An open-source automated PEG precipitation assay to measure the relative solubility of proteins with low material requirement

AbstractThe solubility of proteins correlates with a variety of their properties, including function, production yield, pharmacokinetics, and formulation at high concentrations. High solubility is therefore a key requirement for the development of protein-based reagents for applications in life sciences, biotechnology, diagnostics, and therapeutics. Accurate solubility measurements, however, remain challenging and resource intensive, which limits their throughput and hence their applicability at the early stages of development pipelines, when long-lists of candidates are typically available in minute amounts. Here, we present an automated method based on the titration of a crowding agent (polyethylene glycol, PEG) to quantitatively assess relative solubility of proteins using about 200 µg of purified material. Our results demonstrate that this method is accurate and economical in material requirement and costs of reagents, which makes it suitable for high-throughput screening. This approach is freely-shared and based on a low cost, open-source liquid-handling robot. We anticipate that this method will facilitate the assessment of the developability of proteins and make it substantially more accessible.

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PlasmoTron: an open-source platform for automated culture of malaria parasites

10.1101/241596 ◽

2017 ◽

Cited By ~ 1

Author(s):

Theo Sanderson ◽

Julian C. Rayner

Keyword(s):

Open Source ◽

Genetic Modification ◽

Malaria Parasite ◽

Scale Up ◽

Malaria Parasites ◽

Parasite Culture ◽

Liquid Handling ◽

Liquid Handling Robot

We have created a system which allows an inexpensive opensource liquid-handling robot to automate most aspects of bloodstage malaria parasite culture. Parasites are cultured in multiwell microplates, with their details recorded in a database. Information in the database is used to generate commands for the robot to feed, monitor and passage parasite cultures. We show that the system is capable of raising cultures after transfection and then maintaining them at desired parasitaemias, facilitiating significant scale up of both routine culture and experimental genetic modification. The PlasmoTron software is available at plasmotron.org.

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Adapting a Low-Cost and Open-Source Commercial Pipetting Robot for Nanoliter Liquid Handling

SLAS TECHNOLOGY Translating Life Sciences Innovation ◽

10.1177/2472630320973591 ◽

2020 ◽

pp. 247263032097359

Author(s):

E. Enoch A. W. Councill ◽

Nathanial B. Axtell ◽

Thy Truong ◽

Yiran Liang ◽

Adam L. Aposhian ◽

...

Keyword(s):

Open Source ◽

Scientific Community ◽

Low Cost ◽

Mass Spectrometry Analysis ◽

Liquid Chromatography Mass Spectrometry ◽

Processing Efficiency ◽

Spectrometry Analysis ◽

Liquid Handling ◽

Fluorescence Measurements ◽

Volume Measurements

Low-volume liquid handling capabilities in bioanalytical workflows can dramatically improve sample processing efficiency and reduce reagent costs, yet many commercial nanoliter liquid handlers cost tens of thousands of dollars or more. We have successfully adapted a low-cost and open-source commercial pipetting robot, the Opentrons OT-1, to accurately aspirate and dispense nanoliter volumes. Based on fluorescence measurements, the modified OT-1 was able to reproducibly transfer 50 nL of water with less than 3% measurement error and 5% coefficient of variation (CV). For 15 nL transfers, the volume measurements indicated less than 4% error and 4% CV. We applied this platform to the preparation of low-nanogram proteomic samples for liquid chromatography–mass spectrometry analysis, demonstrating that the modified OT-1 is an effective platform for nanoliter liquid handling. At a total materials cost of less than $6000, including the commercial liquid handler and all modifications, this system is also far less expensive than other platforms with similar capabilities, placing automated nanoliter handling within reach of a far broader scientific community.

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New Capabilities of EvoBot: A Modular, Open-Source Liquid-Handling Robot

SLAS TECHNOLOGY Translating Life Sciences Innovation ◽

10.1177/2472630316689285 ◽

2017 ◽

Vol 22 (5) ◽

pp. 500-506 ◽

Cited By ~ 5

Author(s):

Farzad Nejatimoharrami ◽

Andres Faina ◽

Kasper Stoy

Keyword(s):

Open Source ◽

Open Source Software ◽

Low Cost ◽

Integrated Analysis ◽

Experiment Data ◽

Time Interaction ◽

Modeling Software ◽

Offline Processing ◽

Liquid Handling Robot

We introduce a robot developed to perform feedback-based experiments, such as droplet experiments, a common type of experiments in artificial chemical life research. These experiments are particularly well suited for automation because they often stretch over long periods of time, possibly hours, and often require that the human takes action in response to observed events such as changes in droplet size, count, shape, or clustering or declustering of multiple droplets. Our robot is designed to monitor long-term experiments and, based on the feedback from the experiment, interact with it. The combination of precise automation, accurately collected experiment data, and integrated analysis and modeling software makes real-time interaction with the experiment feasible, as opposed to traditional offline processing of experiments. Last but not least, we believe the low cost of our platform can promote artificial life research. Furthermore, prevalently, findings from an experiment will inspire redesign for novel experiments. In addition, the robot’s open-source software enables easy modification of experiments. We will cover two case studies for application of our robot in feedback-based experiments and demonstrate how our robot can not only automate these experiments, collect data, and interact with the experiments intelligently but also enable chemists to perform formerly infeasible experiments.

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Open-source personal pipetting robots with live-cell incubation and microscopy compatibility

10.1101/2021.07.04.448641 ◽

2021 ◽

Author(s):

Philip Dettinger ◽

Tobias Kull ◽

Geethika Arekatla ◽

Nouraiz Ahmed ◽

Yang Zhang ◽

...

Keyword(s):

Open Source ◽

Time Lapse ◽

Small Scale ◽

Liquid Handling ◽

Academic Settings ◽

Stem And Progenitor Cells ◽

Cell Incubation ◽

Self Production ◽

Liquid Handling Robot ◽

Laboratory Member

Liquid handling robots have the potential to automate many procedures in life sciences. However, they are not in widespread use in academic settings, where funding, space and maintenance specialists are usually limiting. In addition, current robots require lengthy programming by specialists and are incompatible with most academic laboratories with constantly changing small-scale projects. Here, we present the Pipetting Helper Imaging Lid (PHIL), an inexpensive, small, open-source personal liquid handling robot. It is designed for inexperienced users, with self-production from cheap commercial and 3D-printable components and custom control software. PHIL successfully automated pipetting for e.g. tissue immunostainings and stimulations of live stem and progenitor cells during time-lapse microscopy. PHIL is cheap enough for any laboratory member to have their own personal pipetting robot(s), and enables users without programming skills to easily automate a large range of experiments.

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EvoBot: An Open-Source, Modular, Liquid Handling Robot for Scientific Experiments

Applied Sciences ◽

10.3390/app10030814 ◽

2020 ◽

Vol 10 (3) ◽

pp. 814 ◽

Cited By ~ 3

Author(s):

Andres Faiña ◽

Brian Nejati ◽

Kasper Stoy

Keyword(s):

Fuel Cells ◽

Open Source ◽

Microbial Fuel Cells ◽

Modular Design ◽

Detailed Knowledge ◽

Entire System ◽

Liquid Handling ◽

Scientific Experiments ◽

Biochemical Research ◽

Liquid Handling Robot

Commercial liquid handling robots are rarely appropriate when tasks change often, which is the case in the early stages of biochemical research. In order to address it, we have developed EvoBot, a liquid handling robot, which is open-source and employs a modular design. The combination of an open-source and a modular design is particularly powerful because functionality is divided into modules with simple, well-defined interfaces, hence customisation of modules is possible without detailed knowledge of the entire system. Furthermore, the modular design allows end-users to only produce and assemble the modules that are relevant for their specific application. Hence, time and money are not wasted on functionality that is not needed. Finally, modules can easily be reused. In this paper, we describe the EvoBot modular design and through scientific experiments such as basic liquid handling, nurturing of microbial fuel cells, and droplet chemotaxis experiments document how functionality is increased one module at a time with a significant amount of reuse. In addition to providing wet-labs with an extendible, open-source liquid handling robot, we also think that modularity is a key concept that is likely to be useful in other robots developed for scientific purposes.

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An open-source semi-automated robotics pipeline for embryo immunohistochemistry

Scientific Reports ◽

10.1038/s41598-021-89676-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Timothy Fuqua ◽

Jeff Jordan ◽

Aliaksandr Halavatyi ◽

Christian Tischer ◽

Kerstin Richter ◽

...

Keyword(s):

Open Source ◽

Large Scale ◽

Expression Patterns ◽

Future Research ◽

Developmental Systems ◽

Liquid Handling ◽

Antibody Staining ◽

Automated Pipeline ◽

Precise Expression ◽

Liquid Handling Robot

AbstractA significant challenge for developmental systems biology is balancing throughput with controlled conditions that minimize experimental artifacts. Large-scale developmental screens such as unbiased mutagenesis surveys have been limited in their applicability to embryonic systems, as the technologies for quantifying precise expression patterns in whole animals has not kept pace with other sequencing-based technologies. Here, we outline an open-source semi-automated pipeline to chemically fixate, stain, and 3D-image Drosophila embryos. Central to this pipeline is a liquid handling robot, Flyspresso, which automates the steps of classical embryo fixation and staining. We provide the schematics and an overview of the technology for an engineer or someone equivalently trained to reproduce and further improve upon Flyspresso, and highlight the Drosophila embryo fixation and colorimetric or antibody staining protocols. Additionally, we provide a detailed overview and stepwise protocol for our adaptive-feedback pipeline for automated embryo imaging on confocal microscopes. We demonstrate the efficiency of this pipeline compared to classical techniques, and how it can be repurposed or scaled to other protocols and biological systems. We hope our pipeline will serve as a platform for future research, allowing a broader community of users to build, execute, and share similar experiments.

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EvoBot: An Open-Source, Modular Liquid Handling Robot for Nurturing Microbial Fuel Cells

Proceedings of the Artificial Life Conference 2016 ◽

10.7551/978-0-262-33936-0-ch099 ◽

2016 ◽

Cited By ~ 1

Author(s):

Andrs Faa ◽

Farzad Nejatimoharrami ◽

Kasper Stoy ◽

Pavlina Theodosiou ◽

Benjamin Taylor ◽

...

Keyword(s):

Fuel Cells ◽

Open Source ◽

Microbial Fuel Cells ◽

Liquid Handling ◽

Liquid Handling Robot

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Evaluation of two automated low-cost RNA extraction protocols for SARS-CoV-2 detection

PLoS ONE ◽

10.1371/journal.pone.0246302 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0246302

Author(s):

Fernando Lázaro-Perona ◽

Carlos Rodriguez-Antolín ◽

Marina Alguacil-Guillén ◽

Almudena Gutiérrez-Arroyo ◽

Jesús Mingorance ◽

...

Keyword(s):

Magnetic Beads ◽

Low Cost ◽

Rna Extraction ◽

Positive Control ◽

Acid Extraction ◽

Nucleic Acid Extraction ◽

Handling System ◽

Liquid Handling ◽

Liquid Handling Robot ◽

Commercial Kit

Background Two automatable in-house protocols for high-troughput RNA extraction from nasopharyngeal swabs for SARS-CoV-2 detection have been evaluated. Methods One hundred forty one SARS-CoV-2 positive samples were collected during a period of 10-days. In-house protocols were based on extraction with magnetic beads and designed to be used with either the Opentrons OT-2 (OT-2in-house) liquid handling robot or the MagMAXTM Express-96 system (MMin-house). Both protocols were tested in parallel with a commercial kit that uses the MagMAXTM system (MMkit). Nucleic acid extraction efficiencies were calculated from a SARS-CoV-2 DNA positive control. Results No significant differences were found between both in-house protocols and the commercial kit in their performance to detect positive samples. The MMkit was the most efficient although the MMin-house presented, in average, lower Cts than the other two. In-house protocols allowed to save between 350€ and 400€ for every 96 extracted samples compared to the commercial kit. Conclusion The protocols described harness the use of easily available reagents and an open-source liquid handling system and are suitable for SARS-CoV-2 detection in high throughput facilities.

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Computer simulation study about the dependence of amorphous silicon photonic waveguides efficiency on the material quality

The European Physical Journal Applied Physics ◽

10.1051/epjap/2020190250 ◽

2020 ◽

Vol 90 (3) ◽

pp. 30502

Author(s):

Alessandro Fantoni ◽

João Costa ◽

Paulo Lourenço ◽

Manuela Vieira

Keyword(s):

Amorphous Silicon ◽

High Throughput Screening ◽

Simulation Analysis ◽

Low Cost ◽

Deposition Process ◽

Large Area ◽

Sidewall Roughness ◽

Sensing Applications ◽

Fabrication Defects ◽

The Impact

Amorphous silicon PECVD photonic integrated devices are promising candidates for low cost sensing applications. This manuscript reports a simulation analysis about the impact on the overall efficiency caused by the lithography imperfections in the deposition process. The tolerance to the fabrication defects of a photonic sensor based on surface plasmonic resonance is analysed. The simulations are performed with FDTD and BPM algorithms. The device is a plasmonic interferometer composed by an a-Si:H waveguide covered by a thin gold layer. The sensing analysis is performed by equally splitting the input light into two arms, allowing the sensor to be calibrated by its reference arm. Two different 1 × 2 power splitter configurations are presented: a directional coupler and a multimode interference splitter. The waveguide sidewall roughness is considered as the major negative effect caused by deposition imperfections. The simulation results show that plasmonic effects can be excited in the interferometric waveguide structure, allowing a sensing device with enough sensitivity to support the functioning of a bio sensor for high throughput screening. In addition, the good tolerance to the waveguide wall roughness, points out the PECVD deposition technique as reliable method for the overall sensor system to be produced in a low-cost system. The large area deposition of photonics structures, allowed by the PECVD method, can be explored to design a multiplexed system for analysis of multiple biomarkers to further increase the tolerance to fabrication defects.

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