Human Practices

Integrated Human Practices


Limitations of traditional gene regulation

In research involving genetic engineering, the tools available for the control of gene expression in cell-based systems are limited - whether by timescale, spatial resolution, cost, or a combination of the three. These limitations were identified following a thorough literature review of current synthetic biology approaches to modulating gene expression. As these techniques comprise a fundamental basis of research in many areas of biology from medicine to biomanufacturing we recognised the importance of continuing to develop new methods to the limitations of existing techniques, and so chose to address this need with our project. 


Sonogenetics

To learn more about the technologies available for gene regulation, we contacted the sonogenetics researcher Dr Stuart Ibsen from Oregon’s Health and Science University. Dr. Ibsen has PhDs in zoology and biomedical engineering and has worked on bioacoustics, drug delivery, and drug dosage. Through our meeting with him, we learned about sonogenetic techniques; sonogenetics encompasses a range of non-invasive techniques for the regulation of gene expression using low-pressure ultrasound. Ultrasound is fired into a subject engineered with sensitive channels; at the focal point of the ultrasound, these channels open and a pathway is activated. This has a resolution of approximately 1 cubic millimetre when amplified using injected lipid microbubbles containing perfluorohexane (Ibsen et al., 2015). The technique is powerful but can require large and expensive equipment to set up and is very difficult to focus with high resolution or precision in tissues or organs containing gas because this significantly distorts ultrasound signals. Using sonogenetics also requires a high level of technical expertise, making it impractical for small labs. These restrictions combined with its relative novelty mean it has not yet been widely adopted as a standard method of regulating gene expression although it holds a high degree of potential for future application (Liu et al., 2022; Pan et al., 2018).

Screenshot of zoom call
Interview with Dr. Stuart Ibsen
Pixel art of a magpie holding a microphone Pixel art of a magpie holding a microphone


Optogenetics

A mouse undergoing optogenetic research
A mouse undergoing an optogenetics experiment; credit: Dr Mike J F Robinson
Pixel art of a magpie holding a laser pointer

The more established field of optogenetics is where we looked to next to gain some insight. Optogenetics technology is based on photosensitive ion channels which open upon exposure to specific wavelengths of light. To do this, we contacted an industry representative from an optogenetics firm (anonymous) to learn about how their business is run and further details of the technology not easily accessible online. In this meeting, we discussed the costs and training required to operate optogenetics equipment, as well as the capabilities of the technology. Optogenetics is capable of a high level of both spatial and temporal precision, however can only function in 2 dimensions. This can require live subjects to have surgery, which can significantly disturb the system being studied. This is particularly an issue when studying the brain since if it has been operated on it will produce different signals to a normal brain and so interfere with experiments monitoring brain activity. The reason optogenetics is so prevalent is its relatively simple setup for use cases requiring less precision, requiring equipment in the 5-10 thousand dollar range (from this manufacturer) and can be easily operated. For more complex systems requiring a higher degree of precision though, up to 100 thousand dollars might be required.  Its highly flexible and established pathways make it suited for regulating 2 dimensional systems’ gene expression. One important thing we learned from this interview is that the optogenetics systems sold by this firm are primarily for academic use. This better understanding of the demand for gene regulation systems helped us to guide how we implemented and developed our technology.



Following this, we carefully considered where our project could fill in the gaps in the existing technology, ultimately deciding on a project in magnetogenetics. The system we chose to achieve this focused on the stimulation of pathways using magnetic nanoparticles (MNPs) and a magnetosensitive protein. Magnetic fields hold the rare advantage that they are unaffected by any non-metallic materials so can be used on any organism at any scale if enough power is provided.  We were also intrigued by the emerging use of Boolean logic in Biology, thus deciding on our final goal: to create a system capable of remote and precise 3-dimensional activation of genetic pathways based on a genetic AND gate.

After the speaking to experts and conducting an additional literature review, we compiled our notes and thoughts into one table as below to compare magnetogenetics with the current state of alternative methods of control of gene expression:

Comparison to magnetogenetics
System Advantages Disadvantages
Chemical induction
  • Early technique, so well-established
  • Chemicals can be more useful in biomanufacturing as they may not need to be removed from the product, or can be removed more easily
  • Require little additional initial investment, only the chemical itself
  • Does not work well inside solid culture as it may not diffuse well or could disturb tissue
  • No control over diffusion - low spatial resolution
Optogenetics
  • Does not require the use of of nanoparticles, therefore:
    • Fewer biocompatibility considerations for therapeutic uses
    • Lower material cost
    • Higher purity for biomanufacturing use cases
  • Lower power requirements
  • Millisecond precision - high temporal resolution (Boyden et al., 2005)
  • Poor penetration depth
  • In 3D models (i.e. animals) invasive surgery is required to insert fibre optic cables; this is highly specialised and expensive
  • The invasive preparation required for use in neuroscience means that the brain is not in its usual state
  • Usually only two dimensional
Sonogenetics
  • Does not require the use of nanoparticles
  • Lower long-term costs (at low precision ranges)
  • Microbubbles are very cheap - much cheaper than medical grade nanoparticles
  • Lower resolution - microbubbles improve this but only to some extent
  • Low pressure ultrasound can only penetrate a few cubic millimetres into thin bone and deep tissue, unlike magnetic fields
  • Air pockets distort ultrasound signals, making it impractical to use in some tissues and organs (such as lungs and intestines)
  • Difficult to use since it requires high levels of expertise and training
  • Expensive equipment so high initial cost - typical signal amplifiers required are £10,000 and require professional installation

Setting out our key values

We next set out our key values for the project, in order to guide our motives and questioning of stakeholders.

Accessibility was at the forefront of our design choices throughout our project, including financial accessibility - encompassing the cost of our hardware - and ease of use - the level of skills training which would be required by academics, doctors and industry professionals who may use Magenta. In terms of financial accessibility, we ultimately achieved a low total cost of only £324.80 ($430.80 USD) to build our hardware.

Diligence was a reminder to consider a comprehensive range of stakeholder areas and views, in order for our project to have the greatest positive impact.

Our focus on innovation helped us to minimise redundant overlap with existing technologies.

Diagram containing the phrase 'key values' surrounded by four terms: diligence, ease of use, innovation, and financial accessibility
Our initial key values for the project

Specific applications to guide our engineering process

With the focus of our project confirmed, we set out to refine our eventual application ideas to ensure that the technology we developed would benefit the stakeholders involved. Initially we had three fields to focus on:

  • Organoid research
  • Biomanufacturing
  • Neuroscience

To learn more about each field and how magnetogenetics might influence it, we first approached experts in academia. We aimed to gain an insight into their work and how magnetogenetics might be able to help them, so that their needs and opinions could inform our design process.

To ensure that our discussions remained productive and aligned with our engineering process throughout the project, we also established the ‘Three I Framework’, as shown below.

A cycle between the terms Idea, Interact, and Integrate. Each term is connected to a larger text box. Idea - a way in which magnetogenetics might influence or improve the field considered; Interact - have a discussion with a range of stakeholders about our idea; Integrate - assess how the stakeholder feedback can aid our engineering, and following up on their advice
Our three I framework

To plan for our interactions, we used our key values to inform our initial interview questions.

A repeat of the key values diagram earlier in the page, but each term is now connected to a question. Ease of use - What training would be required for professionals to use this technology? Diligence - What steps should we take to carefully consider each stakeholder involved? Innovation - What are the key USPs of our project versus current methods? Financial accessibility - How expensive is current technology, and how can we make our hardware as inexpensive as possible?
Our key values and their related interview questions

Organoid Research

Organoids are an area of research incredibly important for developing our understanding of organ development and stem cells, which are crucial for the eventual development of lab-grown organs for transplant. Organoid researchers have faced issues with inducing morphogen gradients for setting up development axes of organs - what allows the organ to develop into something recognisable rather than a bundle of tissue. 

Idea: magnetogenetics could be used to express morphogens or transcription factors in organoids to set up development axes and help to guide morphogen development, resulting in an organoid more representative of a real organ rather than unorganised tissues. This could allow organoid researchers new avenues for testing and accelerate existing protocols.


Good potential in organoids research

Interaction: We discussed our ideas with Jonas Cerneckis , a researcher at Yanhong Shi’s lab at City of Hope California. He primarily studies stem cells, organoid development, and neurodegenerative disease with a particular focus on Alzheimer’s. In response to our questions about the feasibility of using a magnetogenetic AND gate in organoid development, Jonas shared our excitement about this idea.

Integration: He advised us to consider the spatial resolution, which would need to be at millimetre precision given that brain organoids can be around 4 mm in diameter. Seeing the need for this level of precision, we therefore designed an AND gate requiring two orthogonal magnetic fields to aim towards this. Our field models indicate that the parameters chosen should theoretically be able to achieve 35mm accuracy.


Interaction: Jonas also suggested magnetogenetics to be a potentially cheaper and easier way to control organ-on-a-chip systems (OOC) which are currently used to model multi-organ systems. OOCs are an expensive but effective method of testing drugs and their effects across multiple organ systems without using a full organism by simulating connections and using cultured tissue (Leung et al., 2022).

Integration: While this is a prospect we found exciting, we judged it to be far beyond the scope of the iGEM project’s time and budgetary limitations.


Interaction: Jonas brought to our attention one of the most significant benefits that magnetogenetics has in neuroscience over optogenetic systems: a brain which has had surgery done on it does not behave normally so becomes significantly less useful for research purposes. With magnetogenetic control, this is not an issue as (MNPs) can simply diffuse across the blood-brain barrier, leaving the brain in an undisturbed state. Responses to the stimulus can then be measured as usual and give a normal response. Seeing how enthusiastically he spoke about this, we realised the potential of magnetogenetics-based systems in neuroscience.


Interaction: In response to our thoughts about potential therapeutic applications, Jonas raised an idea we found particularly exciting: utilising magnetogenetics to reduce off-site toxicity of CAR T cell therapies. CAR T-cell therapy is a form of immunotherapy where a patient's T-cells are genetically modified to express a chimeric antigen receptor (CAR) that enables them to target and destroy cancer cells by targeting overexpressed antigens and triggering apoptosis pathways.

Integration: Building on his suggestion, we proposed that a CAR T cell could be bound to a number of MNPs before re-introduction to the body. Then, using a series of genetic AND gates the T cell would only be able to function in an area where both correct antigens and a set of overlapping magnetic fields are present, thus preventing offsite activity and reducing side effects of the therapy and in theory reducing recovery time. A proof of concept has been done using sonogenetics and we are keen to attempt to replicate this success using magnetogenetics, but unfortunately this would not be possible within the timescale of iGEM (Pan et al., 2018).


Upper image shows a professional headshot. Lower image shows the logo of the City of Hope Orange County hospital
Jonas Cerneckis, researcher at City of Hope, California

Revising our key values following our initial interactions

An important point raised by Jonas was to be cautious about ‘overengineering’ where simpler solutions may work better. This guided us to focus on how our project could solve complex problems beyond the scope of existing technologies. Furthermore, we did not want to risk overselling our project, particularly in the context of vulnerable or less informed stakeholders such as patients or the general public. To remind us of this, we added ‘transparency’ to our key values.

A further expansion of the previous key value images, this time with an extra term 'Transparency', and an associated question (How can we avoid 'overselling' our project?)
Our key values with transparency added

Biomanufacturing

From the beginning of the project, we had been interested in biomanufacturing as a potential use case for magnetogenetics following optogenetics firm Prolific Machines’ recent $55m investment campaign. Biomanufacturing is the group of technologies focused on the production of pharmaceuticals chemicals and proteins using microorganisms.

Idea: Magnetogenetics, like optogenetics, could be used as a way to control cultures in bioreactors to optimise expression timescales. This could maximise yields and potentially allow for generation of chemicals not previously possible to make. Magnetogenetics might hold an advantage as it is capable of penetrating optically dense media effectively

Discussion with industry representative 1

We were able to get in touch with with Dr Jeannette Gebel, an R&D scientist at the optogenetics firm Ningaloo Biosystems which specialises in small-scale bioreactors.

Interaction: Dr. Gebel suggested that if magnetogenetics were to be used in biomanufacturing, the tightness of the system would need to be well-characterised. The system should be capable of a low resting state and high activated state operating uniformly across a single reaction vessel, as well as viable on multiple scales.

Integration: Reflecting on these ideas and the required parameters for larger reaction vessels, we decided that magnetogenetics may not be as suitable for biomanufacturing as we had initially thought. Reaction vessels could not contain any metal which could interact with fields, requiring them to be fully custom and impractical above a few litres. While it is beneficial in penetrating an optically dense medium, the strengths of magnetogenetics lie in its spatial precision. For most biomanufacturing use cases, optogenetically and chemically induced systems represent a more appropriate solution.

Upper image: A professional headshot; Lower image: the logo of Ningaloo biosystems
Dr Jeannette Goobel, R&D scientist at Ningaloo biosystems

Discussion with industry representative 2

Image of team member Will Cassie looking at his laptop

Interaction: A meeting with another industry-leading optogenetics firm that wished to remain anonymous provided similar insights into a magnetogenetics biomanufacturing application. Almost all of their optogenetics products were designed for spatial precision and flexibility rather than biomanufacturing.

Integration: This inspired us to also focus on the strengths of magnetogenetics and to give up on optimising for bioreactor use. With this in mind, we narrowed our focus on optimising the spatial precision our system would be capable of. As mentioned previously, our modelling has indicated that the parameters chosen should theoretically achieve an accuracy of 35mm.

Neuroscience

In recent years, neuroscience research has been revolutionised by the development of optogenetics. Its ability to spatially control the activity of neurons using photostimulation has allowed researchers to gain important insights into brain function and dysfunction. This research is hoped to be translated into clinical applications in central nervous system disease in the near future. Given the success of optogenetics in neuroscience research - but also the limitations we had discovered - we were keen to find out where our project could aid neuroscientists and be used in medical applications (Emiliani et al., 2022).

Upper image: Dr. Shilei Ni; Lower image: Shandong University logo
Dr. Shilei Ni, an academic and practising neurosurgeon

Discussing our project applications in neuroscience

To discuss our ideas in neuroscience, we reached out to Dr Shilei Ni, an academic in neuro-oncology and a practising neurosurgeon at the Qilu Hospital of Shandong University (linked), China, who currently serves on the committee for the Chinese Medical Association of Neurosurgery. Dr Ni’s expertise has also allowed him considerable success in scientific competition, including winning the Wang Zhongcheng Neurosurgical Young Physician Award in 2019. With Dr Ni’s twenty years of experience as a neurosurgeon and research focus on using minimally invasive surgical technology to treat CNS tumours, we were keen to discuss our ideas about the blood-brain barrier and brain cancers. 

We suggested an idea regarding the delivery of larger molecule drugs into the brain, by increasing the permeability of the blood-brain barrier (BBB). To do this, the magnetic nanoparticles would be targeted and bound to the endothelial cells of the blood-brain barrier using antibodies of a biomarker specific to these cells. Then, orthogonal magnetic fields would be used (as a 3D AND gate) to downregulate the expression of tight junction proteins in the endothelial cells at a specific site in the blood-brain barrier (e.g. close to a tumour or site of injury) to make the barrier more permeable. Dr Ni informed us about the current strategies for crossing the blood-brain barrier, which often focus on transport using markers such as transferrin, LDLR, GLUT1 and OX26. He encouraged us to remember that the BBB consists of three layers which would pose a challenge, and also pointed out that BBB permeability tends to be incomplete in Alzheimer’s. In terms of the next steps in our project design, we discussed which organism models may be suitable for our project. Although Dr Ni agreed that mouse models - 5xFAD transgenic mice for Alzheimer’s and a GBM model for glioblastoma studies - would be suitable, we chose to keep this as a hypothetical future step, given the time constraints on our project. 

We also talked to Dr Ni about our ideas about the treatment of glioblastomas. Glioblastomas are a particularly aggressive brain cancer which is very difficult to treat; surgery is the current common course of action. However, it is difficult to remove the entire tumour without infringing on the delicate surrounding healthy brain tissue, thus this type of cancer commonly recurs from cells left at the edge of the resection site, leading to poor patient outcomes. Furthermore, chemotherapy often fails to kill the tumour cells, and can lead to the development of new, resistant tumour tissue. (Cruz et al., 2022)

In our earlier discussion with Jonas, he mentioned the possibility of seeding glioblastoma resection sites with MNPs during surgery, then activating them post-surgery to kill cells left at the edge of the resection site. With his neurosurgery expertise, Dr Ni agreed that treating the surgical cavity is a viable approach. He mentioned that recurrence of glioblastomas typically occurs within 2-3 cm of the surgical margin, giving us a target of spatial precision to aim for with our engineering. In addition, Dr Ni pointed out that localised treatment using a spatially precise method would significantly reduce systemic toxicity and bypass the challenges posed by the BBB.


Upper image: Dr. Shilei Ni; Lower image: Shandong University logo
Prof. Dennis Kaetzel, Professor of Applied Physiology

Discussing our project applications in schizophrenia research

After having a promising discussion with Dr Shilei Ni, and discussing potential treatment applications, we sought additional use cases for our system within neuroscience.  

Schizophrenia is an illness which affects approximately 1 in 100 people worldwide, yet current medication options are limited, and there has been little progression in development since the 1960s, when atypical antipsychotics were developed. Current medication is often effective in treating the positive symptoms of schizophrenia such as hallucinations and delusions, but mostly ineffective at treating the negative symptoms, such as cognitive issues, apathy, and lack of motivation. As with most mental health conditions, there is still a lack of understanding of what is physically happening in the brain to cause illness, which slows effective treatment development. Some researchers use optogenetics to specifically recreate certain physiological endophenotypes (brain activation found more often in people with schizophrenia than without) in rodents, to test whether these endophenotypes play a casual role in specific symptoms.

We had the privilege of speaking with Professor Dennis Kaetzel, a researcher at the University of Ulm who is at the forefront of using optogenetics as a tool for studying schizophrenia. We were eager to hear his thoughts on our project and to learn about any limitations in using optogenetics in his research that our device could potentially address in the future. Prof. Kaetzel shared valuable insights and expert advice on what would be required to make our device functional for neuroscience research. He stressed that while promising, there are several challenges we would need to overcome before developing a viable research tool.

One key challenge Prof. Kaetzel highlighted was the issue of optical distraction in optogenetic experiments. In his research, specific regions of a mouse's brain are activated to observe behavioural changes, which can reveal the effects of targeting that part of the brain. However, he hypothesised that the behavioural responses of the mice might sometimes be influenced by the light being visible to them, rather than solely by the brain stimulation. This unintended distraction could be eliminated if our system were implemented, as it does not rely on visible light.

Additionally, Prof. Kaetzel pointed out that for our system to have an advantage over current methods, we would need to ensure that moving test subjects could be reliably and accurately activated. Addressing this would be essential for our method to be practical in dynamic experiments like his.

Oncology

Following on from our initial discussions, our project applications in oncology appeared to be some of the most feasible and exciting. These were concerned with the reduction of glioblastomas after surgery, and the use of CAR T-cell therapy for solid tumours. Therefore, we chose to next look further into therapeutic applications.

Top image: Dr. Rajesh Jena; Middle image: Members of our team at the school of clinical medicine; Bottom image: University of Cambridge logo
Top image: Dr. Rajesh Jena, consultant neuroscientist and academic at the Cambridge Department of Oncology; Middle image: Some members of our team at the University of Cambridge School of Clinical Medicine.

Discussing our project applications in oncology

Interaction: we met with Dr Rajesh Jena, a consultant neuro-oncologist at Addenbrooke’s Hospital and the lead for stereotactic radiosurgery - a minimally invasive, very precise surgery which uses X-rays to treat small abnormalities in the brain and spine. In addition, Dr Jena is an academic at the department of oncology, researching radiotherapy treatment of CNS tumours and mathematical modelling of CNS tumours.



Idea: we discussed the idea of seeding the resection border of glioblastomas with MNPs, for later activation and subsequent lowering of risk of tumour recurrence. We talked first about the problems posed by glioblastoma treatment, such as its infiltrative nature and tendency to spread beyond the resection cavity. These make tumour imaging difficult, which in combination with the low effectiveness of chemotherapy and radiotherapy, results in poor patient prognoses. Dr Jena considered our idea to be interesting and feasible. He also reminded us that since many glioblastoma patients die within a year of diagnosis, therefore long term risks of treatments can often be outweighed by short term benefits. 


When asked about the expertise that would be required by the medical professionals using this proposed technology in conjunction with existing methods, Dr Jena talked about the specialist surgical skills which would be needed to deliver the MNPs. This reminded us of our discussion with Dr Ni about neuroscience; since he was positive about the feasibility of seeding the surgical cavity, this encouraged us to continue to explore this idea. In addition, Dr Jena spoke about the well-established methodology for combining various treatment methods for optimal patient outcome. This includes the assessment of combination toxicity using an isobologram.


Idea: next we discussed our CAR T-cell idea introduced to us by Jonas.

Interaction: Dr Jena talked about the extra considerations that would come with using CAR T-cell therapy for non-solid tumours. For example, with the treatment of leukaemia using CAR T-cell therapy, absorption and distribution of the treatment is not an issue. Whereas, solid tumours have geometric constraints which would need accounting for. Furthermore, at the tissue level, convection could push the MNP constructs away from the tumour. In addition, solid tumours such as pancreatic cancer are surrounded by a dense honeycomb-like material which blocks the entry of immune cells, making many therapies ineffective.

Integration: Dr Jena suggested that the next steps in developing our idea would be tissue models, once we had an idea of how to steer the construct to the tumour location. However, due to the time constraints on our project, this was left as a hypothetical future step. 


Interaction: To aid our determination of tolerances required in magnetic field modelling, we also asked about the typical spatial scales achieved by stereotactic radiotherapy and intensity modulated radiotherapy. For radiotherapy, the resolution is around 1 mm, but can deliver up to 0.8 mm in some cases. We also learned about how the dosages of radiation are important - lower doses may not cause sufficient DNA damage to tumour cells, but too high may cause the collapse and loss of blood supply, thereby inhibiting intravenous drug delivery.

Revising our key values once more

Following on from our discussion with Dr Rajesh Jena, we decided to add a final key value: compassion. This would remind us to consider the end users of our project, and how they may feel about using Magenta technology.

Further expansion of key values page, with added term 'Compassion' and associated question 'What might be the perspectives of patients who may be treated using our technology?
Our key values with compassion added



Experimental Design

Like many teams, we reached out to academics often for advice on protocols and for opinions on potential pathways. This advice helped us to narrow down the proteins and pathways we chose to test and in troubleshooting issues we came across.

Nanoparticles and Model Organisms

Upper image: Dr Andrew Baker; Lower image: University  of Cambridge logo
Dr Andrew Baker, postdoctoral researcher at the Cambridge Department of Pharmacology

Interaction: To assist with our experimental design, we approached Dr Andrew Baker, a postdoctoral researcher in biotechnology at the University of Cambridge. We spoke to him about what magnetic nanoparticle size would me most appropriate for our system. He suggested something in the range of 8nm might be appropriate for the thermal pathways we planned to use. With regards to nanoparticles, he also cautioned us that they may interact with cells in unusual ways due to the charge present on the cell surface of bacteria and yeast. Using a specific binding site may provide a better chance of them sticking to them in the way we might want.

Integration: This led to the eventual inclusion of a his tag in the Wsc1 model.


Interaction:We discussed some of our initial ideas for magnetosensitive systems with Dr. Baker. This included a protein called ferritin, which has been modified to activate (transient receptor potential vanilloid channels) TRPV (Wheeler et al., 2016). However the mechanism of this activation is not understood and research groups have been unable to reproduce results (Latypova et al., 2024).

Integration: This uncertainty compounded with Dr. Baker’s scepticism of the protein led to us deciding not to test it as one of our constructs.


Idea:We also asked him about potentially using C. elegans as a model for animal expression as this is a direction we eventually wanted to take the project.

Interaction:He agreed that it seemed like an appropriate next step, but that within the project timescale it would be implausible to accomplish it without already transformed and working bacterial models.

Integration:This lined up with our existing expectations; with an already ambitious project, producing another working model would not be possible in only 3 months.


Force Quantification

Interaction:Later in the project, we reached out to Dr James Henstock, an associate professor at Newcastle’s Northumbria University to learn more about how to measure the force generated by the 250nm magnetic nanoparticles we were using. He had experience quantifying forces using 300nm MNPs produced by the same manufacturer and directed us to several papers which explained the protocols in more detail.

Integration:After reading these papers, we were able to calculate the magnetic force accurately.

Upper image: Dr James Henstock; Lower image: Logo of Northumbria University
Dr. James Henstock, associate professor at Northumbria University

Yeast Pathways

Upper image: Dr. Marco Geymonat; Lower image: Unviersity of Cambridge logo
Dr Marco Geymonat, Department of Genetics

To get some advice on culturing yeast, we contacted Dr Marco Geymonat, a senior teaching associate at the University of Cambridge department of Genetics.

Idea:We asked him about one of the proteins we were considering as a mechanosensitive pathway: Ste2, a gene expression pathway in yeast triggered by mating pheromones (Cevheroğlu et al., 2017). We had the idea to initiate the dimerisation of the Ste2 proteins and thus trigger the downstream pathway.

Interaction: Dr. Geymonat expressed his scepticism that this would cause the downstream pathway to be activated. We then conducted a subsequent literature review and agreed that the mechanism of Ste2 is unlikely to be the same as we initially thought, with the dimerisation being a consequence rather than a cause of the mating response.

Integration:As such, we decided not to proceed with researching, designing and testing this pathway.


Mechanosensitive Pathway

Upper image: Prof Jurgen Heinisch, Middle image: Osnabruck university logo, Bottom image: screenshot of online meeting
Prof. Jürgen Heinisch

Idea:A protein we were interested in exploring was the Wsc1 protein in yeast cell walls.

Interaction: To learn more about this we contacted Prof. Jürgen J Heinisch from the University of Osnabrück. Prof. Heinisch who had developed an S. cerevisiae strain with extended Wsc1 receptors.

Integration:He generously sent us his plasmids for the modified receptor, which we were then able to use in our experiments (Dupres et al., 2009). He also provided us with a his tagged Wsc1 strain which could interact with our surface functionalised NTA-Ni MNPs. 


Interaction: Through our experimental process, Prof. Heinisch continued to provide support with our troubleshooting, including advising on controls, plasmid design and controls. He suggested the use of glass beads to simulate the mechanical stress which triggers the Wsc1 pathway as a control prior to the use of 250nm MNPs.

Integration: We attempted to use glass beads, however did not have access to ones of the appropriate size. 


Magnetic Nanoparticle Size and Model Organisms

Upper image: Dr. Shilei Ni; Lower image: Shandong University logo
Dr Shilei Ni, academic and practising neurosurgeon

Interaction: For MNP size we should use, Dr. Ni recommended using with a small particle size with a diameter of around 10 nm for applications requiring intravenous injection, potentially alongside organic or polymer nanoparticles which may offer better transformation value. This is since larger MNPs have a higher specific gravity (relative density) which limits their circulation and leads to rapid clearance by the reticuloendothelial system.

Integration:This was factored into our decisions about which sizes of MNP to test in the lab. 


Interaction:Dr. Ni suggested mouse models would be the ideal future step.

Integration: Time constraints forced us to choose E. coli and S. cerevisiae as our model organisms for initial testing.


Plate Reader

Image of the VantaStar plate reader
Vantastar Plate Reader

Integration: After generously lending us a plate reader for our characterisation, BMG Labtech also assisted with the design of some experimental protocols which utilised the plate reader. This included advice on setting up absorbance assays, fluorescence assays and the best ways to use the lent equipment to test the effects of temperature differences on gene expression. 

BMG logo
Group picture of team members with staff from BMG in front of the plate reader
Team members with staff from BMG

New England Biolabs

NEB helped us with troubleshooting our transformations and minipreps. After reviewing our data and troubleshooting process, they concluded that the kit parts were the problem. We greatly appreciate their input on this.

Upper image: Members of the team with staff from NEB, Lower image: NEB logo
Upper image: Members of the team with staff from NEB, Lower image: NEB logo

Magnetic Nanoparticle Toxicity and Size

In our discussion with Dr Jena, we talked about the toxicity of using MNPs in medical applications. Iron oxide MNPs are removed from the body via the lymphatic system so do not accumulate dangerously. They can be fairly inert with no long term side effects. However, clearance can be affected by hemochromatosis so these patients would need to be screened out.

Iron oxide has been suggested to cause Alzheimer’s in some research. However, this is arguably not an issue in glioblastoma applications considering the average survival time of patients and that the onset of Alzheimer’s is commonly in old age.


Regarding nanoparticle size, Dr Jena talked about the need to tune particle size - they should be smaller if they need to be taken up by a cell.

Dr Jena
Dr Jena

System Design

As well as the biological constructs, we also received help and guidance for our hardware design. This allowed us to solve issues with coding and design in addition to making it accessible for production by future users.

Electromagnet Design

Idea: to build 2 different electromagnetic coils - one optimised for high frequency and one optimised for low frequency.

Interaction:to help with optimising these designs while retaining a high degree of precision, we reached out to Mark Huntsman, a member of the electronics development team at the University of Cambridge Engineering Department.

Integration: With his help, the coils we designed worked effectively.

Box Design

We want to say a big thank you to all Engineering Department Dyson Centre technicians who helped us with 3D printing, laser cutting and general manufacture of the boxes used for prototype systems.

Also a big thank you to Richard Roebuck who helped to source the MNPs we ended up using!

Picture of thee sign of the dyson centre for engineering design
The Dyson Centre for engineering design


Pixel art of a magpie holding a screwdriver Pixel art of a magpie holding a spanner

User Testing & Feedback

Interaction: With a finished prototype of our system, we looked for users to give feedback on the hardware and the graphical interface. The Cambridge Makespace provided a good opportunity for that as a place where we could present our prototype to a group with a diverse range of backgrounds from software engineers to medical technology consultants. The MakeSpace is a place for working on personal projects, and once a month has an opportunity to present them and get feedback. We spent an evening there presenting our prototype; this opportunity provided essential insight into how the system could be improved both from an engineering standpoint and for the user interface.

Integration: It let us understand where our explanations might be lacking and what visual designs might help people to understand the hardware and magnetic field system better.

Gus speaking with slides visible behind him
Gus giving background information presentation
10 people around a laptop screen
Gus giving hardware demonstration
Power supply connected to our hardware system and a blank monitor
Prototype system

References

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