Cell Engineering and Synthetic Biology

Analysis of Microbes Generated Using Synthetic Biology

Synthetic biology allows researchers to optimise and create new metabolic pathways, increase yields of key enzymes or metabolites, and even to make new molecules or chassis microorganisms. In order to analyze the performance of new genetic constructs and find high value variants, screening is required as part of the Design-Build-Test-Learn cycle. However, the number of clones within a library is typically in the region of tens to hundreds of thousands, making the screening process a time-consuming and often laborious process.

Our Cyto-Mine® and Research Instruments can be used to miniaturise and speed up the screening process. This can save you large sums on costly consumables and reagents, while increasing throughput and helping you identify rare and valuable products faster than other technologies. We are currently investigating a novel mass spectrometry-based detection platform which may become a future product. If you would like further information, then please contact us.

Find Out More About Our Integrated Systems

The Unique Benefits of Our Systems for Synthetic Biology Applications

Using our Cyto-Mine® system, you can study large libraries of engineered clones that produce intracellular, secreted extracellular or cell-associated proteins and identify unique variants or other cells of interest from this vast population. This is something that is close to impossible to do with other screening processes. While our systems are optimised to work with a wide range of fluorescent assays and reporter systems, you can also retrieve living copies of hits in a label-free manner by using our ESI-Mine™ technology for mass spectrometry (MS) – normally, these samples would be destroyed, but the ESI-Mine™ system splits each sample prior to analysis allowing retrieval of living cells deemed as hits.

The main advantages of our approaches are that Sphere Fluidics’ technology enables high sensitivity and throughput of several millions samples (Cyto-Mine®) or several hundred thousand samples a day (ESI-Mine™). These also give vast cost-savings and high quality results.

Parameter
Microtitre Plate (MPT)
Picodroplet
Throughout samples/day 10² –10³ (LC-MS)
10⁴ (RF-MS)
10⁵–10⁶
Reagent volume (to screen 1M mutants) 100 L
(e.g. very high for 10mM NADPH)
1 mL
(e.g. 100,00 fold lower for 10mM NADPH)
Equipment
  • Qpixx colony picket
  • Multi-plate incubators
  • Centrifuges
  • FX/Tecan liquid handling robots
  • LC-MS or RF-MS
  • MTPs (very high)
  • Syringe or air pressure pumps
  • Fabricated biochips
  • Mass spec
  • Biochip (100-fold lower)

Learn More About Our Technology and its Benefits

Our Systems in Action for Synthetic Biology Applications

A typical synthetic biology project involves engineering cell libraries that can regulate expression of novel and interesting biological molecules. These could be regulatory nucleic acid elements, enzymes, functional RNA molecules or even entire pathways designed to generate a product of interest. These cells must then be screened to find interesting variants. To learn more about how this achieved using our technology, see the accompanying graphic. If you’d like to work with our team to discuss how we can help enhance the synthetic biology work in your lab, get in touch.

Enzyme Evolution and Engineering

Enzymes are commonly engineered to produce the most active, efficient and specific variants possible for a wide range of applications in a range of industries (e.g. chemical, pharmaceutical, fuel, agriculture, cosmetics etc.). This process has historically involved screening billions of clones. Over twenty years ago, enzyme evolution was used to more rapidly direct the evolution of high performance enzymes by focussing on an enzyme’s key areas or ‘hotspots’. This enabled researchers to reduce library sizes to tens of millions of clones. With the introduction of synthetic biology techniques, this number has been even further reduced to tens to hundreds of thousands of clones.

When you combine these industry advances with our technology, you can increase screening throughput to engineer enzymes in an even faster and more cost-efficient way, regardless of whether you are using directed evolution or the latest genetic engineering and synthetic biology techniques.

Find Out More About Our Integrated Systems

The Unique Benefits of Our Systems for Enzyme Evolution and Engineering

One of the first ever applications of picodroplets was to study evolved enzymes, so it’s an area where our team has significant expertise. Our technology has two main applications in this area.

The first is the study of single cells engineered to produce enzyme variants, the performance of which can be assayed using fluorescent reporter assays. Using our Cyto-Mine® system, ultra-high throughput processes can be used to measure extracellular or cell-associated products. The use of picodroplets means that the assays are miniaturised, saving on reagents and minimising costs.

The second is the screening of engineered cell libraries for products using a label-free technique, specifically mass spectrometry (MS). By its very nature, MS destroys each test sample. To overcome this, our ESI-Mine™ system effectively splits each picodroplet into two and accurately tracks every sample and its replicate. This means that the living sample can be safely recovered should the MS suggest it is worth further study. In this case, our technology enables high-throughput (200,000 samples a day compared to 1-10,000, as is usual when using other techniques). As it is label-free, it can offer significant cost and time-savings since no ‘artificial’ assays have to be developed. MS also provides a host of additional information about other molecules(s) being produced.

Parameter
Microtitre Plate (MPT)
Picodroplet
Throughout samples/day 10² –10³ (LC-MS)
10⁴ (RF-MS)
10⁵–10⁶
Reagent volume (to screen 1M mutants) 100 L
(e.g. very high for 10mM NADPH)
1 mL
(e.g. 100,00 fold lower for 10mM NADPH)
Equipment
  • Qpixx colony picket
  • Multi-plate incubators
  • Centrifuges
  • FX/Tecan liquid handling robots
  • LC-MS or RF-MS
  • MTPs (very high)
  • Syringe or air pressure pumps
  • Fabricated biochips
  • Mass spec
  • Biochip (100-fold lower)

Learn More About Our Technology and its Benefits

Our Systems in Action for Enzyme Evolution and Engineering

Pico droplet

Our systems offer a rapid and simple workflow for improving enzyme performance via directed evolution or synthetic biology. The typical process is outlined in the accompanying graphic. To find out more about how you could utilise our technology in your lab, please get in touch.

Committed to Responsible Synthetic Biology

Please note, Sphere Fluidics subscribes to the ethos of a Responsible Innovation Framework for our work in the Synthetic Biology area. We have consulted with UK experts and advisory bodies in the synthetic biology area and are continuing to improve our approach to Responsible Innovation.

We examine ethical, social and regulatory issues and only approve synthetic biology projects that generate products and services that benefit society and/or human wellbeing, make a positive contribution to the environment and that promote sound practices in employment, business behaviour and ethics.

For more information, please see here:

Responsible Innovation