Projects

A complete listing of open projects funded by the Synthetic Biology Strategic Research Initiative at the University of Cambridge, the OpenPlant Synthetic Biology Research Centre and Biomaker Challenge.

OpenPlant Biomaker Challenge Projects

Winter 2020/2021 (projects 180-190)

• Lung physiology monitoring with DIY spirometer

• Accessible and Inclusive STEM: Multisensorial Data Representation

• Microfluidic Device Fabrication using Laser Ablation

• sciTAG: an accessible label design application compatible with existing label printers

• Monitoring Stress In Plants Through Non-Invasive Imaging Techniques

• High throughput Pipetting tool (Plate Z)

• Open-Source Biolistics Enhancement + Automation

• Genetic Characterisation of Maize Landraces using DArTseq for Streak Virus Resistance

• Plant Growth Chamber with real-time monitoring and remote control

• FungiMorph A multipurpose fungal morphology phenotyper

• Pheno3D - a low-cost multi-purpose 3D digital photography phenotyping station

Winter 2019 (projects 153-179)

• Open DLS: an open-source dynamic light scattering device for nanoparticles sizing

• LunaFlow: bioluminescent plankton for 3D flow visualisations of pressure fields

• OpenCM - an open framework for single cell manipulation

• Stress priming for improved production of biotech-relevant compound in green alga

• Mechanisms for direct electron transfer (DIET) between Geobacter and Methanothrix

• Diabetes diagnosis and management using Arduino and mobile user interface

• Developing an open & affordable 3D bioprinter

• CtoD: From Cells to Droplets

• e-CO-SENSE – biophotovoltaic powered soil sensors

• An open toolkit for engineering microbial interactions

• Establishing a joint UK-Kenya Phytoplasma research initiative

• Build your own DNA Dave

• Low cost SLM interface board for advanced microscopy

• SAFE - Safe Air For Everyone

• Variable-time cameras with image recognition for inexpensive, large-scale monitoring of plant pollination events

• Low Cost Oxygen Sensor for Bioreactors

• MACRO IMAGER: a low-cost multi-purpose large area macro digital photography phenotyping station

• A behavioural chamber to evaluate rodent forelimb grasping performance

• BIOFAB INCUBATOR: low cost programmable incubator for growing mycelium textile

• Aeroponics for All

• AccuPatch: conductive microelectrode array for cancer tissue screening

• In-situ 3D visualization using X-ray CT during mechanical testing of natural cellular materials

• BrewerMicro – DIY microscope for counting yeast

• IoHeat: a contained oasis in the coldroom

• Engineering low-cost turbidostat systems for running microbial evolution experiments

Winter 2018-2019 (projects 145-152)

• A XOD node for the Bosch BNO055 9-axis absolute orientation sensor

• Simple GPS modules

• Automating the output of genetic circuits using light adjustable promoter systems

• Aquaneers: a full suite of monitoring sensors and actuation tools for aquariums

• Fully automated optimal home grow chamber

• Ultrasonic hydrometer for remote monitoring of beer fermentation

• Facile optical measurement of real time liquid microbial growth

• Menu-driven user-interface construction tool for XOD

Summer 2018 (projects 135-144)

• Temperature controlled container for sample transportation

• Automated water irrigation, lighting and monitoring system for plant growth

• Agarose device to generate and study an in vitro embryonic model system

• Wearable biosensor for monitoring vaginal discharge

• Evolution under temporally-controlled selection: The Oscillostat

• Open bioreactor for local enzyme manufacturing

• Visual Programming for Biomakers

• Improving dual-view imaging in a custom-built light sheet microscope

• Spectre - Palm-sized Spectrophotometer

• LyseeFlask

Summer 2017 (projects 94-134)

• A cell-free sensor platform for the quantification of arsenic concentrations in drinking water

• A Device for Real-Time Monitoring of Protein Synthesis

• A low cost reusable microfluidic device for the detection of antibiotic  resistant genes in bacteria isolated from patient samples

• A low cost, point-of- care device to measure blood haemoglobin  levels, using calorimetry and infrared spectroscopy

• A low-cost colorimeter for accurate detection of colour changes in medical diagnostic tests

• A low-cost, pressurized liquid chromatography system for protein  purification

• An accessible, low cost, hand-held device for detecting counterfeit antimalarial drugs, using quartz crystal microbalance technology

• A microdroplet incubator to establish 3D organoids cultures from oesophageal  adenocarcinoma

• A sensor to improve the accuracy of stereotactic brain biopsies for the  diagnosis of brain tumours

• An artificial habitat to investigate  Boquila trifoliata mimicry

• Cheap Do-It- Yourself Small Volume UV Spectrometer for  Nucleic Acid and Protein Quantitation

• Detecting alterations in ionic concentrations associated with  different cellular states

• Detecting pathogens in sewage sludge

• Developing a self-regulating control system for intravenous drug  administration -- using aminoglycosides as an example

• Development of an anti-TFF3 functionalized surface to capture of Barrett’s oesophagus cells

• DIY bioacoustics

• Field portable colorimeter

• Functional membrane-based integrated biosensing devices for detection and  quantitation of specific nucleic acids and other biomolecules

• Handheld syringe pump with heating element

• KNOW-FLOW/ A low-cost programmable blood flow system

• Low Cost Wearable Sensors Strain Sensors for illness  identification via Gait, Posture and muscle usage

• Low-Cost Multispectral Imagery for UAV-based Vegetation Monitoring

• Macrophotography of fern gametophytes using a DIY focus stacking system

• Microfluidic Turntable for molecular  diagnostic testing

• OptoFlow/ Optical flow rate measurement for microfluidics

• Puzzle-solving Bacterial Pet/ Imaging Platform for Microfluidics-based Reinforced Learning with  Motile Bacterial Cells

• Remote Environment Controller for  Experiments in Extreme Environments

• Sci-Fi Cam

• Ultrasonic Plant Height System for High-Throughput Plant Phenotyping

• Real-Time monitoring of cell proliferation

• A light intensity meter to measure plant growth conditions

• The Charge on Cancer: Using Induced Dipole Moment to Electrostatically Separate Healthy and Cancer Cell-Metal Nanoparticle Complex

• Automatic size and weight measurements of fish

• Building DeepSkin: a low-cost state-of-the-art digital dermatoscope

• PiRMA: A low-cost rodent physiology monitoring bed for pre-clinical experiments

• Using stem cells to sense and report developmental signalling gradients: towards advanced spatial in vitro models of embryogenesis

• Improving Open Source Motion Control With Arduino

• A Place in the Sun: Creating bespoke spectral recipes using a simple LED Array

• An open source electro-pneumatic controller for integrated microfluidic chips

• iLAB: next-generation coding for physiological monitoring

• Open-source Lasercut Portable Incubator for Microbiology

OpenPlant Fund Projects

November 2019 (projects 92-93)

• ‘Reach and Teach Science in Africa’: Strengthening Agricultural Research Capacity to Tackle Food Insecurity in Africa

• Speed Breeding for Accelerated Crop Improvement in East Africa Workshop

July 2018 (projects 82-91)

• Molecular Biotechnology Laboratory Training Workshop and the UK-Africa Food Security Symposium

• Extending the type IIS toolkit for subcellular localisation in Marchantia

• Developing a frugal transcription factor relative affinity measurement pipeline (TRAMP)

• Site-directed integration of transgenes into the nuclear genome of plants using CRISPR/Cpf1/ssDNA

• Harnessing cytosine DNA hypomethylation to explore the potential for crop improvement in wheat

• Receptor-like kinases at the initiation and maintenance of AM symbiosis

• Visualizing genetic circuits in space and time with paper-based cell-free translation

• Optimizing open enzyme purification using 3D-printing and automation

December 2017 (projects 72-81)

• Focus Stacking for Teaching and Publication in Plant Sciences

• Actin visualization: to disclose mechanisms of host cell reorganisation during interactions with microbes

• Comparative analysis of cell free and in planta protein synthesis systems

• Cell-free proteins synthesis as a resource for generating plant proteins

• R for Proteomics' training proposal

• Open-Cell: An Open-Source 3D Printable System for High-Throughput Cell-Free Screening

• Development of open source camera trap powered by plant microbial fuel cell (pMFC)

• Open Source Resources for Teaching Synthetic Biology in Low-Resource Settings

• Design of synthetic plant and mammal gene regulatory networks using nonparametric Bayesian approaches

July 2017 (projects 62-71)

• A cell-free sensor platform for the quantification of arsenic concentrations in drinking water

• Development of Manufacturing Capability for Rare Sugar Nucleotides

• Engineering of Chlamydomonas reinhardtii to produce betalain pigments and the use of riboswitches to direct metabolic flux

• CGSENS: Visualization of CG methylation using a fluorescence protein biosensor

• GardenSeq: Chasing the invisible diversity of microbial life forms in vegetable garden beds with a portable DNA-sequencer

• Plug and play synthetic biology education resource

• Single cell pollen meiosis screening in wheat

• Harvesting the genetic value of interspecific wheat introgressions

• Identifying nutrient-status dependent elements regulating the wheat transcriptional response to neighbours

• Bench-top Controlled Environment Growth Chamber for Speed-Breeding and Crop Transformation

December 2016 (projects 52-61)

• Plant-ProChip 2.0: High throughput transformation of plant protoplast

• Translating Nitrogen Use Efficiency from models to crops

• The Green Mother Machine Reloaded

• Development of a Low-Cost Micro-Environment Device for Root-Nutrient Interaction

• DNA-mediated fusion of spheroplasts with synthetic liposomes

• Ambient temperature preservation of cell-free TX-TL reagents for use in synthetic biology

• Developing teaching resources for rapid, open and combinatorial genetic circuit fabrication in cell-free systems

• Accessible 3D Models of Molecules

• Light sheet microscopy of cell sheet folding in Volvox

• Bacterial photography and edge detection: engineering light sensitive circuits in E. coli

January 2016 (projects 38-51)

• Hot Tomato: Complementation of the Capsaicin Biosynthetic Pathway to Engineer Spicy Tomatoes

• Implementation of a synthetic transcriptional AND gate in the chloroplast of Chlamydomonas reinhardtii

• Advancing the ability to image single RNA molecules at the cellular level

• Establish a Procedure for Rapid Identification of Genetic Parts for Use in Algal Biotechnology

• A synthetic biology approach to investigating arbuscular mycorrhizal symbiosis in Marchantia paleacea

• Desktop plant experiment box

• Environmental sensor networks based on plant electrical signalling.

• Plant electro-mechanics

• Establishing 3D Printed Microfluidics for Molecular Biology Workflows

• Universal precise large area colony scanning stage with measurement and selection tool integration

• Development of an Open Source Autonomous Imaging Station for Distribution in High Schools, Universities, and Emerging DIY Scientific Communities.

• Co-lab OpenPlant - interdisciplinary workshops of science art and design

• Synthetic Biology for Schools: A multidisciplinary approach

• Genetic resources in the age of the Nagoya Protocol and gene/genome synthesis

July 2015 (projects 22-37)

• Channeling targeted DNA double strand breaks into alternative repair pathways

• Engineering Marchantia polymorpha chloroplasts for the production of high-value specialized terpenes

• Open Pi-Image: A low cost-open source plant growth imaging and analysis platform

• Open Labware for plant electrophysiology

• Documentation Tool for Open Plant Technologies

• Whiskeroscope: rodent whisker inspired sensor for use in analysis of plant tissue structure

• The use of synthetic biology tools to define the roles of LysM receptor-like kinases in legumes and cereals

• Developing novel selection markers for plant transformation to advance live-imaging techniques

• Quick analytical system for plastid genome modifications

• Wireless, portable, low cost, open source hardware for monitoring plant electrophysiology

• Strengthening synthetic biology capacity in Kenya through bioinformatics training

• Setting up an open synthetic biology lab in Abuja, Nigeria

• The Big Algal open Experiment

• Facilitating synthetic biology literature mining and searching for the plant community

• Responsible innovation and open innovation with large bioresources: goals, challenges and proposals

• Development of new codon optimization tools and development of a synthetic gene expression system in the green alga Chlamydomonas reinhardtii

SynBio IRC Biomaker Challenge Projects

November 2015 (projects 10-21)

• SynBio Student Society

• SynBioHub: Patent information system for synthetic biology

• Synthesis of novel optimised lux reporters for eukaryotic systems

• CamOptimus: Self-contained user-friendly multi-parameter optimisation platform for non-specialist experimental biologists

• Reliable IP-free system for inter-chassis transfer of the high molecular weight DNA

• A piezoelectric bio-platform to image and stimulate cellular interactions

• Interactive web-based software tool for biological circuit design (Extension plan)

• Development of a microfluidic device for high-throughput analysis of genetic circuits in plant protoplasts

• Bio-Hackathon

• Low cost solution for high throughput bacterial electrotransformation

• CELLUWIN: 3D printing for cellulose

• Organotypic cultures as tools for functional screening of drugs to promote oligodendrocyte differentiation and CNS myelination

March 2015 (projects 1-9)

• Engineering of self­ cloning brewer’s yeast for novel terpene profiles in beer

• Open source 3D-printed microscope

• Interactive web­ based software for genetic circuit design

• Novel bioluminescent reporters

• DIY Biolab

• Flexible, low cost, live­ cell imaging platform

• Faster engineering of cyanobacteria

• Finding new recombinases

• The Green Mother Machine: A microfluidics device for cyanobacteria