Visualising genetic circuits in space and time, with paper-based cell-free translation

We are a pair of scientists at Medical Research Council Laboratory of Molecular Biology (MRC LMB), who are passionate about helping students learn about modern science.

Synthetic biology is particularly interesting to us as we both work at the forefront of this field and appreciate how biology has transformed into more of an engineering discipline, where we learn about life by building biological systems. The same principle, i.e., learning biology by doing it, is very efficient for studying complex concepts in schools. However, performing modern synthetic biology experiments in the classroom is an expensive activity, due to the reagents, media, bacteria and lab instruments needed, not to mention the paperwork burden of dealing with genetically modified organisms.

We believe that teaching modern science can be accessible, cheap and straightforward. We are not alone in this and there are significant developments that have been done by Amino Labs, Cell-free tech and Biobits, which pursue the same goal as us: to make cutting-edge science accessible and affordable. We chose to work with the cell-free transcription-translation system (TXTL) as it is cheap to make, there is no need for safety regulations and they are highly customizable: the only thing you need is a genetic construct.

Our aim is to teach students the principles of genetic control, the foundation of synthetic biology. The first thing that struck us was the ease with which children study electric circuits by directly connecting electrical parts in chains and experimenting with them. We wanted to reiterate this logic for biology. Luckily, the major principles of genetic regulation have already been established with electrical engineering in mind; the only puzzle piece missing: to connect them physically on a breadboard.

Figure A: Cell-free transcription-translation system (TXTL) using filter paper

Figure A: Cell-free transcription-translation system (TXTL) using filter paper

The TXTL is meant to be a magic mixture that produces practically any genetic part (such as Green Fluorescent Protein or T7 RNA polymerase). As a material support where the reaction is contained, we chose a filter paper. The idea was to turn these pieces of paper into functional modules by expressing proteins in them. Therefore, connecting paper pieces later will let expressed proteins move from one paper piece to another with the water flow (Fig.A).

In the end, a protein expressed in one module can affect the reaction in the other. This experimental setup simplifies studying gene circuitry, as triggers and products of the circuit are physically separated and therefore theoretically it should be easier to deal with this kind of system as opposed to a black box mixture in the tube. Also, the possibilities are practically endless as this system is highly customizable and pieces could be connected in any way that should help children to experiment with material in an unconstrained manner.

 

Figure B: comparison of activity between commercial mixture (Promega T7 high yield S30) and inhouse  E.coli  mixture.

Figure B: comparison of activity between commercial mixture (Promega T7 high yield S30) and inhouse E.coli mixture.

The project started with the production of highly active TXTL E.coli mixtures. To help other laboratories that have access to only basic equipment, we used a cheap and easy protocol for preparing cell-extracts, so that our work is easily reproducible. We have prepared cell extracts either traditionally with a French press (Emulsiflex) and high-speed centrifuge, or using a cheaper and more streamlined approach by using ultrasound cell-lysis and a cooled table top centrifuge. Independent of the protocol we used for the preparation of E.coli lysate, activity was on par with the commercial mixture (Promega T7 high yield S30) (Fig.B).

 

Figure c: TXTL mixtures showing more active in solution than on paper.

Figure c: TXTL mixtures showing more active in solution than on paper.

The challenges began when we tried to run the TXTL reaction on paper: the cell-free mixtures are always active in the solution, their paper-based counterpart only gives a low signal which could only be visualized with expensive instrumentation and thus could not be used in any low-resource environments (Fig.C).

 

For now, we have found a viable alternative that is suitable for outreach: as opposed to lyophilizing TXTL on the paper, we freeze-dry TXTL in the tube. Surprisingly, the reaction mix was as active as the original one, and according to previous reports the reaction components retain their activity for weeks, and even months. Thus, we aim to use this ‘halfway’ TXTL product in the upcoming summer outreach. However, the battle is not over yet; we have now turned our attention to other support materials such as agarose, that does not interfere with TXTL, is cheap, could be freeze-dried and be cast in any form.

Follow the projects progress on twitter @zakir_tnimov

Project Manager (HE) GPSEP [Maternity Cover], Sainsbury Lab Cambridge

DEPARTMENT/LOCATION: Sainsbury Laboratory, Cambridge

SALARY: £36,261-£48,677

REFERENCE: PT19452

CATEGORY: Academic-related

PUBLISHED: 5 June 2019

CLOSING DATE: 30 June 2019

Applications are invited for the post of Project Manager Gatsby Plant Science Education Programme (Higher Education) in the Sainsbury Laboratory, to manage a high-profile undergraduate plant science summer school and other post-16 student engagement projects as part of a programme funded by the Gatsby Charitable Foundation.

This post offers an exciting opportunity for those with experience and interest in undergraduate education and post-16 student engagement to build on an existing, successful programme of work. The Gatsby Plant Science Summer School has demonstrable impact on some of the brightest UK biology students, and this post will manage alumni support for graduates of the summer school. The successful candidate will also have the opportunity to use their creativity and passion for plant science to devise ways of inspiring future participants in the programme and develop post-16 student plant science engagement activities.

The Gatsby Plant Science Education Programme aims to increase participation and interest in plant science in UK schools and universities, through online resources for students, school and college teachers, support for education professionals, and an annual undergraduate plant science summer school.

Applicants should have a first degree (or equivalent professional experience) in the biological sciences, preferably plant science, with a demonstrable broad knowledge of the UK Higher Education context and experience of a plant science research environment. A broad network of contacts in the plant science and/or science education communities is essential, alongside an understanding of at least one of the following fields: undergraduate bioscience education, evaluation of student engagement. Previous experience of developing partnerships on a national and local scale would be advantageous.

Successful candidates will have excellent project management skills, in addition to experience in managing financial budgets. Strong interpersonal and communication skills are required, with the ability to work in a helpful and diplomatic manner with a wide range of people at all levels.

Most importantly, we are looking for a project manager who, working with the current Summer School team will build upon the continuing success of the projects with enthusiasm.

The Laboratory provides a welcoming and collaborative environment with a wide-range of family-friendly benefits and development opportunities. More about the Sainsbury Laboratory, further information for the role and details of what the University offers to employees, can be found at: http://www.slcu.cam.ac.uk/.

Start date: The post will be available from 12 August 2019

Maternity cover: This post is fixed-term for one year or the return of the post holder, whichever is the earlier.

Applications are welcome from internal candidates who would like to apply for the role on the basis of a secondment from their current role in the University.

The interview date is Thursday 11 July 2019.

Further information: http://www.jobs.cam.ac.uk/job/21876/

Regius Professorship of Botany, Cambridge University

DEPARTMENT/LOCATION: Department of Plant Sciences

REFERENCE: PD17932

CATEGORY: Professorships/Directorships

PUBLISHED: 30 April 2019

CLOSING DATE: 28 June 2019

The Board of Electors to the Regius Professorship of Botany invite applications for this Professorship from persons whose work falls within the general field of the Professorship to take up appointment on 1 January 2020 or as soon as possible thereafter.

This appointment arises at a vibrant time for the study of plant science in Cambridge. The Department seeks to make the appointment of a scientist of outstanding calibre to this prestigious professorship who will have the opportunity to shape the direction and emphasis of plant science research, teaching and impact in Cambridge itself, and provide leadership in the subject nationally and internationally.

Candidates will have an outstanding research record of international stature in plant biology and the vision, leadership, experience and enthusiasm to build on current strengths in maintaining and developing a leading research presence. They will also have a commitment to the recruitment, training and mentoring of the next generation of researchers. They will hold a PhD or equivalent postgraduate qualification.

Standard professorial duties include teaching and research, examining, supervision and administration. The Professor will be based in Cambridge. A competitive salary will be offered.

Further information: http://www.jobs.cam.ac.uk/job/20155/

Research Associate in Plant Sciences (Fixed Term), Cambridge University

DEPARTMENT/LOCATION: Department of Plant Sciences

SALARY: £32,236-£39,609

REFERENCE: PD17760

CATEGORY: Research

PUBLISHED: 10 June 2019

CLOSING DATE: 9 July 2019

A position is open for a Leverhulme Trust-funded postdoctoral research associate based within the Department of Plant Sciences at the University of Cambridge, and supervised by Professor Beverley Glover and Professor Alex Webb.

The appointee will investigate the evolution of the WDR proteins TTG1, LWD1 and LWD2. WDR proteins form a scaffold which supports the interaction of transcription factors, allowing the regulation of diverse suites of downstream genes. Our project aims to compare TTG1 and LWD protein function and identify changes important for their functional specificity. We aim to use mutant analyses to define biological function, in combination with yeast 2-hybrid analyses to determine which proteins are involved in the interacting complexes specifying different outcomes. RNAseq and ChIPseq will be used to establish the downstream targets resulting from the activities of these protein complexes.

We are looking for a highly motivated post-doctoral scientist to work in this area. The successful candidate must be able to demonstrate a strong background in the molecular genetic analysis of Arabidopsis, including a PhD in a relevant area. Experience with some of: mutant analysis, microscopy, RNAseq and ChIPseq will be necessary. Prior experience of yeast 2-hybrid analyses and/or circadian analyses will also be an advantage.

Fixed-term: The funds for this post are available for 3 years in the first instance.

Further information: http://www.jobs.cam.ac.uk/job/19960/

Programme Manager (Earth Biogenome Project), Earlham Institute, Norwich

Salary range: £39,150 - £47,850

Post No. 1003698

Contract length: 24 months

Department: Faculty

Opening date: 04 June 2019

Closing date: 01 July 2019

Applications are invited for a Programme Manager (Earth Biogenome Project) to join the Research Faculty Office at the Earlham Institute, based in Norwich, UK.


Background:
The Earlham Institute is looking for a Programme Manager to join the new Darwin Tree of Life Programme that aims to sequence the genomes of 66,000 known species of animals, plants, protozoa and fungi in the UK. This is part of a global effort (Earth Biogenome Project) to sequence the genomes of 1.5 million species on Earth.

Work at the Earlham Institute will focus on analysing genomes to further our understanding of evolutionary processes that drive biodiversity in populations and ecosystems. We are also involved in applying genomics to the conservation and management of valuable ecosystems and to the sustainable use of biodiversity for public good.

EI is seeking a highly skilled Programme Manager to support the Institute’s involvement in the Earth Biogenome Project - a global, collaborative initiative which aims to sequence the genomes of all species of life on Earth in the next 10-20 years.


The role:
The role will be key in the application for further funding to expand our engagement in these UK and global projects. This is a diverse, vital role and an excellent opportunity for someone seeking to move away from the bench into full time project management or seeking to move to project management in this exciting area of research.

This varied and dynamic role will involve providing high quality project management for activities in the Research Faculty Office in all aspects of implementing the Institute research strategy, taking responsibility for spearheading new activities.


The ideal candidate:
To be considered for this post, applicants must possess a PhD in a relevant scientific field. Candidates should have excellent experience of managing complex research programmes/projects and a working knowledge of project management productivity tools. Financial management experience is desirable.

Candidates should have prior experience of working in an academic environment and have a good track record of scientific writing. Excellent interpersonal skills and the ability to draft scientific documents is essential for this post. Candidates should be resilient, adaptable, organised and able to work well as part of a team.


Additional information:
Salary on appointment will be within the range £39,150 to £47,850 per annum depending on qualifications and experience. This is a full time post for a contract of 2 years.

We welcome applications from candidates seeking job share, part time or alternative working patterns.

As a Disability Confident employer, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy.

Postdoctoral Research Scientist (Plant Metabolic Diversity), Earlham Institute, Norwich

Salary range: £31,250 - £38,100

Post No. 1003678

Contract length: 18 months

Department: Engineering Biology

Opening date: 04 June 2019

Closing date: 01 July 2019

Applications are invited for a Postdoctoral Research Scientist (Plant Metabolic Diversity) to join the Patron Lab at the Earlham Institute, based in Norwich, UK. In collaboration with the Osbourn Lab at the John Innes Centre, this project will be linked to the Darwin Tree of Life Project, which aims to sequence all known UK eukaryotes.


Background:
The Earlham Institute is looking for a Postdoctoral Research Scientist (Plant Metabolic Diversity) to join the new Darwin Tree of Life Programme that aims to sequence the genomes of 66,000 known species of animals, plants, protozoa and fungi in the UK.

Work at the Earlham Institute will focus on analysing genomes to further our understanding of evolutionary processes that drive biodiversity in populations and ecosystems. We are also involved in applying genomics to the conservation and management of valuable ecosystems and to the sustainable use of biodiversity for public good.

EI is seeking a Postdoctoral Research Scientist (Plant Metabolic Diversity) to support the Institute’s involvement in the Earth Biogenome Project a global, collaborative initiative which aims to sequence the genomes of 1.5 million species of life on Earth in the next 10-20 years.


The role:
This project will generate and compare genomic, transcriptomic and metabolomic datasets for a group of related plant species. The scientist will be responsible for conducting comparative analyses with the aim of exploring the genetic basis of metabolic diversity and identifying genes responsible for the presence of target metabolites.

They will work in collaboration with other scientists at the Earlham Institute and John Innes Centre to characterise candidate genes, with the eventual aim of enabling biological production of novel, high-value metabolites.


The ideal candidate:
The candidate must have a PhD in Plant Biology, Biochemistry, Bioengineering, Synthetic Biology, Evolutionary Biology, Bioinformatics or a related subject.

The project would suit either a molecular biologist or biochemist experienced in the analysis of RNA-seq/metabolomic datasets, or a bioinformatician interested in applying their expertise to understanding metabolic diversification in plants. The candidate must be motivated and interested in the application of innovative technologies to natural product biology.


Additional information:

Salary on appointment will be within the range £31,250 - £38,100 per annum depending on qualifications and experience. This is a full time post for a contract of 18 months.

As a Disability Confident employer, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy.

Postdoctoral Researcher (Osbourn Lab), John Innes Centre, Norwich

Closes: 27th June 2019 

Salary: £31,250 to £38,100 depending on qualifications and experience 

Contract: Full time until 31 March 2021.

Applications are invited for a Postdoctoral Researcher to work on a collaborative project between the laboratories of Professor Anne Osbourn (John Innes Centre) and Dr Yang Bai (Institute of Genetics and Developmental Biology, Beijing).

The successful candidate will be based at the John Innes Centre but will also visit Dr Bai’s lab at IGDB to carry out key aspects of this work relating to microbiome analysis.

This project is funded by the John Innes Centre – Chinese Academy of Sciences Centre of Excellence in Plant and Microbial Science Alliance (CEPAMS).

The role

Building on recently published work from the Osbourn and Bai labs (‘A specialized metabolic network selectively modulates Arabidopsis root microbiota’ Science 10 May 2019:Vol. 364, Issue 6440, eaau6389), the successful candidate will investigate the impact of the environment on production of host metabolites that sculpt root microbial communities. Specifically, they will:

  1. Use available in silico transcriptome resources to investigate the expression of Arabidopsis biosynthetic gene clusters in roots in response to different abiotic and biotic stresses and verify the effects of different environmental conditions on gene expression experimentally by qPCR.  The impact of different environmental stresses on root microbial communities in wild type Arabidopsis will be established by root microbiome sequencing. The impact of mutation/overexpression of triterpene pathway genes on root microbiota establishment and plant fitness under different environmental conditions will then be investigated

  2. Carry out in vitro tests of the effects of purified Arabidopsis root triterpenes on the growth of representative bacterial strains cultured from the Arabidopsis soil microbiota and evaluate the effects of different microbial strains on plant growth and development

  3. Investigate the impact of different triterpenes (avenacins) on root microbiome establishment in oat using a suite of available thoroughly characterised avenacin pathway mutants. These experiments will reveal the role of the avenacin pathway in regulating oat root microbiota and enable comparisons to be made with findings for Arabidopsis

The ideal candidate

The post holder will work independently and ensure research and record keeping is carried out in accordance with good practice, Scientific Integrity and in compliance with local policies and any legal requirements.

The successful applicant will have a PhD in plant biology or microbiology and extensive experience of plant and/or microbial genetics and molecular biology. Experience of plant stress biology, and/or microbiome analysis are desirable.  Excellent communication and interpersonal skills are essential.

Additional information

Salary on appointment will be within the range £31,250 to £38,100 per annum depending on qualifications and experience.  This is a full time post available until 31 March 2021.

Further information and details of how to apply can be found here or contact the Human Resources team on 01603 450462 or nbi.recruitment@nbi.ac.uk  quoting reference 1003704.  Click here to find out more about working at the John Innes Centre.

We are an equal opportunities employer, actively supporting inclusivity and diversity.  As a Disability Confident organisation, we guarantee to offer an interview to all disabled applicants who meet the essential criteria for this vacancy. The John Innes Centre is also proud to hold a Gold Award from Athena SWAN and is a member of Stonewall’s Diversity Champions programme.

The closing date for applications will be 27 June 2019.  

The John Innes Centre is a registered charity (No. 223852) grant-aided by the Biotechnology and Biological Sciences Research Council and is an Equal Opportunities Employer.

Postdoctoral Researcher (Smith Lab), John Innes Centre, Norwich

Closes: 4th July 2019 

Salary: £31,250 - £38,100 per annum depending on qualifications and experience 

Contract: Fixed Term Contract

Applications are invited for a Postdoctoral Researcher to join the Laboratory of Professor Alison Smith.

Background

Starch in the endosperm of cereal seeds is the single largest source of calories in the human diet, and an important raw material for industry. Despite its importance we know very little about how starch granules are formed during endosperm development. It is apparent that the temporal and spatial patterns of initiation of starch granules have diverged and diversified enormously during the 66 million years of evolution of the Pooideae subfamily to which temperate cereals and forage grasses belong.

The project will be conducted in the Alison Smith lab, in close collaboration with the David Seung lab. Both labs have strong interests and expertise in molecular, genetic and biochemical aspects of the synthesis and turnover of starch in model and crop plants, and access to a wide range of other expertise and technologies that may be necessary for the project.

The project is a collaboration with Steve Kelly and his team in Plant Sciences, University of Oxford, who have expertise in comparative transcriptomics analyses.

The role

The aim of this project is to identify the genetic basis of starch granule diversity in endosperms, using techniques including screens of mutant populations, transgenesis, cell biology and microscopy, and modelling.

The postholder will use a range of visualisation and quantitation techniques to deduce how different spatial and temporal patterns of starch granule formation arise during seed development. They will work alongside and collaborate with a researcher using transcriptomic and bioinformatic approach to identify genes that underlie seed starch diversity

The post holder will be encouraged to attend courses in technical and professional skills, to travel to national and international meetings, and to present their discoveries to internal and external audiences.

The ideal candidate

Applicants must have a background that includes plant biochemistry/metabolism, genetics and molecular biology. Experience of working with cereals or grasses and with transgenic plants is desirable. The project requires good interpersonal skills and the ability to work both independently and as part of a team.

Additional information

Salary on appointment will be within the range £31,250 to £38,100 per annum depending on qualifications and experience.  This is a fulltime contract of 3 years.

Interviews will be held on 22 July 2019.

Further information and details of how to apply can be found here. Or contact our Human Resources team on 01603 450462 or nbi.recruitment@nbi.ac.uk, quoting reference 1003664.

Facility Manager, Edinburgh Genome Foundry

Are you keen to develop your project and people management skills in one of the most fast moving areas of biomedical research: lab automation and synthetic biology?

We are looking for a molecular biologist, with extensive project and people management skills, to drive forward an automated genome assembly platform – Edinburgh’s Genome Foundry.

The Foundry is a world-leading facility, based within the School of Biological Sciences at the University of Edinburgh, devoted to the design and building of DNA constructs and provision of a wide range of laboratory automation services. The Facility Manager at Edinburgh Genome Foundry will be responsible for the implementation of the Foundry’s business strategy, the effective management of its projects, people, resources and budgets.

This is a unique opportunity to apply and develop your skills within an exciting, challenging and collaborative work environment.

This post is offered on a full time, open ended basis.

Salary: £40,792 - £48,677

For further Information, please contact Dr Liz Fletcher (liz.fletcher@ed.ac.uk)

Closing date is 25 June 2019 at 5 pm.

For the full job description and to apply, visit:

https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.jobspec?p_id=048000

Hive BioLab, the first community/DIYBio lab in Ghana, launches @hivebiolab

HiveBioLABS.jpg

Hive BioLab is the first community/DIYBio lab in Ghana dedicated to the rapid prototyping of ideas in biology, research, enterprising bio-startups by helping and providing resources to students and graduates to translate science to businesses.

HiveBioLab is now active on twitter: @hivebiolab

A Biomaker team has made it to the final of the BBSRC Innovator of the Year 2019 Awards

Close-up-cabinet-615x340.png

A Biomaker team with participants from Quadram Institute Bioscience (QIB), the Earlham Institute (EI), the John Innes Centre (JIC) and the University of Oxford, has developed a small scale speed breeding cabinet, which has qualified them for the final of the BBSRC Innovator of the Year 2019 Awards. Read more about this story here:

https://www.jic.ac.uk/news/norwich-research-park-team-in-line-for-early-career-innovator-award/

A specialized metabolic network selectively modulates Arabidopsis root microbiota

Osbourn Science 2019.large.jpg

OpenPlant scientists Hans-Wilhelm Nützmann and Anne Osbourn demonstrate that model plant Arabidopsis thaliana produces a range of specialized triterpenes that direct the assembly and maintenance of a specific microbial community within and around its roots. Their work, which was part of a collaborative effort, was recently published in Science:

Ancheng C. Huang, Ting Jiang, Yong-Xin Liu, Yue-Chen Bai, James Reed, Baoyuan Qu, Alain Goossens, Hans-Wilhelm Nützmann, Yang Bai, Anne Osbourn

A specialized metabolic network selectively modulates Arabidopsis root microbiota

Science (2019) Vol. 364, Issue 6440, eaau6389
DOI: 10.1126/science.aau6389

https://science.sciencemag.org/content/364/6440/eaau6389

Abstract

Plant specialized metabolites have ecological functions, yet the presence of numerous uncharacterized biosynthetic genes in plant genomes suggests that many molecules remain unknown. We discovered a triterpene biosynthetic network in the roots of the small mustard plant Arabidopsis thaliana. Collectively, we have elucidated and reconstituted three divergent pathways for the biosynthesis of root triterpenes, namely thalianin (seven steps), thalianyl medium-chain fatty acid esters (three steps), and arabidin (five steps). A. thaliana mutants disrupted in the biosynthesis of these compounds have altered root microbiota. In vitro bioassays with purified compounds reveal selective growth modulation activities of pathway metabolites toward root microbiota members and their biochemical transformation and utilization by bacteria, supporting a role for this biosynthetic network in shaping an Arabidopsis-specific root microbial community.

Biomaker Training in Ghana: Introducing biologists and non-biologists to “Building science hardware for biology”

Participants tinkering with XOD and the Open Smart Rich UNO 3 microcontroller

Participants tinkering with XOD and the Open Smart Rich UNO 3 microcontroller

The Biomaker Africa Programme is an initiative by the Open Plant fund, Synthetic Biology Strategic Research Initiative (Synbio SRI) and University of Cambridge. The programme, which is the first of its kind in Africa, aims to train biologists and non-biologists to design, prototype and share science hardware designs critical to building tools for laboratory use and for environmental sensing.

The Biomaker Africa Programme is geared towards enabling teams to design and build solutions to problems in agriculture, health, research and education specific to Africa. The programme is currently spread across 4 countries, Ghana (Kumasi Hive), South Africa (University of Pretoria), Egypt (Mansoura University) and Ethiopia (Bahir Dar University).

Kumasi Hive, one of the implementing nodes of the Biomaker Africa Programme, designed a two-month intensive training programme for students and graduates with backgrounds in biology and engineering. Ten participants were subsequently selected and began their training from March 2, 2019 to April 13, 2019. The curriculum driving the training was divided into various sections including:

  1. Introduction to fundamentals of biology

  2. Introduction to electronics and programming with XOD

  3. Introduction to 3D printing and laser cutting

  4. Design thinking

Participants of the Biomaker Training putting to use their 3D printing skills and 3D modelling skills.

Participants of the Biomaker Training putting to use their 3D printing skills and 3D modelling skills.

The curriculum was designed with the aim of equipping participants with transdisciplinary knowledge and skills in biology, electronics, programming, 3D printing and design thinking. We believe this will enable the selected participants to build biology solutions to real world challenges specific to the Ghanaian context.

Each training track lasted for two weeks and took place on Saturdays and Sundays. The training sessions were characterized by short presentations by trainers, brainstorming sessions and research presentations by the participants. The training ended with a Biomaker hackathon, where the participants were provided with the Biomaker kits to build working prototypes in a day. After a design thinking session to expose the participants to the design thinking process and a human centred design approach, the participants came out with projects such as:

  1. A solar-powered power pack for gel-electrophoresis to be used for field research and indoor laboratory use

  2. Colorimeter for urine analysis

  3. Water quality sensor for testing mercury and lead levels in water samples in mining areas in Ghana

  4. Air quality sensor for environmental monitoring

  5. Smart DIY biological safety cabinet for BSL1 work

By Harry Akligoh, Kumasi Hive, Ghana and Open Bioeconomy Lab.

 

Cas9-mediated mutagenesis of potato starch branching enzymes generates a range of tuber starch phenotypes

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OpenPlant scientists Aytug Tuncel, Nicola Patron and Alison Smith demonstrate that Cas9-mediated mutagenesis of starch-branching enzymes has the potential to generate new, potentially valuable starch properties.

Aytug Tuncel, Kendall R. Corbin, Jennifer Ahn‐Jarvis , Suzanne Harris, Erica Hawkins, Mark A. Smedley, Wendy Harwood, Frederick J. Warren, Nicola J. Patron, Alison M. Smith

Cas9-mediated mutagenesis of potato starch branching enzymes generates a range of tuber starch phenotypes

Plant Biotechnology Journal https://doi.org/10.1111/pbi.13137

Abstract

We investigated whether Cas9‐mediated mutagenesis of starch‐branching enzymes (SBEs) in tetraploid potatoes could generate tuber starches with a range of distinct properties. Constructs containing the Cas9 gene and sgRNAs targeting SBE1, SBE2 or both genes were introduced by Agrobacterium‐mediated transformation or by PEG‐mediated delivery into protoplasts. Outcomes included lines with mutations in all or only some of the homoeoalleles of SBE genes, and lines in which homoeoalleles carried several different mutations. DNA delivery into protoplasts resulted in mutants with no detectable Cas9 gene, suggesting the absence of foreign DNA. Selected mutants with starch granule abnormalities had reductions in tuber SBE1 and/or SBE2 protein that were broadly in line with expectations from genotype analysis. Strong reduction of both SBE isoforms created an extreme starch phenotype, as reported previously for low‐SBE potato tubers. HPLC‐SEC and 1H NMR revealed a decrease in short amylopectin chains, an increase in long chains and a large reduction in branching frequency relative to wild‐type starch. Mutants with strong reductions of SBE2 protein alone had near‐normal amylopectin chain length distributions and only small reductions in branching frequency. However, starch granule initiation was enormously increased: cells contained many granules of < 4 μm and granules with multiple hila. Thus large reductions in both SBEs reduce amylopectin branching during granule growth, whereas reduction of SBE2 alone primarily affects numbers of starch granule initiations. Our results demonstrate that Cas9‐mediated mutagenesis of SBE genes has the potential to generate new, potentially valuable starch properties without integration of foreign DNA into the genome.

Various job opportunities at Tropic Biosciences in Norwich

Tropic Biosciences:

“Based in Norwich, UK, Tropic Biosciences utilizes advanced genome editing (CRIPSR) and plant breeding technologies in developing new commercial varieties of tropical crops (e.g. coffee, banana, cacao). These multi-billion dollar crops play a critical role in supporting global nutrition and trade income but face intensifying disease and supply-chain challenges. We aim to solve these challenges through non-GMO genetic innovation.”

“CRIPSR technology is already transforming the agricultural industry at the hands of major seed companies like DuPont and Monsanto (‘Big Seed’) who use it to develop their future varieties of corn, soy and cotton. Our goal is to employ and further innovate this proven tool in the massive, largely untapped, tropical crops sector. To achieve this goal, we built a team of successful AgriTech entrepreneurs and world-class researchers with unique expertise in our target markets.”

Tropic Biosciences is currently looking for the following:

For more information about Tropic Biosciences visit https://www.tropicbioscience.com/.

Developing a frugal and medium throughput method for assessing protein-DNA binding affinity

What are we doing?

Project collaborators Dr Susana Sauret-Gueto and Dr Eftychios Frangedakis, from the University of Cambridge.

Project collaborators Dr Susana Sauret-Gueto and Dr Eftychios Frangedakis, from the University of Cambridge.

We live in an era in which we can thoroughly investigate all the genetic material that makes up an organism, at the level of the whole genome. Understanding gene regulation, the set of processes that control the decoding of DNA, is an essential part of modern synthetic biology. Although the expression of a gene can be regulated at different levels, transcription is one of the most important steps in this complex multistage process. Transcription is the process of creating messenger sequences, known as RNA, which allow the translation machinery of the cell to build proteins according to the DNA instructions. The efficiency of transcription determines of how much of these messenger RNAs are produced.

Transcription is triggered by a collection of functional proteins known as transcription factors (TFs), which bind onto the DNA sequence in front of the part of the gene that encodes a protein (the coding sequence). This section of DNA is called the promoter. Previous research has demonstrated that the strength of a binding event between a TF and the part of a DNA sequence in the promoter that it can ‘recognise’, is pivotal in affecting the transcription of the associated gene. The strength of this binding event between a TF and its binding site (TFBS) is referred to as binding affinity. Our OpenPlant funded project, based at the Earlham Institute and the University of Cambridge, is focused of finding out how much variation in binding affinity exists in nature, and subsequently creating synthetic promoters with varying binding affinities. We aim to develop a new method to test how variation in TFBS sequence might affect binding affinity. With the knowledge gained, we can then build promoter sequences that activate transcription at the level we design, in the place in a plant we want.

Methods of assessing the binding affinity of TFs and DNA sequences already exist, but have limited scope for asking questions such as ours, either due to low throughput or high cost. One such method, which has been established for decades, is the Electrophoretic Mobility Shift Assay (EMSA). EMSA is based on visualising the travel of the bound TF-DNA complex through a jelly like matrix, or gel. Because each sequence and TF have to be made, and then individually ‘run’ through the EMSA gel, this method is difficult to scale up.

Figure 1: Comparing current protein-DNA binding assays.

Figure 1: Comparing current protein-DNA binding assays.

Another option for testing the binding affinity of TFBS is based on a high-density DNA chip, also known as DNA microarray. This is essentially a glass slide with hundreds of thousands of short DNA sequences attached to the surface. The TF of interest can be synthesised in the lab and then hybridised with the chip. Hybridisation is just letting the binding between TF and TFBS occur as is would in the cell and, following this, the amount of TF bound on to each DNA sequence can be detected. However, the process of creating and reading such a chip is expensive and needs specific devices (Figure 1).

The aim of our work is to design and test a methodology which overcomes the shortcomings of available methods for testing TF binding affinity. Our goal is to provide a medium-throughput test of binding affinity, and we are designing our methodology to be easily replicable using affordable, readily available components. Approaching the problem from both synthetic and evolutionary backgrounds, we want to be able to test a range of binding sites for affinity, with enough replication to validate hypotheses. To do this we have developed the transcription factor relative affinity measurement pipeline (TRAMP).

Where did the ideas come from?

Inspired by the design of the DNA chip-based methods described above, we set out to design a method for assessing TF-DNA binding with as high a throughput as possible, whilst avoiding the high cost and specific requirements of the chip-based assay. We use a simple and cheap commercially available product to immobilise DNA onto the widely available lab workhorse; the 96-well plate. We have also used a recently developed method to tag our TF protein with a small peptide that, when bound to another peptide, gives off a signal. This signal is detectable in a plate reader, a piece of equipment widely used in modern labs. This new method allows us to easily quantify the amount of TF binding at a given TFBS, by measuring the brightness of the glow given off by the cumulative amount of the signal. These two components have allowed us to create a biochemical method of assaying protein-DNA binding affinity (Figure 2).

Figure 2: Assaying protein-DNA binding affinity using the transcription factor relative affinity measurement pipeline (TRAMP)

Figure 2: Assaying protein-DNA binding affinity using the transcription factor relative affinity measurement pipeline (TRAMP)

To maximise the efficiency of selecting TFBS to test in the assay we are designing, we have developed a novel computational tool. This allows us to leverage naturally occurring genetic variation in TFBS sequences gathered from publicly available population wide datasets. Instead of assaying thousands of random DNA sequences before finding a desirable one, we use several analytical methods to categorise natural variation along several parameters. We have been able to use a computational approximation of the binding event itself to score potential affinity. We also model the shape of the DNA double helix where the TFBS lies, allowing us to investigate the role of this physical property of DNA that has been suggested to be important in the efficiency of binding events.

These methods allow us to rapidly generate a set of suggested TFBS that should exhibit a range of binding affinities. This set of TFBS can be passed into the plate-based assay to be tested, and the findings used to test and further develop our understanding of binding affinity.

 

Where can this assay be applied?

We think that our work will be of interest to a wide range of biologists looking to understand the role of TF binding affinity in gene regulation. We hope by using TRAMP, we can find DNA sequences that exhibit different binding affinities to their corresponding TFs. Our aim is to be able to then replace the native TFBS in a promoter with the sequences we discover. We will use this approach to validate our findings, by linking the predictions and lab assays we have conducted back to transcription, the biological function we are interested in understanding.

It is our hope that our synthetic promoters will allow us to alter the activity of the promoter, meaning that when transcription occurs, the target gene will generate a different amount of messenger-RNA. If we can do this, we think our work will help scientists who want to use very specific gene expression patterns as part of synthetic biology strategies to synthesise valuable compounds like medicines. Our pipeline could also be useful for testing the effect of variation in TFBS between individuals, populations, or species.

By Dr Yaomin Cai and Dr Will Nash, Postdoctoral researchers at the Earlham Institute.

www.earlham.ac.uk

@EarlhamInst

[Closes 28th April 2019] Biomaker Challenge Africa Coordinator (Fixed Term), Department of Plant Science, University of Cambridge.

 The Global Challenges Research Fund is supporting a pump-priming programme to take the Biomaker Challenge to centres in Africa. Biomaker is an interdisciplinary programme that brings together multiple teams to build low-cost sensor devices and instruments for biology (https://www.biomaker.org). The Biomaker Africa programme is co-organised by the Synthetic Biology Strategic Research Initiative, the BBSRC-EPSRC OpenPlant, Centre for Global Equality, and OpenBioeconomy Lab in Cambridge. We are looking for a Challenge Coordinator for 12 weeks during May-Jul 2019 to take responsibility for coordinating participating teams and managing online communications and social media. This includes organising and publicising events and highlighting interesting projects online through writing and multimedia presentations, coordinating training and connecting teams who might be able to share knowledge and skills.


The appointee will form part of a team to deliver:

  • A set of informational and training materials for biologists, engineers and interested public (e.g. the Maker community)

  • Blog posts, photos, videos and social media content about Biomaker Africa

The position will provide an opportunity to travel to sites in Africa to help organise starter and training events, and to build a wide range of contacts in this area.


Skills gained include:

  • Coordination, planning and organisation

  • Networking skills between academia and industry, including sponsor liaison

  • Communications including writing, photography, video production and social media

  • Public speaking and presentations

  • Introduction to technologies such as 3D-printing, electronics and DIY approaches to scientific instrumentation

The placement would suit someone with an interest in electronics, biology, and maker technologies e.g. 3D printing. Experience in other coordination and communication roles (paid or voluntary) is desirable. 

For full job description.

For enquiries, please email Alexandra Ting at synbio@hermes.cam.ac.uk.

To apply, send a covering letter explaining your interests and suitability for the role and a CV to synbio@hermes.cam.ac.uk

Joint OpenPlant Fund/ Biomaker call opens Monday 8 April and closes Monday 13 May

The next call for OpenPlant Fund applications is announced!

This year’s OpenPlant Fund call is joined with the Cambridge-Norwich Biomaker Challenge. More information on this joint call can be found at: https://www.biomaker.org/cambridge-norwich-challenge.

A summary of the important dates can be found below:

Call Opens: Monday 8 April

Mixer event in Cambridge: Thursday 25 April (Transport Norwich - Cambridge can be provided)

Call closes: Monday 13 May

Challenge Begins: Friday 24 May

Progress reports and presentations: Monday 29 July (OpenPlant Forum Event)

Challenge Closes/Open Technology Workshop: Saturday 2 November

FinalBCPoster2019.png

Cambridge Science Festival

Cambridge Science festival.jpg

For this year's Cambridge Science Festival, Alex Ting (Cambridge OpenPlant coordinator) teamed up with Biomakespace, SciArt in Cambridge, and independent events producer Sophie Weeks to host The Art & Science Soirée. The event brought together scientists, engineers, artists and designers engaged in DIY science for an exciting evening of speed meets, snap-talks, hands-on demos, and unexpected encounters. 

The event opened with slam poetry by Peter Bickerton (Science Communicator, Earlham Institute) followed by a talk by Jim Ajioka (Co-founder, Colorifix) and Giulia Tomasello (Interaction Designer specialising in women's healthcare.) Inside the house, Biomaker Challenge teams exhibited their low-cost, open-source projects. The aim of the event was to provide inspiration for open science projects (talks and demos), showcase the tools available to pursue such projects (Biomaker Challenge), and highlight a community-access space for biology and prototyping (Biomakespace). We hope that the event will inspire and provide an avenue for artists, designers, and other non-scientists to get involved in open science. 

Photos of the event can be found here: https://www.flickr.com/photos/synbiosri/albums/72157679436063798

Students recieve CRISPR training thanks to OpenPlant-funded project.

Thanks to the support of OpenPlant 4K fund, summer student Nandor Hegyi (University of Aberdeen) and final year undergraduate student Darius Zarrabian (University of Cambridge) received hands-on CRISPR training from Dr Gonzalo Mendoza Ochoa in the lab of Alison Smith (Cambridge).

 

Host species  Chlamydomonas reinhardtii

Host species Chlamydomonas reinhardtii

The OpenPlant-funded project entitled “Site-directed integration of transgenes into the nuclear genome of algae and plants using CRISPR/Cpf1/ssDNA” aimed to solve drawbacks associated with current methods for nuclear transformation, which results in random integration of transgenic DNA. The plan was to firstly develop the method for the green alga and biotech host Chlamydomonas reinhardtii, and then try to adapt this specific method for land plants and compare it with similar methods being developed.

 

The students quickly learned that research can present unexpected challenges. Nonetheless, they remained determined to tackle the problem! Having achieved half of the tasks of the project, Nandor returned to Aberdeen to continue his degree with the thought “I wish I would have had more time to work on this interesting project”. Darius came to the rescue soon after and, with equal enthusiasm, took up where Nandor left off. He is currently in the final stage of his final year research project and is gathering data that indicate that single-stranded DNA fixes nuclease-induced DNA cuts (via homologous recombination) better than exogenous double-stranded DNA.

 

Darius’s words “I have really enjoyed making progress with the project and learning about CRISPR, despite the inevitable multitude of 96-well plates I have had to face!” capture both the joy and hard work of scientific research.

 

We thank again OpenPlant for the support and will be sharing progress in the near future.

By Dr Gonzalo Mendoza (University of Cambridge)