonances

Publisher: IOP Publishing

Date: 19-01-2010

DOI: 10.1088/0957-0233/21/2/027002

The nature of proximate damped Lyman α systems★

Publisher: Oxford University Press (OUP)

Date: 05-2010

DOI: 10.1111/J.1365-2966.2010.16780.X

Time delays in coupled multibubble systems (L)

Publisher: Acoustical Society of America (ASA)

Date: 2005

DOI: 10.1121/1.1828573

Abstract: D ing constants of free oscillations of coupled gas bubbles change considerably when time delays due to the finite speed of sound in the surrounding liquid are taken into account. This effect is illustrated analytically by the ex le of a two-bubble system and numerically by the ex le of a bubble chain. By comparing the numerical data with experimental measurements, it is shown that allowing for time delays considerably improves agreement between theory and experiment.

On using Helmholtz-type resonance to reduce the size of dual-purpose offshore oscillating water column wave energy converters

Publisher: AIP Publishing

Date: 09-2023

DOI: 10.1063/5.0165334

Chaotic micromixing in open wells using audio-frequency acoustic microstreaming

Publisher: Future Science Ltd

Date: 10-2009

DOI: 10.2144/000113242

Abstract: Mixing fluids for biochemical assays is problematic when volumes are very small (on the order of the 10 µL typical of single drops), which has inspired the development of many micromixing devices. In this paper, we show that micromixing is possible in the simple open wells of standard laboratory consumables using appropriate acoustic frequencies that can be applied using cheap, conventional audio components. Earlier work has shown that the phenomenon of acoustic microstreaming can mix fluids, provided that bubbles are introduced into a specially designed microchamber or that high-frequency surface acoustic wave devices are constructed. We demonstrate a key simplification: acoustic micromixing at audio frequencies by ensuring the system has a liquid-air interface with a small radius of curvature. The meniscus of a drop in a small well provided an appropriately small radius, and so an introduced bubble was not necessary. Microstreaming showed improvement over diffusion-based mixing by 1–2 orders of magnitude. Furthermore, significant improvements are attainable through the utilization of chaotic mixing principles, whereby alternating fluid flow patterns are created by applying, in sequence, two different acoustic frequencies to a drop of liquid in an open well.

Production of monodispersed micron-sized bubbles at high rates in a microfluidic device

Publisher: AIP Publishing

Date: 05-10-2009

DOI: 10.1063/1.3242019

Abstract: A polydimethylsiloxane microchip consisting of a T-junction microchannel network and a thin glass capillary has been developed for the generation of microbubbles. The glass capillary is used to produce an ultrathin gas jet and to controllably block the straight liquid channel, thereby increasing the local liquid velocity near the intersection. Liquid flow rate, liquid viscosity, gas pressure, and inner diameter of the gas jet are varied to investigate the effect on bubble generation. Bubbles with a diameter down to 4.5 μm can be produced at a high rate of 7.5 kHz using a capillary with an inner diameter of 2 μm.

The effects of coupling and bubble size on the dynamical-systems behaviour of a small cluster of microbubbles

Publisher: Elsevier BV

Date: 03-2010

DOI: 10.1016/J.JSV.2009.09.037

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

Publisher: Acoustical Society of America (ASA)

Date: 05-2022

DOI: 10.1121/10.0010377

Abstract: 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.

Modelling underwater noise mitigation of a bubble curtain using a coupled-oscillator model

Publisher: Elsevier BV

Date: 12-2023

DOI: 10.1016/J.JSV.2023.117903

Three-dimensional direct numerical simulation of flow induced by an oscillating sphere close to a plane boundary

Publisher: AIP Publishing

Date: 09-2021

DOI: 10.1063/5.0065651

Abstract: The dynamic interaction of submerged spherical structures with ocean waves alters the local flow field and is responsible for the movement of sediments over the seabed, which would have detrimental effects on the ecosystems. The present research aims to gain insight into the effect of a plane boundary on the vorticity dynamics and shear modifications on the plane boundary induced by the flow due to an oscillating sphere. The flow field around an oscillating sphere close to a plane boundary is investigated numerically by three-dimensional direct numerical simulation of the Navier–Stokes equations. The sphere oscillates perpendicular to the plane boundary modeling the seabed. The flow structure, resulting mean and fluctuating shear stress distribution on the plane boundary, and the Lagrangian particle transport are investigated as a function of the sphere oscillation litude, Reynolds number, and the distance of the sphere from the plane boundary. The systematic correlations for the variation of maximum shear stress on the plane boundary are estimated from scaling parameters. The time-mean results are then linked to the Lagrangian particle transport where it is observed that the Lagrangian path lines track the mean streamlines closely. Further, the particles at the stagnation zone cease drifting and oscillate about a constant mean position. The practical significance of this result is that a ring of zero mean shear on the seabed is found toward where particles congregate. This provides a guide for the optimum location for the mooring anchors, minimizing the risk of anchor scour or undermining.

A coupled damped harmonic oscillator model for arbitrary arrays of floating cylinders using homotopy methods

Publisher: AIP Publishing

Date: 10-2023

DOI: 10.1063/5.0165305

The role of surfactant headgroup, chain length, and cavitation microstreaming on the growth of bubbles by rectified diffusion

Publisher: American Chemical Society (ACS)

Date: 18-11-2011

DOI: 10.1021/JP208862P

Symmetric mode resonance of bubbles attached to a rigid boundary

Publisher: Acoustical Society of America (ASA)

Date: 11-2005

DOI: 10.1121/1.2062268

Abstract: Experimental results are compared with a theoretical analysis concerning wall effects on the symmetric mode resonance frequency of millimeter-sized air bubbles in water. An analytical model based on a linear coupled-oscillator approximation is used to describe the oscillations of the bubbles, while the method of images is used to model the effect of the wall. Three situations are considered: a single bubble, a group of two bubbles, and a group of three bubbles. The results show that bubbles attached to a rigid boundary have lower resonance frequencies compared to when they are in an infinite uniform liquid domain (referred to as free space). Both the experimental data and theoretical analysis show that the symmetric mode resonance frequency decreases with the number of bubbles but increases as the bubbles are moved apart. Discrepancies between theory and experiment can be explained by the fact that distortion effects due to buoyancy forces and surface tension were ignored. The data presented here are intended to guide future investigations into the resonances of larger arrays of bubbles on rigid surfaces, which may assist in surface sonochemistry, sonic cleaning, and micro-mixing applications.

On the propagation of acoustic energy in the vicinity of a bubble chain

Publisher: Elsevier BV

Date: 10-2007

DOI: 10.1016/J.JSV.2007.05.025

Nonlinear dynamic behavior of microscopic bubbles near a rigid wall

Publisher: American Physical Society (APS)

Date: 12-06-2012

DOI: 10.1103/PHYSREVE.85.066309

Discovery Projects - Grant ID: DP130101744

Start Date: 01-2013

End Date: 06-2018

Amount: $435,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP200102671

Start Date: 09-2020

End Date: 02-2024

Amount: $525,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0347947

Start Date: 02-2003

End Date: 06-2006

Amount: $314,599.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP110200499

Start Date: 07-2011

End Date: 09-2016

Amount: $300,000.00

Funder: Australian Research Council

Industrial Transformation Training Centres - Grant ID: IC140100023

Start Date: 04-2015

End Date: 06-2019

Amount: $1,800,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE130100088

Start Date: 2013

End Date: 12-2014

Amount: $275,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP180101109

Start Date: 07-2021

End Date: 06-2024

Amount: $427,000.00

Funder: Australian Research Council

Linkage Infrastructure, Equipment And Facilities - Grant ID: LE0775715

Start Date: 2007

End Date: 12-2008

Amount: $370,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP210101965

Start Date: 06-2021

End Date: 12-2024

Amount: $250,000.00

Funder: Australian Research Council