0 Introduction

1 Designing the Bioreactor

2 Overview of single components

3 Assembly instructions

0 Introduction

Producing reliable cultivation data can be fairly difficult, time consuming and pricey.
We decided to adress this problem by creating OPEN PBR, a modular cultivation setup for photosynthetic organisms with up to 9 separate cultivation vessels.
While gathering knowledge with our efforts in Human Practices, we quickly recognized the need for a platform that enables the user to vary many parameters during cultivation of microalgae while still being affordable and capable of generating reproducible data.
The OPEN PBR fulfills these demands by providing a modular setup for cultivation of algae in turbido- or chemostat mode. With all components defined an openly available, it remains highly modular while using standardized vessels to provide reproducibility.
By using an existing model of general equations describing a chemostat with light as limiting substrate, we were able to pin down necessary functions and devices for performing them. For easy assembly of the device, files for lasercutting, a list of components and where to order them and an assembly guideline are provided below.

Our Open PBR — Klick on part-labels for more information

1 Modeling and Design

Chemostat equation
Light Gradient
OD Measurement
???

Chemostat Equation

This chapter gives an overview over important parameters for cultivation resulting from the general chemostat equation.

Overview of the hierarchical and modular cloning system

WHAAT?

Fig. 1. Universal MoClo fusion sites.

Figcap

WHAAAT?

Fig. 2. Blablabla.

Figcaption.

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Light Gradient

An important aspect of photosynthetic growth is illumination. Read about the light environment in a cultivation vessel here.

WHAAT?

Fig. 1. Universal MoClo fusion sites.

Figcap

WHAAAT?

Fig. 2. Blablabla.

Figcaption.

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OD Measurement

With the same equation describing the light gradient inside the culture, we can define a relationship to measure cell density and other parameters.

WHAAT?

Fig. 1. Universal MoClo fusion sites.

Figcap

WHAAAT?

Fig. 2. Blablabla.

Figcaption.

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2 Overview of single components

Sensors
Illumination
Gas mixing and pumps
Cultivation vessel
Casing

In this chapter, we give an overview for all functions and components of the system. The aim is to serve as an introduction for assembling the system with the instructions provided in the last chapter.

Container preview

WHAAT?

Fig. 1. Universal MoClo fusion sites.

Figcap

WHAAAT?

Fig. 2. Blablabla.

Figcaption.

Read more Read less

Crozet, P., Navarro, F. J., Willmund, F., Mehrshahi, P., Bakowski, K., Lauersen, K. J., ... Lemaire, S. D. (2018). Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii. ACS Synthetic Biology, 7(9), 2074-2086. Retrieved from https://doi.org/10.1021/acssynbio.8b00251. doi:10.1021/acssynbio.8b00251

Ebrahim, A., Lerman, J. A., Palsson, B. O., & Hyduke, D. R. (2013). COBRApy: COnstraints-Based Reconstruction and Analysis for Python. BMC Systems Biology, 7(1), 74. https://doi.org/10.1186/1752-0509-7-74

Engler, C., Kandzia, R. & Marillonnet, S. (2008). A One Pot, One Step, Precision Cloning Method with High Throughput Capability. PLOS ONE, 3(11), e3647. Retrieved from https://doi.org/10.1371/journal.pone.0003647. doi:10.1371/journal.pone.0003647

Greiner, A., Kelterborn, S., Evers, H., Kreimer, G., Sizova, I. & Hegemann, P. (2017). Targeting of Photoreceptor Genes in Chlamydomonas reinhardtii via Zinc-Finger Nucleases and CRISPR/Cas9. The Plant Cell. 29. tpc.00659.2017. 10.1105/tpc.17.00659.

Imam, S. , Schäuble, S. , Valenzuela, J. , López García de Lomana, A. , Carter, W. , Price, N. D. and Baliga, N. S. (2015), A refined genome‐scale reconstruction of Chlamydomonas metabolism provides a platform for systems‐level analyses. Plant J, 84: 1239-1256. doi:10.1111/tpj.13059

Kelterborn, S., Boehning, F., Evers, H., Sizova, I., Baidukova, O., & Hegemann, P. (2019). Gene editing in green alga Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins. Unpublished work.

Kliphuis, A. M. J., Klok, A. J., Martens, D. E., Lamers, P. P., Janssen, M., & Wijffels, R. H. (2012). Metabolic modeling of Chlamydomonas reinhardtii: Energy requirements for photoautotrophic growth and maintenance. Journal of Applied Phycology, 24(2), 253–266. https://doi.org/10.1007/s10811-011-9674-3

Loera‐Quezada, M. M., Leyva‐González, M. A., Velázquez‐Juárez, G. , Sanchez‐Calderón, L. , Do Nascimento, M. , López‐Arredondo, D. and Herrera‐Estrella, L. (2016), A novel genetic engineering platform for the effective management of biological contaminants for the production of microalgae. Plant Biotechnol J, 14: 2066-2076. doi:10.1111/pbi.12564

Ma, Y., Yao, M., Li, B., Ding, M., He, B., Chen, S., ... & Yuan, Y. (2018). Enhanced poly (ethylene terephthalate) hydrolase activity by protein engineering. Engineering, 4(6), 888-893. Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E., and Church, G. M. “RNA-Guided Human Genome Engineering via Cas9,” Science, vol. 339, pp. 823–826, feb 2013.

Merchant, S. S., Prochnik, S. E., Vallon, O., Harris, E. H., Karpowicz, S. J., Witman, G. B., … Grossman, A. R. (2007). The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (New York, N.Y.), 318(5848), 245–250. doi:10.1126/science.1143609

Patron, N. J., Orzaez, D., Marillonnet, S., Warzecha, H., Matthewman, C., Youles, M., . . . Haseloff, J. (2015). Standards for plant synthetic biology: a common syntax for exchange of DNA parts. New Phytologist, 208(1), 13-19. Retrieved from https://doi.org/10.1111/nph.13532. doi:10.1111/nph.13532

Weber, E., Engler, C., Gruetzner, R., Werner, S., & Marillonnet, S. (2011). A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLOS ONE, 6(2), e16765. Retrieved from https://doi.org/10.1371/journal.pone.0016765. doi:10.1371/journal.pone.0016765

Palm, G. J., Reisky, L., Böttcher, D., Müller, H., Michels, E. A., Walczak, M. C., ... & Weber, G. (2019). Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate. Nature communications, 10(1), 1717.

Strenkert, S., Schmollinger, S., Gallaher, S. D., Salomé, P. A., Purvine, S. O., Nicora, C. D., Mettler-Altmann, T., Soubeyrand, E., Weber, A. P. M., Lipton, M. S., Basset, G. J., Merchant, S. S. Proceedings of the National Academy of Sciences Feb 2019, 116 (6) 2374-2383; DOI:10.1073/pnas.1815238116

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Team:Humboldt Berlin/Hardware

Hardware

0 Introduction

1 Designing the Bioreactor

2 Overview of single components

3 Assembly instructions

0 Introduction

1 Modeling and Design

Chemostat equation

Light Gradient

OD Measurement

???

Chemostat Equation

Light Gradient

OD Measurement

2 Overview of single components

Sensors

Illumination

Gas mixing and pumps

Cultivation vessel

Casing

Sensors

Illumination

Gas mixing and pumps

Cultivation vessel

Casing

Github Project

Tools

PDF Instructions