OpenPlant Blog — OpenPlant
, ,

Plant Science SAW projects at Tunstead primary School

, ,

Guest blog from Emma McKechnie-Welsch, a PhD student from the John Innes Centre who spent three months doing an internship in Science Engagement with OpenPlant and the SAW Trust.

 

Plant Science SAW projects at Tunstead primary School

Arabidopsis apical meristem. Image by Emma McKechnie-Welsch

Arabidopsis apical meristem. Image by Emma McKechnie-Welsch

My name is Emma and I am a PhD student working in the Cell and Developmental Biology department at the John Innes Centre. My research looks at genes functioning to facilitate controlled plant growth and development from the shoot apical meristem in Professor Robert Sablowski’s research group. My PhD funding from the BBSRC includes a three month work placement and I was keen to gain experience in science communication and outreach so arranged a joint placement with OpenPlant and the SAW trust.

On my placement I had the opportunity to design two SAW projects to discuss science relevant to my research with primary school children at Tunstead primary school. For the year 1/2 class I worked with writer Julia Webb and artist Lara Nicole and the aim was to get children thinking about the functions of different parts of a plant. For the year 5/6 class I was worked with writer Mike O’Driscoll and artist Chris Hann with a day themed around plant evolution.

 

We used scientific images at the start of the day to catalyse inquisitiveness about the science we were going to explore, and provide inspiration for the poetry and art sessions.

 

Practical Science with Year 1/2

Build a plant game, played with year 1/2 class

Build a plant game, played with year 1/2 class

To start off the lesson we played a “build a plant” game to get more familiar with the main parts of a plant, their function, and what plants use from their environment to grow. Each child also put a cut flower in coloured water to think about the use of the stem. Then the children were given a selection of fruit and vegetables and asked to decide what part of the plant each came from. They were given a flower to look more closely at the reproductive parts and think about how seeds are formed by pollination. Finally, they looked at different types of seeds in a seed kit and we discussed the different types of seed dispersal tactics plants use.

 

Practical Science with Year 5/6

The children dissected plants to look up close at the reproductive parts under the microscope.

The children dissected plants to look up close at the reproductive parts under the microscope.

We began by guessing the number of different plant species on earth and the children suggested why plants are useful. In groups, they were given cards representing each component of photosynthesis and had to arrange them to think about the process. We covered pollination and its importance for increasing genetic variation.

The children dissected plants to look up close at the reproductive parts under the microscope. I covered different types of seed dispersal and the importance of varying environmental conditions for evolution. Then children carried out DNA extraction from strawberries after learning a bit about what DNA was and how important it was in controlling the appearance of the plant, with a single mutation in a gene coding region potentially greatly changing this. Following on from DNA extraction there was a game to match the numbers of genes to different organisms.

 

 

After the morning science sessions the children had poetry and art sessions based on the content. Here are some poems and images from the Year 5/6 group (age 10/11):

Poem 1.png
Yr 6 art work.jpg
Poem 1.png

 

The Year 1/2 children (age 4/5) wrote poems as if they were a seed growing up, and made flower hand puppets after designing a flower:

sock puppets.jpg

The children really engaged with the scientific learning aspect of the day which was great. Lots of the children thought about the questions I asked to the classes and gave insightful answers, as well as wanting to ask questions throughout the lesson/ activities. When asked about their favourite part of the day, at least half the children listed specific sections of the science morning.

The poems produced by the year 5/6 children really showcased the children’s interest in understanding genetics and how growth and development of organisms are controlled. The younger children were enthusiastic about looking at different types of seeds, bringing back different types they had found in their school grounds at break time to show me. It was great for them to think about the different stages of growth a plant goes through from seed to eventually producing a flower, including difficulties different environmental conditions could cause, while writing their poems.

The children were really excited about getting to do an afternoon of art although the activities designed weren’t quite as expected. The art didn’t centre around drawing on paper but producing 3D art pieces. The younger children gave lots of personality to their individual hand puppets and used them to help communicate their poetry whilst the older children focused on the scientific pictures provided and gave interpretations of pollen and seed dispersal, as well as the protective mechanism of the cactus.

From this experience, I could see how integration of science with writing and art can help children associate science more closely with creative thought, rather than a regimented, inflexible learning process, which makes the subject inaccessible to some children. The teachers were impressed with the pieces the children managed to produce and the level of thought about scientific processes they reached, which I think was largely down to the different approach to education SAW days take.

[Closes 31 Aug 2017] Call for Fellows at CRI Research

Information from the website of the Centre Recherches Interdisciplinaires (CRI): https://cri-paris.org 

The CRI collaboratory is recruiting fellows to join their adventure. They are inviting applications for three types of fellows: short (3-6 months), long (1-3 years) and core (5 years): https://cri-paris.org/research/call-for-fellows/

The CRI is broadening its research activities, creating a collaboratory at the crossroads across the life, learning, and digital sciences.

We are developing an open, collaborative research program to tackle the world’s health and education challenges, focusing on the following broad topics, amenable to bridge foundational research and societal impact:

  • Open health – from data-rich research to development of frugal software and hardware solutions.
  • Open learning – from understanding learning to human-machine paradigms
  • Open synthetic and systems biology – from foundational understanding of living systems to open biotech and open pharma solutions.
  • Open transitions – from tracing past major transitions to understanding and shaping current digital transition.
  • Open phronesis – tackling ethical challenges of our time.

The Collaboratory will host short (3-6 months), long (1-3 years) and core (5 years) research fellows alongside with their affiliated postdocs and PhD students. They will be accompanied by associate faculty members from France and abroad that will take part in the selection and mentoring the incoming fellows and students. Anyone capable of carrying an autonomous research project, from young graduates to established researchers (including sabbaticals) is eligible to apply to become a CRI Research Fellow.  We expect a gradual recruitment build-up to reach a 60-70 strong cohort within our dedicated building at the historical heart of Paris (the Marais) that will open its doors within a year. This 6500m2 building will include state-of-the-art wet lab space, makerspace, pedagogic facilities and studio apartments for young researchers.

[Closes 9 Aug 2017] DNA Foundry, Science and Technology Lead

Applications are invited for a DNA Foundry, Science and Technology Lead to join the Engineering Biology Group at the Earlham Institute. Using start-of-the-art laboratory automation and synthetic biology approaches, the Foundry has automated nanoscale pipelines for (i) part-based assembly and bacterial transformation, (ii) quality control of assemblies and (iii) delivery of constructs to chassis organisms. The mission of the Foundry is to bring these capabilities to bear on research in academia and industry. The post holder will establish and manage synthetic biology workflows at the Earlham DNA Foundry. This will include working with automation specialists and technical assistants to develop and execute protocols in DNA assembly, biosynthesis and genome engineering. In addition, they will engage and communicate with researchers in academia and industry to promote the mission of the Earlham Foundry and to establish and develop new collaborations. The ideal candidate will possess a PhD in Molecular Biology, Biotechnology, Synthetic Biology or a related subject. They will have an in depth understanding of molecular biology laboratory techniques and experience of collaborating with internal and external stakeholders on large scale projects. They must possess excellent communication and interpersonal skills. This position is open to applicant of all nationalities.

All applications must be made through the portal link: http://www.earlham.ac.uk/dna-foundry-science-and-technology-lead

Contact: nicola.patron@earlham.ac.uk

OpenPlant and the OpenMTA feature in 'Learning by Sharing' at SB 7.0

Prof Jim Haseloff, Dr Nicola Patron and BioBricks Foundation Legal Director Dr Linda Kahl who pioneers the OpenMTA initiative with which OpenPlant is collaborating, all presented in the 'Learning by Sharing' session at SB 7.0 in Singapore, 13-16 June 2017.

The videos of all talks are now online at the BioBricks Vimeo site.

Prof Jim Haseloff (Director, OpenPlant at University of Cambridge)

Dr Nicola Patron (Earlham Institute)

Dr Linda Kahl (BioBricks Foundation)

Share
,

OpenPlant researchers advance a translational synthetic biology platform for rapid access to new drug-like molecules

,

Researchers in Prof Anne Osbourn's lab at the John Innes Centre, including Prof Osbourn and OpenPlant PDRA Dr Michael Stephenson, have published a new paper detailing their advances in rapidly creating and purifying gram-scale quantities of natural products that were previously not possible to synthesise. This has the potential to reinvigorate drug discovery pipelines by opening up whole regions of chemical diversity for testing and production of potentially medicinally important molecules.

OAlogo.png

Reed, J., Stephenson, M.J., Miettinen, K., Brouwer, B., Leveau, A., Brett, P., Goss, R.J., Goossens, A., O’Connell, M.A. and Osbourn, A., 2017. A translational synthetic biology platform for rapid access to gram-scale quantities of novel drug-like molecules. Metabolic Engineering. DOI: 10.1016/j.ymben.2017.06.012

Fig 2 from paper: Generation of gram quantities of triterpene using vacuum infiltration a, Vacuum infiltration of N. benthamiana plants. Plants are retained by a bespoke holder, inverted into a bath containing 10 L of A. tumefaciens suspen…

Fig 2 from paper: Generation of gram quantities of triterpene using vacuum infiltration a, Vacuum infiltration of N. benthamiana plants. Plants are retained by a bespoke holder, inverted into a bath containing 10 L of A. tumefaciens suspension, and a vacuum applied. Upon release of the vacuum the infiltration process is complete. b, GFP expression in leaves from a vacuum-infiltrated plant 5 days after infiltration (leaves arranged from top left to bottom right in descending order of their height on the plant). The youngest leaves (top left) were formed post-infiltration. c, β-Amyrin purified from vacuum-infiltrated plants following transient expression.

Abstract

Plants are an excellent source of drug leads. However availability is limited by access to source species, low abundance and recalcitrance to chemical synthesis. Although plant genomics is yielding a wealth of genes for natural product biosynthesis, the translation of this genetic information into small molecules for evaluation as drug leads represents a major bottleneck. For example, the yeast platform for artemisinic acid production is estimated to have taken >150 person years to develop. Here we demonstrate the power of plant transient transfection technology for rapid, scalable biosynthesis and isolation of triterpenes, one of the largest and most structurally diverse families of plant natural products. Using pathway engineering and improved agro-infiltration methodology we are able to generate gram-scale quantities of purified triterpene in just a few weeks. In contrast to heterologous expression in microbes, this system does not depend on re-engineering of the host. We next exploit agro-infection for quick and easy combinatorial biosynthesis without the need for generation of multi-gene constructs, so affording an easy entrée to suites of molecules, some new-to-nature, that are recalcitrant to chemical synthesis. We use this platform to purify a suite of bespoke triterpene analogs and demonstrate differences in anti-proliferative and anti-inflammatory activity in bioassays, providing proof of concept of this system for accessing and evaluating medicinally important bioactives. Together with new genome mining algorithms for plant pathway discovery and advances in plant synthetic biology, this advance provides new routes to synthesize and access previously inaccessible natural products and analogs and has the potential to reinvigorate drug discovery pipelines.

 

 

Share

Twenty-nine Biomaker Challenge projects funded plus extra deadline for proposals - 21 July 2017

Twenty-nine Biomaker Challenge projects were funded by the SRI, OpenPlant and CamBridgSens covering a huge range of biology and engineering tasks from cell-free synthetic biology to clinical devices to lab automation solutions. Due to late interest, we have added a later deadline of 21 July.

Starting in this summer for the first time, the Biomaker Challenge is a four-month programme challenging interdisciplinary teams to build low-cost sensors and instruments for biology. From colorimeters to microfluidics and beyond, we were looking for frugal, open source and DIY approaches to biological experiments and we found them! The proposals contained a rich set of interdisciplinary project ideas from across the University of Cambridge and Norwich Research Park, with many external collaborators from local industry, the Royal College of Art and further afield.

 The 29 awardees have now been announced (see full list below) and will shortly be documented on GitHub and the Biomaker.org website, where some proposals are already online.

Biomaker Challenge Coordinator Kyata Chihbalabala has recently joined the SRI for ten weeks to manage the programme and arrange training and meetups. The Biomaker Toolkits are now being distributed so watch this space for events coming soon!

Apply by 21 July for Biomaker Challenge Round Two!

Due to a rush of late interest, we have decided to open another round. You still have an opportunity to apply for a Biomaker Toolkit (worth £250) and £750 additional support for your biological instrumentation project.

Find out more about how to apply >>

Acknowledgements

Judging Panel: Dr Emre Ozer (ARM Ltd), Dr Stephanie Reichel (CRUK Cambridge Institute), Dr Dan MacLean (Earlham Institute), Prof Jim Haseloff (Department of Plant Sciences, University of Cambridge), Dr Alexandre Kabla (Engineering Department, University of Cambridge), Dr Oliver Hadeler (Chemical Engineering and Biotechnology, University of Cambridge).

Sponsors: ARM Ltd, New England Biolabs

 

The Funded Projects

  1. A cell-free sensor platform for the quantification of arsenic concentrations in drinking water.
  2. A Device for Real-Time Monitoring of Protein Synthesis.
  3. A low cost reusable microfluidic device for the detection of antibiotic resistant genes in bacteria isolated from patient samples.
  4. A low cost, point-of- care device to measure blood haemoglobin levels, using calorimetry and infrared spectroscopy.
  5. A low-cost colorimeter for accurate detection of colour changes in medical diagnostic tests
  6. A low-cost, pressurized liquid chromatography system for protein purification
  7. A microdroplet incubator to establish 3D organoids cultures from oesophageal adenocarcinoma.
  8. A sensor to improve the accuracy of stereotactic brain biopsies for the diagnosis of brain tumours
  9. An artificial habitat to investigate Boquila trifoliata mimicry
  10. Cheap Do-It- Yourself Small Volume UV Spectrometer for Nucleic Acid and Protein Quantitation
  11. Detecting alterations in ionic concentrations associated with different cellular states
  12. Detecting pathogens in sewage sludge
  13. Developing a self-regulating control system for intravenous drug administration -- using aminoglycosides as an example
  14. Development of an anti-TFF3 functionalized surface to capture of Barrett’s oesophagus cells
  15. DIY bioacoustics
  16. Field portable colorimeter
  17. Functional membrane-based integrated biosensing devices for detection and quantitation of specific nucleic acids and other biomolecules
  18. Handheld syringe pump with heating element
  19. KNOW-FLOW: A low-cost programmable blood flow system
  20. Low Cost Wearable Sensors Strain Sensors for illness identification via Gait, Posture and muscle usage
  21. Low-Cost Multispectral Imagery for UAV-based Vegetation Monitoring
  22. Macrophotography of fern gametophytes using a DIY focus stacking system.
  23. Microfluidic Turntable for molecular diagnostic testing
  24. OptoFlow: Optical flow rate measurement for microfluidics
  25. Puzzle-solving Bacterial Pet: Imaging Platform for Microfluidics-based Reinforced Learning with Motile Bacterial Cells
  26. Remote Environment Controller for Experiments in Extreme Environments
  27. Sci-Fi Cam
  28. Ultrasonic Plant Height System for High- Throughput Plant Phenotyping
  29. Real-Time monitoring of cell proliferation

 

Biomaker Challenge is sponsored by BBSRC/EPSRC through OpenPlant Synthetic Biology Research Centre (www.openplant.org) and the University of Cambridge Research Policy Committee through the Synthetic Biology Strategic Research Initiative (www.synbio.cam.ac.uk) and the Sensors Strategic Research Network (www.sensors.cam.ac.uk).

Share