Biomaker Fayre

The Biomarker Challenge is an annual competition that funds creative interdisciplinary projects at the interface of biology and engineering.

Each of the 20(+) teams that took part this year, have been supported to produce low cost, open access resources and instruments, for biology. This year, a whole array of innovative and creative projects returned to Cambridge to showcase their final products.

The event also hosted inspiring talks from; Karen Sarkisan (Imperial College) on his start-up company Planta, where they are creating self-luminous plants, Oscar Gonzalez (Quadram Institute) on his team’s speed breeding chamber and Harrison Steel (Oxford University), who spoke of his innovative robotic platform Chi:Bio.

Best Biomaker Spirit awarded to the OpenCM biomaker team

As usual, awards were given out to three outstanding projects. This year the Best Technology prize was given to the LunaFlow team for their incubator which uses a tomographic camera system to measure the luminescent response of pressure sensitive diatoms.

The Best Biology award was given to the team behind creating an Open and Affordable 3D Bioprinter, which provides temperature controlled printing of bacteria and algae.  Lastly, the OpenCM team was given the Best Biomaker Spirit award, for their project which judges stated was a great example of the combined use of open technologies.

Congratulations to the three winning teams and to all the teams who made it to the fayre to exhibit their exciting projects.

For more information on the projects check out the Biomaker hackster page to see what the teams have been up to this year.

LunaFlow winners of this year’s Best Technology award.

Open and Affordable 3D Bioprinter team, winners of this year’s Best Biology award

IoHeat: a nice oasis in the cold room

The problem

Temperature is a crucial, yet often overlooked condition that affects the growth efficiency of mammalian and bacterial cell cultures. To achieve maximal growth rate, the temperature of the culture media needs to be maintained at the optimal level throughout the experiment.

While during a culture the media are maintained at the optimal for the organism level, their composition often dictates that they are stored at a lower (~2-8 °C) temperature. A typical culture medium for mammalian cells is composed of a complement of amino acids, vitamins, inorganic salts, glucose, and serum as a source of growth factors, hormones, and attachment factors; in addition to nutrients, the medium also helps maintain pH and osmolality. Many of these components are not stable for extended periods of time at elevated temperatures.

Sustaining mammalian cell cultures requires regular changes of the medium and/or subcultures (passages) into fresh culture medium. In many cases, the survival of the cells during these processes depends on the thorough pre-conditioning of the media at the desired temperature. Oftentimes, this means pre-incubating the media in a water bath for more than an hour, before they are ready to use.

This can impose time restrictions when experiments need to run at different time-points or need to be carried out early in the day or during out-of-hours, as access can be limited at these periods. Time optimization is needed. 

The Idea

Our project was focusing on developing a remotely-controlled heated compartment, which can be kept in a cold environment.

Schematic of a remotely-controlled heated compartment prototype

The device can be used in laboratories to control specific working temperature (37 °C) of cell culture medium or reagents, shortly before use.

Specifically, the heating device finds application in the laboratories where microbiological or cell culture work are carried out.

The function of incubator is to maintain optimal temperature, humidity and other conditions such as the CO (CO2) and oxygen content of the atmosphere inside. Incubators are essential for a lot of experimental work in cell biology, microbiology and molecular biology and are used to culture both bacterial as well as eukaryotic cells.

With our mini-incubator we aimed to achieve the proper functionality of an incubator, but with the time optimization improvement due to the remote controls of temperature.

In May 2019, we had the great opportunity to take part in the OpenPlant Biomaker Challenge to develop our first prototype. For the first challenge we built an insulator polyester box mimicking the incubator and remotely controllable by the Telegram interface. This represented our proof of concept.

We then developed a set of scripts to locally control the electronic components, designing each command to work with a file-lock system that avoids collision when multiple users operate the device. The scripts allow to start the heating cycle, to report the current status of the device (temperature, humidity, heating status). To allow remote control of the device, a Telegram bot has been developed. The bot has a simple authentication system to allow only white-listed users to operate the device, a queue system allows to schedule multiple heating cycles, and the queue can be queried, and new tasks can be added, through the bot.

Following a series of successful tests our next task was to down-scale the device. We developed a customized 3D printed structure that allows us to efficiently organize the electrical components. In addition, 3D designed incubators can be customized to accommodate a range of different vessels and types of samples.

We also decided to organize a workshop for scientists at the Norwich Research Park. The main aim was to let the participants familiarizing with the programming in RasbperryPi, stressing that behind any problem there is a solution that can be achieved with a multidisciplinary approach.

What’s next?

We think that Biomaker Challenge was a great experience and a big opportunity for develop our idea. Now that we are able to obtain a proof of concept, we are aiming to further optimize our device and hopefully make it available as lab equipment to be used by researchers.

Blog written by IoHeat Team.

Plant genome engineer vacancy with Phytoform Labs

Phytoform Labs enables plant breeding innovation in specialty crops and focuses on sustainability in agriculture.

The company, based at Rothamsted Research centre in Harpenden, is currently looking for a plant genome engineer to join their multidisciplinary team. Offering the right individual a competitive salary in a fast-paced start-up environment.

For more information on the position visit their website or contact Nicolas Kral of Phytoform Labs.

Plant molecular biologist vacancy with Phytoform Labs

Phytoform Labs enables plant breeding innovation in specialty crops and focuses on sustainability in agriculture.

The company, based at Rothamsted Research centre in Harpenden, is currently looking for a plant molecular biologist to join their multidisciplinary team. Offering the right individual a competitive salary in a fast-paced start up environment.

For more information on the position visit their website or contact Nicolas Kral of Phytoform Labs.

PhD studentship available in Prof. Cathie Martin's lab

To divide or not divide? The importance of division to hair formation in plants.

The project aims to compare regulation of multicellular hair development in tomato with single-celled hair development in Arabidopsis and to establish how the induction of DNA replication without cell division (endoreduplication) came to be the key regulatory step in hair development in Brassica species like Arabidopsis.

Application deadline: 25th November 2019.

Project start date: 1st October 2020.

Read more about this position here.

Group Leader Vacancies

Group leader positions currently available at the John Innes Centre.

John Innes Centre would particularly welcome applicants who are working in the areas of population genetics, chemistry and biology of plants and microbial natural products, cell biology, biotic interactions of plants and the interface of agriculture and the natural environment.

Entry deadline is December 16th 2019.

For more more information visit the website.

An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat (Triticum aestivum L.)

Dr Sadiye Hayta and Prof Wendy Harwood from the John Innes Centre published their work on an efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat, which has important implications for synthetic biology approaches to crop improvements:

Hayta et al. (2019) Fig 6: Transgenic plants showing GUS expression

An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat (Triticum aestivum L.)

Sadiye Hayta, Mark A. Smedley, Selcen U. Demir, Robert Blundell, Alison Hinchliffe, Nicola Atkinson & Wendy A. Harwood

Plant Methods Volume 15, Article number: 121 (2019)

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0503-z

Abstract:

Background

Despite wheat being a worldwide staple, it is still considered the most difficult to transform out of the main cereal crops. Therefore, for the wheat research community, a freely available and effective wheat transformation system is still greatly needed.

Results

We have developed and optimised a reproducible Agrobacterium-mediated transformation system for the spring wheat cv ‘Fielder’ that yields transformation efficiencies of up to 25%. We report on some of the important factors that influence transformation efficiencies. In particular, these include donor plant health, stage of the donor material, pre-treatment by centrifugation, vector type and selection cassette. Transgene copy number data for independent plants regenerated from the same original immature embryo suggests that multiple transgenic events arise from single immature embryos, therefore, actual efficiencies might be even higher than those reported.

Conclusion

We reported here a high-throughput, highly efficient and repeatable transformation system for wheat and this system has been used successfully to introduce genes of interest, for RNAi, over-expression and for CRISPR–Cas9 based genome editing.

Combining Transient Expression and Cryo-EM to Obtain High-Resolution Structures of Luteovirid Particles

OpenPlant PI George Lomonossoff and colleagues published their work on combining transient expression and cryo-EM to obtain high-resolution structures of luteovirid particles:

Byrne et al. (2019) Graphical abstract

Combining Transient Expression and Cryo-EM to Obtain High-Resolution Structures of Luteovirid Particles

Matthew J. Byrne, John F.C.Steele, Emma L. Hesketh, Miriam Walden, Rebecca F. Thompson, George P. Lomonossoff, and Neil A. Ranson

Structure (2019) https://doi.org/10.1016/j.str.2019.09.010

Abstract:

The Luteoviridae are pathogenic plant viruses responsible for significant crop losses worldwide. They infect a wide range of food crops, including cereals, legumes, cucurbits, sugar beet, sugarcane, and potato and, as such, are a major threat to global food security. Viral replication is strictly limited to the plant vasculature, and this phloem limitation, coupled with the need for aphid transmission of virus particles, has made it difficult to generate virus in the quantities needed for high-resolution structural studies. Here, we exploit recent advances in heterologous expression in plants to produce sufficient quantities of virus-like particles for structural studies. We have determined their structures to high resolution by cryoelectron microscopy, providing the molecular-level insight required to rationally interrogate luteovirid capsid formation and aphid transmission, thereby providing a platform for the development of preventive agrochemicals for this important family of plant viruses.

Improving plant transient expression through the rational design of synthetic 5′ and 3′ untranslated regions

Dr. Heydrien Peyret, Prof. James Brown and OpenPlant PI Prof. George Lomonossoff published their work on improving plant transient expression through the rational design of synthetic 5' and 3' untranslated regions in expression vectors:

Peyret et al. (2019): “Fig 1: The Synth expression cassette.”

Improving plant transient expression through the rational design of synthetic 5′ and 3′ untranslated regions

Hadrien Peyret, James K. M. Brown & George P. Lomonossoff

Plant Methods Volume 15, Article number: 108 (2019)

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0494-9

Abstract:

Background

The growing field of plant molecular farming relies on expression vectors that allow high yields of recombinant proteins to be produced through transient gene expression. While numerous expression vectors currently exist for this purpose, there are very few examples of systematic efforts to improve upon these. Moreover, the current generation of expression systems makes use of naturally-occurring regulatory elements, typically selected from plant viruses, to maximise yields. This study aims to use rational design to generate synthetic sequences that can rival existing ones.

Results

In this work, we present the rational design of novel synthetic 5′ and 3′ untranslated regions (UTRs) which can be used in various combinations to modulate accumulation levels of transiently-expressed recombinant proteins. Using the pEAQ-HT expression vector as a point of comparison, we show that pre-existing expression systems can be improved by the deployment of rationally designed synthetic UTRs. Notably, we show that a suite of short, synthetic 5′UTRs behave as expression enhancers that outperform the HT 5′UTR present in the CPMV-HT expression system. Furthermore, we confirm the critical role played by the 3′UTR of cowpea mosaic virus RNA-2 in the performance of the CPMV-HT system. Finally, we use the knowledge obtained from these results to develop novel expression vectors (named pHRE and pHREAC) that equal or outperform pEAQ-HT in terms of recombinant protein yield. These new vectors are also domesticated for the use of certain Type IIS restriction enzymes, which allows for quicker cloning and straightforward assessment of different combinations of UTRs.

Conclusions

We have shown that it is possible to rationally design a suite of expression modulators in the form of synthetic UTRs. We have created novel expression vectors that allow very high levels of recombinant protein expression in a transient expression context. This will have important consequences for future efforts to develop ever-better plant transient overexpression vectors for research or industrial applications.