The BioMimetic Systems Engineering (BMSE) Laboratory

The BioMimetic Systems Engineering Laboratory (BMSE) at the University of Queensland combines Tissue EngineeringBiomedical Image Analysis, and Computational Biology to study and solve biological and medical problems using biomimetic systems.

We focus on blood vessels and vascularised systems as these are the essential building blocks of mass transport in functional tissue. Our work aligns with chemical engineering fundamentals and clinical collaborators in vascular surgery, neurosurgery, and radiology. Our systems engineering approaches allow us to examine, model, engineer, optimise, control, scale, and automate dynamic systems of several entities such as multi-cellular tissues or cell-material and cell-fluid systems. We engineer biomimetic systems through experimental and computational techniques.

The BMSE Lab is hiring! We will be hiring one postdoctoral research associate and two PhD researchers to start January 2022. We will then be hiring additional PhDs researchers as part of Mark's ARC DECRA project April 2022. We are looking for candidates that have experience in engineered cell culture platforms and data science or computational modelling. The postdoc candidate must have published experience in engineered cell culture systems. Additional details and formal job advertisements are currently under the 'Available Projects' tab of Mark's webpage, and interested candidates are encouraged to email Mark now.

This lab website has recently been launched and is incomplete. Please check back as we update it. Contact us with any problems or questions. 

Further information on BMSE lab's activities, research, projects, and staff can be found through the tabs below:

Contact us

Dr Mark C Allenby
Group Leader, Senior Lecturer

UQ Researchers@MCAllenby

 

We are advertising Postdoc and PhD positions in the BMSE laboratory. Visit Mark's webpage for details.

Dr Mark C Allenby, Senior Lecturer in Biomedical Engineering

Mark leads the BioMimetic Systems Engineering (BMSE) Lab and is a Senior Lecturer in UQ's School of Chemical Engineering. Mark is a future ARC DECRA Fellow (2022-2025), an Advance Queensland Fellow (2019-2022) and an Adjunct Senior Lecturer at QUT. Mark has principally supervised 3 PhDs and 2 MPhil/RAs, co-supervised 7 PhDs and has been awarded $1.7M of funding as chief investigator across 16 competitive funding rounds in 3 years. Mark received a PhD and MSc in chemical engineering from Imperial College London and has undergraduate degrees in mathematics and chemistry. Mark's background includes the engineering of dynamic stem cell bioreactors for tissue biomanufacturing, automated signal and image processing for tissue diagnostics, and model-based optimisation and control of 4D cell systems.

Email: m.allenby@uq.edu.au

Ms Sabrina Schoenborn, 2nd Year PhD Student

Sabrina is a second-year PhD Student at the UQ BioMimetic Systems Engineering (BMSE) Lab and focuses her research on the numerical and experimental characterisation of lower peripheral arteries and vascular graft anastomoses. During her work, Sabrina utilises numerical simulations (FEA, CFD, FSI), computer-aided design (CAD), additive manufacturing (3D printing), medical image segmentation, and plastics and silicone processing to create and validate patient-specific vascular models. She received her Bachelor of Science (Mechanical Engineering) and Master of Science (Plastics and Textile Technology) from RWTH Aachen University in Aachen, Germany and has made the biomedical application of mechanical, textile, and plastics engineering methods the main focus of her work and studies. Her passion is creating real-world impact with medical engineering to improve patient outcomes via science communication and translational research.

Email: s.schoenborn@uq.edu.au

Mr Mitchell Johnson, 1st Year MPhil Student

Mitchell is a first-year MPhil Student at the UQ BioMimetic Systems Engineering (BMSE) Lab and focuses on computational methods to identify, locate, and morphologically analyse Unruptured Intracranial Aneurysms (UIAs). His work focuses on MRA-TOF imagery, voxel visualisation tooling, mesh analysis, and ways to apply deep learning and traditional image analysis techniques towards detection and rupture prediction. He is passionate about using deep learning to produce medical assistance systems that will save lives. Mitchell’s project focuses on using deep learning and traditional image analysis (combined with computational mesh analysis techniques) to understand the ways in which aneurysms can be detected within MRA-TOF imagery. He is working towards a cross-platform 3D voxel annotation system, algorithms for automated aneurysm identification, segmentation, and structure analysis, and an open dataset of aneurysm data for other researchers to use.

Email: mitchell.johnson@uq.edu.au

Mitchell, Mark, and Sabrina catching a beer after a first week at UQ!
Sabrina, Cody, Trent, and Mark after winning the Bionics Queensland Accelerator Grand Challenge (2020)

 

Tissue Engineering

The field of tissue engineering aims to recreate tissue within the laboratory. We engineer synthetic platforms and culture cells to mimic or controllably grow complex and functional tissue at high density and scale. This artificial tissue may have future applications for therapeutics and grafts, testing and optimising interventions, and cellular agriculture. Topics: Biomaterial Fabrication, Bioreactor Engineering, Stem Cell & Tissue Culture.

Biomedical Image Analysis

Imaging remains the gold standard technique to assess tissue quality and function. We capture microscopy and medical images and program algorithms and software to rapidly, automatically, and precisely diagnose our engineered tissue or patient tissue. This imaging data links our experiments to our computational models and to clinical data. Topics: Microscopy, MRI, CT, Segmentation, Statistical Shape Analyses, Co-Localisation, Motility & Fate Tracking

Computational Biology

Predictive models of cell and tissue behaviour are necessary to optimise tissue manufacturing or guide clinical decision-making. Leveraging image analyses and culture experiments, we program multiscale mathematical or statistical models in single-cell, tissue-wide, or multi-tissue systems to link experiments to theory to practice. Topics: Cell Population Models (DE's), Single-Cell Models (Agent-Based), Tissue Biomechanics (FEA).

 

Biofabrication for Personalised Vascular Surgery Prognosis, Training, and Treatment 

Advanced Queensland Industry Research Fellowship (2019-2022)

  • Development of a numerical and experimental model to optimise graft anastomosis in peripheral arteries (Sabrina Schoenborn - UQ)

The primary cause of mid-term occlusive graft failure in small-diameter vascular bypass grafts is the development of intimal hyperplasia. Major causes of intimal hyperplasia have been identified as the tubular compliance mismatch between artery and graft and the anastomotic compliance mismatch between artery and anastomosis device, such as a stiff suture, which attaches the graft to the artery. With advanced vascular grafts offering physiological tubular compliance and biodegradable vascular grafts showing promising results in animal models and clinical trials, the development of compliant biodegradable anastomosis solutions has become an emerging clinical issue. To address this unmet need, a numerical fluid-structure interaction simulation platform is being developed in this project to aid in the design and testing of artery-graft anastomosis strategies and to allow the study of fluid flow and mechanical behaviour around anastomosis sites. Experimental validation is facilitated via compliant silicone arterial phantoms with matched compliance which are manufactured using additive manufacturing technology.

  • A diagnostic software suite using machine learning to predict intracranial aneurysm rupture (Mitchell Johnson - UQ)

Intracranial aneurysms are bulging, weak outpouchings of arteries that supply blood to the brain. They are relatively common, and in rare cases, burst and become subarachnoid haemorrhages with catastrophic 35% mortality and 35% lifelong morbidity rates. While surgical treatments are available to decrease  aneurysm rupture risk, aneurysms are rarely detected prior to rupture and there remains little guidance over which aneurysms are prone to future rupture. Leveraging medical image analysis and data science, this project seeks to develop computational algorithms which can automatically identify aneurysms from brain images and develop fundamental understanding around aneurysm imaging factors which are indicative of rupture risk, such as shape, location, and more. An ultimate goal of this research program is to develop an automated radiology software that can serve as a second set of eyes for the untrained radiologist, rapidly searching through the many unrelated brain images in a healthcare service to screen for aneurysms and, if an aneurysm is identified, predict whether the aneurysm is particularly at-risk of rupture. 

  • Soft robotic devices for emulating vascular mechanobiology (Cody Fell - QUT)

Tissue biomanufacturing aims to produce laboratory-grown stem cell grafts, complex organoid systems, and engineered organs-on-a-chip for clinical therapies and pharmaceutical models. However, biomanufacturing systems remain expensive, inconsistent, and limited in their recapitulation of native tissue mechanics. Soft robotics are ideal platforms for emulating physiologically complex mechanical stimuli to enhance patient-specific tissue maturation. The kneecap’s femoropopliteal artery (FPA) represents a highly flexible tissue across multiple axes during blood flow, walking, standing, and crouching, and these complex biomechanics are implicated in the FPA’s frequent presentation of peripheral artery disease. To investigate how patient-specific FPA mechanics effect lab-grown arterial tissue, we developed a bio-hybrid soft robot (BSR) bioreactor to recapitulate patient-, disease-, and lifestyle-specific mechanobiology for disease understanding, treatment simulations, and for lab-grown tissue grafts.

  • Combining additive manufacturing and soft robotics for improved biomimetic tissue engineered constructs (Brenna Devlin - QUT)

Movement is critical to healthy tissue development. The mechanical forces apparent during a heartbeat, during breathing, and during everyday exercise regulate the performance of individual cells, such as muscle and bone cells, and their interactions within their local tissue microenvironment. Current cell culture platforms fail to recapitulate these mechanical forces, which are necessary to faithfully recreate healthy or diseased tissue in the laboratory. We propose a soft robotic bioreactor able to plug-in 3D cell culture cartridges and impart physiological mechanical loading conditions. We have demonstrated the capabilities of our bioreactor in mimicking flexible arterial tissue in 2D, which we redesign to incorporate melt electrowritten 3D scaffolds. The bioreactor’s multi-axial mechanical biomimicry is a first of its kind, offering tailored tissue morphology and differentiation, well-suited for future musculoskeletal, osteochondral, or dermal tissue regeneration or drug testing.

  • 3D-printed composite biomaterials for personalised vascular implants (Trent Brooks-Richards - QUT)

Bioresorbable vascular stents (BVS) are a highly anticipated transition from metallic stents, potentially reducing common latent complications while allowing restoration of vasomotion. Initial clinical trials of BVS indicate a need for materials with improved mechanical and degradation characteristics. Here, we show a preliminary investigation using graphene oxide (GO) to mechanically reinforce medical-grade poly(ɛ-caprolactone) (PCL) fabricated using fused deposition modelling and melt electrowriting (MEW) toward use in patient-specific bioresorbable stent technology. We evaluate nanocomposite printing ink quality and rheology. Once printed into cylindrical scaffolds of different scales and geometries, we evaluate the improved multi-axial mechanics of the composite ink and endothelial cell regeneration kinetics. Additive manufacturing techniques combined with resorbable, reinforced composite biomaterials such as GO-PCL hold promise as patient-specific stenting solutions to arterial lesions for improved patient outcomes with reduced latent complications.

 

Engineering Tissue Organisation Using Intelligent Additive Biomanufacturing

Australian Research Council DECRA Fellowship (2022-2025)

Replacing wounds with surgical grafts remains challenging as an insufficient mass transfer of nutrients and metabolites can lead to tissue necrosis. Blood vessels must rapidly incorporate throughout tissue grafts for survival, but this is difficult for large grafts or for impaired (diabetic) host tissue. The intra-operative placement of vessel conduits within or around grafts has improved tissue revascularisation and regeneration. However, adding vessels to grafts requires additional morbidity sites and their angiogenic effect remains inconsistent. The project aims to manufacture lab-grown patient-specific grafts with inbuilt vascular conduits optimally designed for defect-specific regeneration and patterned tissue maturation with minimal patient morbidity. These conduit-grafts will be manufactured and validated in bioreactor tissue culture, with an aim toward future animal trials.

Surgical treatments of cerebrovascular conditions, such as intracranial aneurysms, are difficult to optimise for patient-specific conditions due to the variety of presentations and low margin for error. The ability to trial different medical, endovascular or surgical approaches on patient-specific presentations prior to open craniotomy could develop better therapies, but no models recapitulate cerebrovascular: (1) anatomy (2) mechanics and (3) biology simultaneously, all of which influence long-term treatment success rates. These cerebrovascular models would help solve fundamental questions of whether to operate, when to operate, and how to operate. This project will develop a manufacturing framework to generate a soft material macro/microfluidic cerebrovascular mimicry from patient images which in its first design is able to incorporate endothelial cells and medium perfusion to simulate physiological mechanobiology. Cerebrovascular surgery (stent, coil implants) will be simulated in the brain model, which aims to act as a preoperative testbed to compare surgical approaches and engineer better implant designs.

  • Engineering tissue organisation under 3D printed microconfinement and bioreactor mass transport (PhD scholarships avaliable soon)

PhD scholarships related to a ARC DECRA grant aiming to organize and shape the formation of lab-grown tissue by 3D printing structures which control the behaviour of cells. This cell behaviour control will be accomplished through an interdisciplinary and multiscale pipeline of additive micromanufacturing, bioreactor engineering, cell culture, single-cell imaging, and computational modelling. In contrast with current empirical approaches, this quantitative and predictive understanding of how to control biological processes within 3D printed environments will design and engineer more robust, customisable, scalable, and economical cell culture platforms able to optimally manufacture bespoke and complex 3D tissues for future biomedical products. In collaboration with Prof Maria Woodruff (QUT).

    Upcoming Events

    November 15th-19th, 2021: Cody, Sabrina, and Mark will be delivering oral presentations virtually at TERMIS-WC
    • Cody: 3:30pm-5pm on Tuesday 16th November maastricht time – 1130pm-1am brisbane time
    • Mark: 3:30pm-5pm on Tuesday 16th November maastricht time – 1130pm-1am brisbane time
    • Sabrina: 1:30pm-3pm on Wednesday 17th November maastricht time – 930pm-11pm brisbane time
    • Mark: 8:30am-10am on Friday, 19th November maastricht time – 430pm-6pm brisbane time

    October 26th, 2021: Mark will deliver a pre-recorded talk at the Effective Altruism UQ event Alternative Meats at 6pm.

    October 22nd, 2021: Mark will deliver an invited talk at the Queensland Cardiovascular Research Network (QCVRN) at 4:15pm.

    News and Past Events

    September 29th, 2021: Mark's paper 'A spatiotemporal microenvironment model to improve design of a three-dimensional bioreactor for red cell production' has been published in Tissue Engineering Part A  (led by Prof Sakis Mantalaris, Georgia Tech).

    September 28th, 2021: Sabrina and Trent presented their PhD projects at the International Society of Biofabrication Conference! Sabrina presented 'Numerical and Experimental Platform for the Characterisation of Patient Specific Small-Diameter Vascular Graft Anastomoses for Translation to Tissue Engineering' and Trent presented 'Towards Patient-Specific Vascular Stents: Additive Manufacturing of Poly(ɛ-Caprolactone) Mechanically Enhanced with Graphene Oxide'.

    September 25th, 2021: Cody's preprint 'Bio-hybrid soft robotic bioreactors for mimicking multi-axial femoropopliteal artery mechanobiology' is online at bioRxiv  (collaboration with Prof Mia Woodruff, QUT).

    September 24th, 2021: Matt's paper developing 'A quantitative analysis of cell bridging kinetics on a scaffold using computer vision algorithms' has been published in Acta Biomaterialia (led by Prof Mia Woodruff, QUT).

    September 5th, 2021: Habib's paper reviewing 'The effects of COVID-19 on the placenta during pregnancy' has been published in Frontiers in Immunology (led by Dr Arutha Kulasinghe, UQ).

    August 18th, 2021: Mark was awarded a DECRA entitled 'Engineering tissue organisation using intelligent additive biomanufacturing' which will run from March 2022 through 2025. 

    August 5th, 2021: Mark welcomed his first child into the world, Giulia Letizia Allenby! Bring on the sleepless nights!

    August 3rd, 2021: Alex's paper on 'Model-based data analysis of tissue growth in thin 3D printed scaffolds' has been published in the Journal of Theoretical Biology (led by Prof Matthew Simpson, QUT).

    July 20th, 2021: Maureen's paper using 'Using melt-electrowritten microfibres for tailoring scaffold mechanics of 3D bioprinted chondrocyte-laden constructs' has been published in Bioprinting (led by Prof Mia Woodruff, QUT)

    July 10th, 2021: Jared's paper on 'A deep learning method for automatic segmentation of the bony orbit in MRI and CT images' has been published in Scientific Reports (led by Dr. David Alonso-Caneiro, QUT)

    July 5th, 2021: The BMSE Lab started at UQ!