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Article ; Online: Designing a Model-Driven Approach Towards Rational Experimental Design in Bioprocess Optimization.

Yeoh, Jing Wui / Poh, Chueh Loo

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2553, Page(s) 173–187

Abstract: To enable a more rational optimization approach to drive the transition from lab-scale to large industrial bioprocesses, a systematic framework coupling both experimental design and integrated modeling was established to guide the workflow executed from ... ...

Abstract	To enable a more rational optimization approach to drive the transition from lab-scale to large industrial bioprocesses, a systematic framework coupling both experimental design and integrated modeling was established to guide the workflow executed from small flask scale to bioreactor scale. The integrated model relies on the coupling of biotic cell factory kinetics to the abiotic bioreactor hydrodynamics to offer a rational means for an in-depth understanding of two-way spatiotemporal interactions between cell behaviors and environmental variations. This model could serve as a promising tool to inform experimental work with reduced efforts via full-factorial in silico predictions. This chapter thus describes the general workflow involved in designing and applying this modeling approach to drive the experimental design towards rational bioprocess optimization.
MeSH term(s)	Bioreactors ; Hydrodynamics ; Research Design
Language	English
Publishing date	2022-09-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2617-7_9
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Editorial.

Kitney, Richard I / Poh, Chueh Loo

Engineering biology

2021 Volume 5, Issue 1, Page(s) 1

Language	English
Publishing date	2021-03-25
Publishing country	United States
Document type	Editorial
ISSN	2398-6182
ISSN (online)	2398-6182
DOI	10.1049/enb2.12006
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Article: Toward Multiplexed Optogenetic Circuits.

Dwijayanti, Ari / Zhang, Congqiang / Poh, Chueh Loo / Lautier, Thomas

Frontiers in bioengineering and biotechnology

2022 Volume 9, Page(s) 804563

Abstract: Owing to its ubiquity and easy availability in nature, light has been widely employed to control complex cellular behaviors. Light-sensitive proteins are the foundation to such diverse and multilevel adaptive regulations in a large range of organisms. ... ...

Abstract	Owing to its ubiquity and easy availability in nature, light has been widely employed to control complex cellular behaviors. Light-sensitive proteins are the foundation to such diverse and multilevel adaptive regulations in a large range of organisms. Due to their remarkable properties and potential applications in engineered systems, exploration and engineering of natural light-sensitive proteins have significantly contributed to expand optogenetic toolboxes with tailor-made performances in synthetic genetic circuits. Progressively, more complex systems have been designed in which multiple photoreceptors, each sensing its dedicated wavelength, are combined to simultaneously coordinate cellular responses in a single cell. In this review, we highlight recent works and challenges on multiplexed optogenetic circuits in natural and engineered systems for a dynamic regulation breakthrough in biotechnological applications.
Language	English
Publishing date	2022-01-05
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2021.804563
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Article ; Online: A biological camera that captures and stores images directly into DNA.

Lim, Cheng Kai / Yeoh, Jing Wui / Kunartama, Aurelius Andrew / Yew, Wen Shan / Poh, Chueh Loo

Nature communications

2023 Volume 14, Issue 1, Page(s) 3921

Abstract: The increasing integration between biological and digital interfaces has led to heightened interest in utilizing biological materials to store digital data, with the most promising one involving the storage of data within defined sequences of DNA that ... ...

Abstract	The increasing integration between biological and digital interfaces has led to heightened interest in utilizing biological materials to store digital data, with the most promising one involving the storage of data within defined sequences of DNA that are created by de novo DNA synthesis. However, there is a lack of methods that can obviate the need for de novo DNA synthesis, which tends to be costly and inefficient. Here, in this work, we detail a method of capturing 2-dimensional light patterns into DNA, by utilizing optogenetic circuits to record light exposure into DNA, encoding spatial locations with barcoding, and retrieving stored images via high-throughput next-generation sequencing. We demonstrate the encoding of multiple images into DNA, totaling 1152 bits, selective image retrieval, as well as robustness to drying, heat and UV. We also demonstrate successful multiplexing using multiple wavelengths of light, capturing 2 different images simultaneously using red and blue light. This work thus establishes a 'living digital camera', paving the way towards integrating biological systems with digital devices.
MeSH term(s)	DNA/genetics ; DNA Replication ; Light ; High-Throughput Nucleotide Sequencing
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-07-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-38876-w
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Book ; Online: Two Cellular Resource Based Models Linking Growth and Parts Characteristics Aids the Study and Optimization of Synthetic Gene Circuits

Wang, Huijuan / Ling, Maurice HT / Chua, Tze Kwang / Poh, Chueh Loo

2023

Abstract: A major challenge in synthetic genetic circuit development is the inter-dependency between heterologous gene expressions by circuits and host's growth rate. Increasing heterologous gene expression increases burden to the host, resulting in host growth ... ...

Abstract	A major challenge in synthetic genetic circuit development is the inter-dependency between heterologous gene expressions by circuits and host's growth rate. Increasing heterologous gene expression increases burden to the host, resulting in host growth reduction; which reduces overall heterologous protein abundance. Hence, it is difficult to design predictable genetic circuits. Here, we develop two biophysical models; one for promoter, another for RBS; to correlate heterologous gene expression and growth reduction. We model cellular resource allocation in E. coli to describe the burden, as growth reduction, caused by genetic circuits. To facilitate their uses in genetic circuit design, inputs to the model are common characteristics of biological parts [e.g. relative promoter strength (RPU) and relative ribosome binding sites strength (RRU)]. The models suggest that E. coli's growth rate reduces linearly with increasing RPU / RRU of the genetic circuits; thus, providing 2 handy models taking parts characteristics as input to estimate growth rate reduction for fine tuning genetic circuit design in silico prior to construction. Our promoter model correlates well with experiments using various genetic circuits, both single and double expression cassettes, up to a relative promoter unit of 3.7 with a 60% growth rate reduction (average R2 ~ 0.9).
Keywords	Quantitative Biology - Molecular Networks ; Mathematics - Numerical Analysis ; Quantitative Biology - Quantitative Methods
Subject code	612
Publishing date	2023-02-19
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Designing and Assembling Plasmids for the Construction of Escherichia coli Biosensor for Vibrio cholerae Detection.

Holowko, Maciej B / Poh, Chueh Loo

Methods in molecular biology (Clifton, N.J.)

2018 Volume 1772, Page(s) 445–456

Abstract: In the process of constructing and characterizing the whole cell biosensor for Vibrio cholerae detection, two main techniques have been employed-DNA assembly using the Gibson isothermal assembly reaction was used for the assembly of the PCRed plasmid ... ...

Abstract	In the process of constructing and characterizing the whole cell biosensor for Vibrio cholerae detection, two main techniques have been employed-DNA assembly using the Gibson isothermal assembly reaction was used for the assembly of the PCRed plasmid fragments (DNA parts), and microplate fluorescence readings were used for bacterial strain characterization. The general workflow can be summed up as: the in silico designed DNA fragments were assembled by isothermal assembly to be later transformed into Escherichia coli that, in turn, was characterized using the microplate reader. As fine-tuning of the sensor design was required, the process was repeated iteratively until the final strain was created with desired characteristics. This chapter describes in detail this workflow for different constructs which finally led to the creation of the first whole cell biosensor in E. coli for V. cholerae detection.
MeSH term(s)	Biosensing Techniques/methods ; DNA/genetics ; Escherichia coli/genetics ; Plasmids/genetics ; Vibrio cholerae/genetics
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2018-05-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7795-6_26
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Article ; Online: Regulating exopolysaccharide gene wcaF allows control of Escherichia coli biofilm formation.

Zhang, Jingyun / Poh, Chueh Loo

Scientific reports

2018 Volume 8, Issue 1, Page(s) 13127

Abstract: While biofilms are known to cause problems in many areas of human health and the industry, biofilms are important in a number of engineering applications including wastewater management, bioremediation, and bioproduction of valuable chemicals. However, ... ...

Abstract	While biofilms are known to cause problems in many areas of human health and the industry, biofilms are important in a number of engineering applications including wastewater management, bioremediation, and bioproduction of valuable chemicals. However, excessive biofilm growth remains a key challenge in the use of biofilms in these applications. As certain amount of biofilm growth is required for efficient use of biofilms, the ability to control and maintain biofilms at desired thickness is vital. To this end, we developed synthetic gene circuits to control E. coli MG1655 biofilm formation by using CRISPRi/dCas9 to regulate a gene (wcaF) involved in the synthesis of colanic acid (CA), a key polysaccharide in E. coli biofilm extracellular polymeric substance (EPS). We showed that the biofilm formation was inhibited when wcaF was repressed and the biofilms could be maintained at a different thickness over a period of time. We also demonstrated that it is also possible to control the biofilm thickness spatially by inhibiting wcaF gene using a genetic light switch. The results demonstrate that the approach has great potential as a new means to control and maintain biofilm thickness in biofilm related applications.
MeSH term(s)	Acyltransferases/genetics ; Acyltransferases/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Biofilms/growth & development ; CRISPR-Associated Protein 9/genetics ; CRISPR-Associated Protein 9/metabolism ; CRISPR-Cas Systems ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Gene Editing/methods ; Gene Expression Regulation, Bacterial ; Genetic Engineering/methods ; Plasmids/chemistry ; Plasmids/metabolism ; Polysaccharides/biosynthesis ; Polysaccharides/genetics ; Polysaccharides, Bacterial/biosynthesis ; Polysaccharides, Bacterial/genetics ; RNA, Guide, CRISPR-Cas Systems
Chemical Substances	Bacterial Proteins ; Polysaccharides ; Polysaccharides, Bacterial ; colanic acid (9012-87-7) ; Acyltransferases (EC 2.3.-) ; CRISPR-Associated Protein 9 (EC 3.1.-)
Language	English
Publishing date	2018-09-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-31161-7
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Article: Thermogenetics: Applications come of age

Chee, Wai Kit David / Yeoh, Jing Wui / Dao, Viet Linh / Poh, Chueh Loo

Biotechnology advances. 2022 Mar., Apr., v. 55

2022

Abstract: Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to ... ...

Abstract	Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications. In all, the review aims to convey both the exhilarating recent technological developments underlying the advancement of thermosensors and the exciting opportunities the nascent thermogenetic field holds for biomedical and biotechnology applications.
Keywords	biosafety ; biotechnology ; synthetic biology ; temperature
Language	English
Dates of publication	2022-03
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	47165-3
ISSN	0734-9750
ISSN	0734-9750
DOI	10.1016/j.biotechadv.2022.107907
Database	NAL-Catalogue (AGRICOLA)

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Zs.A 3730: Show issues

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Article ; Online: Blue Light-Directed Cell Migration, Aggregation, and Patterning.

Zhang, Jingyun / Luo, Yuhuan / Poh, Chueh Loo

Journal of molecular biology

2020 Volume 432, Issue 10, Page(s) 3137–3148

Abstract: Bacterial motility is related to many cellular activities, such as cell migration, aggregation, and biofilm formations. The ability to control motility and direct the bacteria to certain location could be used to guide the bacteria in applications such ... ...

Abstract	Bacterial motility is related to many cellular activities, such as cell migration, aggregation, and biofilm formations. The ability to control motility and direct the bacteria to certain location could be used to guide the bacteria in applications such as seeking for and killing pathogen, forming various population-level patterns, and delivering of drugs and vaccines. Currently, bacteria motility is mainly controlled by chemotaxis (prescribed chemical stimuli), which needs physical contact with the chemical inducer. This lacks the flexibility for pattern formation as it has limited spatial control. To overcome the limitations, we developed blue light-regulated synthetic genetic circuit to control bacterial directional motility, by taking the advantage that light stimulus can be delivered to cells in different patterns with precise spatial control. The circuit developed enables programmed Escherichia coli cells to increase directional motility and move away from the blue light, i.e., that negative phototaxis is utilized. This further allows the control of the cells to form aggregation with different patterns. Further, we showed that the circuit can be used to separate two different strains. The demonstrated ability of blue light-controllable gene circuits to regulate a CheZ expression could give researchers more means to control bacterial motility and pattern formation.
MeSH term(s)	Bacterial Physiological Phenomena/drug effects ; Chemotaxis/drug effects ; Escherichia coli/physiology ; Gene Expression Regulation, Bacterial/drug effects ; Light/adverse effects ; Methyl-Accepting Chemotaxis Proteins/genetics ; Promoter Regions, Genetic ; Synthetic Biology
Chemical Substances	Methyl-Accepting Chemotaxis Proteins ; cheZ protein, E coli
Language	English
Publishing date	2020-04-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2020.03.029
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Zs.A 867: Show issues

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Article ; Online: Novel Modalities in DNA Data Storage.

Lim, Cheng Kai / Nirantar, Saurabh / Yew, Wen Shan / Poh, Chueh Loo

Trends in biotechnology

2021 Volume 39, Issue 10, Page(s) 990–1003

Abstract: The field of storing information in DNA has expanded exponentially. Most common modalities involve encoding information from bits into synthesized nucleotides, storage in liquid or dry media, and decoding via sequencing. However, limitations to this ... ...

Abstract	The field of storing information in DNA has expanded exponentially. Most common modalities involve encoding information from bits into synthesized nucleotides, storage in liquid or dry media, and decoding via sequencing. However, limitations to this paradigm include the cost of DNA synthesis and sequencing, along with low throughput. Further unresolved questions include the appropriate media of storage and the scalability of such approaches for commercial viability. In this review, we examine various storage modalities involving the use of DNA from a systems-level perspective. We compare novel methods that draw inspiration from molecular biology techniques that have been devised to overcome the difficulties posed by standard workflows and conceptualize potential applications that can arise from these advances.
MeSH term(s)	DNA/genetics ; High-Throughput Nucleotide Sequencing ; Information Storage and Retrieval ; Sequence Analysis, DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2021-01-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	47474-5
ISSN	1879-3096 ; 0167-7799
ISSN (online)	1879-3096
ISSN	0167-7799
DOI	10.1016/j.tibtech.2020.12.008
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Zs.A 2750: Show issues

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