Post Doctoral Research Assistant, University of Edinburgh

Post Doctoral Research Assistant  – Experiments of Topologically Active Polymers & DNA Origami
From June 2021 or soon after to June 2024 (3 years) & potentially extendible
Salary high-end UE07 ~ £41k/year

We are looking for an experienced and motivated PDRA with background in experimental soft matter, polymer physics and/or molecular biology. The ideal candidate should have direct expertise on DNA biophysics and/or rheology of complex fluids. 

The project involves developing and performing experiments on polymers that can change topology in time and that are based on DNA. It also involves experiments with DNA origami and super-resolution microscopy. The aim of the project is to understand the rheological properties of polymeric materials and complex fluids made of “topologically active” polymers and DNA origami. 

This position is for a senior PDRA, who is expected to be semi-independent, have supervision responsibilities on a day-to-day basis and to propose and lead side-projects.

More info: https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.jobspec?p_id=052998

Contact: Davide Michieletto, davide.michieletto@ed.ac.uk
Group website: www2.ph.ed.ac.uk/~dmichiel/eutopia.unitn.eu

CtoD: From Cells to Droplets

The aim and rationale

Real biological systems are complicated by the massive number of components and highly complex cellular network. Establishing a cell-like environment in vitro would allow us to disentangle basic mechanisms underlying cellular networks under well-controlled settings. We are a small but interdisciplinary team between the Department of Chemistry and the Department of Plant Sciences, aiming to apply microfluidic droplet system to studying physiological processes in plants, transforming the objects of research from plant tissues into artificial cells.

Microdroplets generation and in-droplet protein expression for mimicking physiological pathways.

The project and more

In this project, we aimed to develop an artificial cellular system using microfluidic droplets that allows the in vitro expression of proteins from plants in a compartmentalised cell-like environment. The biosynthetic pathway of a class of plant pigments, betalains, was used as a simple model to test the methodology, and the TNT® SP6 High-Yield Wheat Germ Protein Expression System from Promega was selected as a reliable in vitro protein expression system. The cell-free protein expression components together with betalain biosynthetic genes were enclosed in microdroplets and intermediate and final products measured.

Betalain biosynthetic pathway from L-Tyrosine to two groups of betalains. DOPA, 3,4 dihydroxyphenylalanine. DODA, 4,5 DOPA dioxygenase. cDOPA5GT, cyclo-DOPA 5-O glucosyltransferase.

Up to this point, we have tested the expression of various proteins in microdroplets. Betalain biosynthetic enzymes were produced and confirmed by fluorescent protein fusions in microdroplets. However, simply co-expressing enzymes from the betalain biosynthetic pathway in the cell-free protein expression solution was not sufficient to drive detectable production of pigment molecules. Following these, optimisation of buffer composition was made and various substrates fed into the system, which led to realisation of parts of the pathway in the in vitro environment.

In addition to the project itself, the various events and training organised by OpenPlant/Biomaker were even more remarkable. The annual OpenPlant Forum gathered an incredibly diverse range of subjects and the low-cost DIY instruments for automating laboratory experiments were mind-blowing.

Future perspective

The OpenPlant/Biomaker project has built solid foundation and connection for us to move forward in the future. Communication between cells plays a central role in many metabolic pathways of multicellular organisms, yet it remains difficult to reproduce in vitro. To this end, an artificial multicellular system with droplet-to-droplet communication will be explored to mimic metabolic pathways which rely on the communication between cells. This platform would open more opportunities for synthetic biology and allow hypotheses and models based on cell-to-cell communications to be tested in vitro.

Last but not least, we thank the OpenPlant/Biomaker teams for the wonderful events and generous help that they have provided!

Written by Zhengao Di, University of Cambridge

Developing an open and affordable 3D bioprinter

Background

Friends had Central Perk cafe, the gang from How I Met Your Mother had MacLaren’s Pub and we have Charlie’s Pizza joint. What started as a trivial discussion about printing human organs over a stone-baked Margherita quickly evolved into us applying for a bid to participate in the BioMaker Challenge, with the objective of Developing an open & affordable 3D bioprinter. 

The beginnings of 3D printing date back to the 1980’s, when it was commonly known as its more mouthful synonym stereolithography (SLA), a technology pioneered by Charles W. Hull. Revolutionized with SLA, one could translate a 3D design from a data file into a physical object, in a relatively short time. The household notion of 3D printing is testament to the success of SLA, which originated from the company 3D Systems Corporation. 

Fast forward 40 years, my neighbours are at home 3D printing little elves for their garden, my cousin is buying a 2-story building printed by an enormous SLA machine, my doctor is offering his patients custom 3D printed ear implants, heart valves or bones - SLA has already infiltrated many aspects of our lives, economy and medical care. Much of this progress came about because of the RepRap project, whose aim was to create an open-source 3D printer capable of printing most of the parts needed to replicate itself, making it cheap enough for hobbyists. Today’s consumer 3D printer companies, and the widespread use of 3D printing, grew out of the RepRap hobbyist community. 

The field of regenerative medicine could hugely benefit from 3D printing techniques to offer personalized medicine to its patients, by for example printing organs made of one’s own cells. However, these applications are challenged by the complex architecture of human organs, the difficulties of supporting living cells, introducing foreign materials in a human body and working at a microscale. 

Addressing these issues, companies and academic researchers have built 3D printing platforms, specialized for biological materials, hence 3D bioprinting. Not surprisingly, these come at a prohibitive cost, up to £200K for the printer only.

BioMaker Challenge

During our weekly pizza gatherings we talked about how it would be great to have an open-source bioprinting project, along the same lines as the original RepRap project. It could make the technology more accessible and bring printing human organs for transplantation a step closer. None of our backgrounds were in bioprinting, but our combined skillsets did range from engineering and programming to cell biology, with diverse backgrounds in start-ups, industry and academia. The Biomaker challenge would be a great way to work together on a project where we could contribute something to the 3D printing community, and learn a lot along the way. Plus it would be fun! 

Bertie the 3D bioprinter.

So as part of the BioMaker Challenge, we set out to address the lack of reasonably priced open-source 3D bioprinters in the market by Developing an open & affordable 3D bioprinter. With this project still in its infancy, working with human cells was out of the scope due to ethical and practical reasons. Nevertheless, we attempted to design our 3D printer to potentially print corals, an application with a shorter timeline, more amenable to working in the absence of a biological laboratory and with direct benefits to a problem close to our hearts, the depreciation of the ocean’s corals. Our project branched into two components outlined below: 

1. Converting an existing open-source 3D printer into a 3D bioprinter capable of extruding biomaterial.

Our inspiration to address this first problem is drawn from a paper by an American group (Push et., 2018), in which they describe the design of a syringe pump large volume extruder (LVE) of low cost, compatible with printing biomaterial. This involves the purchase of standard materials (e.g: 60mL syringe, bolt nuts) and the 3D printing of other assembly components with a PLA extruder from a standard 3D printer. The newly assembled LVE would then replace the printer’s standard PLA extruder and allow the printing of biomaterials. 

With this in mind, many hours of research and discussions went into selecting the right 3D printer as a foundation for our bioprinter - we were certain about two things: it had to be open-sourced and stay within a reasonable budget. We finally settled on the RepRap Ender 5 3D-printer. In addition to the syringe extruder, we were interested in trying to integrate a peristaltic pump in our system because it would allow us to extrude multiple bio-inks at once. 

Adding a valving architecture between the reservoirs and the pump enables the switching of the reservoir that bioinks are aspirated from on the go, thereby enabling the interlinking of multiple inks of different cell types in 3D space. 

After a few months of putting all the hardware together and with a sprinkle of software, Bertie the Bioprinter was born!

2. Developing a bioink suitable for sustaining living cells.

Regardless of the organism in question, a bioink should: 

a) Contain the right nutritional environment for specialized cells.

b) Maintain a single-cell suspension (prevent cells from clumping together and/or from dying from being separated from their friends).

c) Provide a physical scaffold once printed to keep the shape of the 3D model.

d) Use materials that are safe to insert in the receiving environment. 

Printing human cells was out of the scope of Biomaker, so we initially turned our attention to another challenging bioprinting application, trying to 3D print coral (which not all of us knew was a living organism!). Coral numbers and health have declined rapidly as a result of environmental conditions and their slow growth cycle. If coral could be 3D bioprinted, perhaps it could be transplanted back into reefs to bring them back to life.

We dove into the scientific literature and identified two such bioink formulas, which are, in theory, capable of supporting the life cycle of corals and providing an “ocean-friendly” physical scaffold. It turned out however that coral species are high maintenance, requiring expensive aquariums and daily care. Even the most experienced coral growers find it challenging to maintain a community of the families of coral that were the right size to fit our bioprinter. We realised that we didn’t have the funds or the time to manage coral during the Biomaker Project, but we did make connections with coral researchers who we hope to work with on this project in the longer term. 

Printed phytoplankton using Bertha the bioprinter.

We were however determined to evaluate the efficacy of our bioinks, and didn’t let coral’s needy demands deter us. One of the bioinks we identified is based on the chemical interaction of sodium alginate and calcium chloride, which create a solidified gel upon contact. At the concentration used, these chemicals didn’t affect the survival of phytoplankton, a single cell organism we chose to work with for its relative low cost, ease of maintenance and ability to survive as single cells. 

By the end of the project we were able to print a very slimy collection of phytoplankton, and affectionately named it Bertha. Bertha still sits in someone’s fridge for posterity.

Future

The BioMaker Challenge was an incredible opportunity for us to concretise an idea and start along the path to our long term goal. We also got to meet a wonderful community of makers and with their help and feedback we hope to further refine Bertie the Bioprinter. Moving forward, we plan to improve Bertie’s performance in terms of printing precision and its ability to run complex modes (e.g: multiple bioinks printing at once), as well as make him suitable for sterile work (e.g: ventilation, UV lights). We also plan to develop  application specific bioinks for Bertie to print. 

We’d like to take this opportunity to thank the BioMaker Organisers (special thanks to Alexandra, Jenny & Jim) for arranging this event, Professor Ludovic Vallier (Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre) for supporting our ideas and administrative needs as well as the BioMakeSpace Cambridge who welcomed us in their community.  Thanks to the BioMaker Challenge, we are now one small step closer to 3D printing organs, and in the meantime, Bertie is on standby for printing COVID-19 related materials (with the original PLA extruder) if need be. 

Julie, Sebastian, Monica, Robin, Ben & Tejas

PS, For more details of the project, check out our Hackster :-)

OpenCM - an open framework for single cell manipulation

Introduction

Microscopic studies of single cells, their dynamics, signalling and behaviour require a whole toolbox of different microscopic techniques, highly specific gadgets and methods that can easily exceed the budget for new lab equipment.

OpenCM team (left to right): Maziyar Jalaal, Nico Schramma, Stephanie Höhn and Kyriacos Leptos

The open technology community is continually developing new, innovative and inexpensive solutions for easy-to-build microscopes and other equipment, aiming to democratize microscopy and enhancing the applicability of custom-built devices to approach novel questions. The OpenCM team aimed to provide one of the solutions needed to make open-source microscopes even more utile, namely a setup for micromanipulation.

Multi-axis micromanipulation is used for in-vitro fertilization, imaging of highly motile cells, microinjections, patch-clamp methods, mechanical probing of cells with micropipettes and is - simply put - the microscopists tiny helping hand to interact with the sample mechanically.

The project

Key to the OpenCM project is the close collaboration with Benedict Diederich and René Lachmann from the UC2 group, which started after the OpenPlant forum in July 2019. UC2 builds 3D-printed modular optical elements, which can be easily assembled into various microscopes. The OpenCM project aims to make this system even more versatile, by adding a module for micromanipulation.

During the BioMaker challenge the team was able to design the first prototype two-axis micromanipulator, which fitted the UC2 system and was controlled via Arduino. The team followed the online documentation of their collaborators in order to 3D-print a microscope, which is controlled with an open source Python based GUI on a Raspberry Pi. The team was among the first to reproduce the UC2 microscope and helped evaluate and enhance their current quality of the online documentation.

In the end, the team was able to build a fully integrated microscope and micromanipulation system and to showcase it at the BioMaker Fayre. The most important outcome of the BioMaker Challenge is establishing a very close collaboration with the UC2 project, which is still persisting.

Future work

The team plans to undertake the final steps in developing a 3-axis micromanipulator (OpenCM2). The hardware will be integrated into the UC2 system, and free software will be provided for position controlling with a wireless joystick and the UC2 GUI via Raspberry PI and wifi controllers.  

First prototype as presented at the BioMaker Fayre 2019, an inverted microscope with 2 axis micro
manipulator.

The project will continue in close collaboration with the laboratory of UC2 in Jena, Germany, and the financial support in the context of the programme “Creativity and Studies” of the University of Gottingen by the AKB Stiftung, a non-profit foundation of the Büchting Family (secured by Nico Schramma and Björn Kscheschinski).

Furthermore, the team found the UC2 setup very useful to provide hands-on experience at the intersection between physics, mechanical engineering, microscopy and cell biology. Hence, as a side project, the team also started preparing workshops for children and students.

In a joint effort, and with the financial help of the UK's Women Engineering Society and the Public Engagement office at the University of Cambridge, the members of UC2 and OpenCM participate at the Women in Engineering Society 100 Violets Challenge in order to give a first "Optics for Everybody" workshop. Unfortunately, due to the pandemic, the exhibition at the Brunel Museum in London has been postponed.

During the BioMaker challenge and driven by the community's open-mindedness, the team was encouraged to branch out ideas, communicate openly, and team up with others to find and combine new and innovative solutions. In the end, the BioMaker spirit inspired the OpenCM team to reach out to the broader community.

Acknowledgments

We thank David Page-Croft for fruitful discussions and his help with 3D printing. We also thank Benedict Diederich, René Lachmann and Barbora Marsikova from the UC2-Project, and Alexandra Ting, Dieuwertje van Esse - van der Does and Jim Haseloff from the BioMaker Challenge.

Written by Maziyar Jalaal, Nico Schramma, Stephanie Höhn and Kyriacos Leptos.

References

Diederich, Benedict, et al. "UC2-A Versatile and Customizable low-cost 3D-printed Optical Open-Standard for microscopic imaging." bioRxiv (2020).

Research Assistant/ Lab Manager position in Chemical Biotechnology, University of Edinburgh

3.5-year Research Assistant / Lab Manager position in Chemical Biotechnology (Wallace Lab - IQB3)

We are looking for a highly-motivated MSc/PhD-level Research Assistant to join our lab in IQB3 from Dec/Jan. The role will be primarily research based and will continue our work on the combined use of chemical and biological tools in microbes for the sustainable production of industrial small molecules. This will include the assembly and optimisation of biosynthetic pathways in bacteria, the screening of new biocompatible catalysts, and the analysis of novel metabolites using a variety of analytical techniques. The post will also include a significant supervisory role, including the management of day-to-day research activities in the group, organisation of lab strains, coordination of group meetings and seminars.

Applicants can contact Stephen directly (stephen.wallace@ed.ac.uk) including a CV and cover letter, or apply directly using the link below.

Closing Date: 12th October 2020

Link here: https://www.jobs.ac.uk/job/CBP647/research-assistant

Website: http://wallacelab.bio.ed.ac.uk 

Twitter: @Dr_StephenW and @Wallace_Lab

Research Associate in Protein Design and Synthetic Biology, University of Bristol

Research Associate in Protein Design and Synthetic Biology

With Dr Fabio Parmeggiani, University of Bristol  

The group of Dr Fabio Parmeggiani is seeking a talented and enthusiastic postdoc interested in protein design and synthetic biology. The project will be focused on designing custom modular protein architectures as robust and reliable scaffolds for the development of novel functional protein-based nanomaterials and multivalent ligands to modulate cell response.

The aim of the project is to develop a robust, fast and high throughput design platform to rapidly build new proteins and complexes. The researcher will be responsible for developing the experimental part of the pipeline (involving DNA assembly, protein expression and purification, validation of designs through biophysical and structural characterization) and spearhead applications in nanomaterials and cell biology. The position would be best suited to a researcher with a keen interest in applying de novo protein design in synthetic biology.  Essential skills for this role would include: design, construction and expression of synthetic genes in E. coli; biochemical and biophysical characterisation of proteins; strong structural biology expertise, in particular with cryo-electron microscopy and x-ray crystallography.

Closing date: 14 October 2020 

More information can be found here.