scholarly journals Computational Analysis of Dynamic Light Exposure of Unicellular Algal Cells in a Flat-Panel Photobioreactor to Support Light-Induced CO2 Bioprocess Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Nicolò S. Vasile ◽  
Alessandro Cordara ◽  
Giulia Usai ◽  
Angela Re
Keyword(s):  
Light Transmission ◽  
Light Exposure ◽  
Model Organism ◽  
Cell Factory ◽  
Bioprocess Development ◽  
Cultivation Conditions ◽  
Flat Panel ◽  
Modeling Framework ◽  
Cell Factories ◽  
Cell Trajectories

Cyanobacterial cell factories trace a vibrant pathway to climate change neutrality and sustainable development owing to their ability to turn carbon dioxide-rich waste into a broad portfolio of renewable compounds, which are deemed valuable in green chemistry cross-sectorial applications. Cell factory design requires to define the optimal operational and cultivation conditions. The paramount parameter in biomass cultivation in photobioreactors is the light intensity since it impacts cellular physiology and productivity. Our modeling framework provides a basis for the predictive control of light-limited, light-saturated, and light-inhibited growth of the Synechocystis sp. PCC 6803 model organism in a flat-panel photobioreactor. The model here presented couples computational fluid dynamics, light transmission, kinetic modeling, and the reconstruction of single cell trajectories in differently irradiated areas of the photobioreactor to relate key physiological parameters to the multi-faceted processes occurring in the cultivation environment. Furthermore, our analysis highlights the need for properly constraining the model with decisive qualitative and quantitative data related to light calibration and light measurements both at the inlet and outlet of the photobioreactor in order to boost the accuracy and extrapolation capabilities of the model.

scholarly journals Nanocellulose-based mechanically stable immobilization matrix for enhanced ethylene production: A framework for photosynthetic solid-state cell factories

2021 ◽  
Author(s):  
Ville Rissanen ◽  
Sindhujaa Vajravel ◽  
Sergey Kosourov ◽  
Suvi Arola ◽  
Eero Kontturi ◽  
...  
Keyword(s):  
Solid State ◽  
Ethylene Production ◽  
Cell Immobilization ◽  
Cell Factory ◽  
Cell Factories ◽  
Solid State Cell ◽  
Immobilization Matrix

Cell immobilization is a promising approach to create efficient photosynthetic cell factories for sustainable chemicals production. Here, we demonstrate a novel photosynthetic solid-state cell factory design for sustainable biocatalytic ethylene...

scholarly journals A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Hongzhong Lu ◽  
Feiran Li ◽  
Benjamín J. Sánchez ◽  
Zhengming Zhu ◽  
Gang Li ◽  
...  
Keyword(s):  
Model Organism ◽  
Metabolic Model ◽  
Phenotypic Traits ◽  
Cell Factory ◽  
Scale Level ◽  
Single Nucleotide ◽  
Multi Scale ◽  
Yeast Strains ◽  
Single Nucleotide Variations ◽  
Genome Scale

Abstract Genome-scale metabolic models (GEMs) represent extensive knowledgebases that provide a platform for model simulations and integrative analysis of omics data. This study introduces Yeast8 and an associated ecosystem of models that represent a comprehensive computational resource for performing simulations of the metabolism of Saccharomyces cerevisiae––an important model organism and widely used cell-factory. Yeast8 tracks community development with version control, setting a standard for how GEMs can be continuously updated in a simple and reproducible way. We use Yeast8 to develop the derived models panYeast8 and coreYeast8, which in turn enable the reconstruction of GEMs for 1,011 different yeast strains. Through integration with enzyme constraints (ecYeast8) and protein 3D structures (proYeast8DB), Yeast8 further facilitates the exploration of yeast metabolism at a multi-scale level, enabling prediction of how single nucleotide variations translate to phenotypic traits.

scholarly journals Intelligent microbial cell factory with genetic pH shooting (GPS) for cell self-responsive base/acid regulation

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Chenyi Li ◽  
Xiaopeng Gao ◽  
Xiao Peng ◽  
Jinlin Li ◽  
Wenxin Bai ◽  
...  
Keyword(s):  
Ph Regulation ◽  
Self Regulation ◽  
Scale Up ◽  
Microbial Cell ◽  
Production Costs ◽  
Cell Factory ◽  
Ph Sensing ◽  
Genetic Circuits ◽  
Microbial Cell Factory ◽  
Cell Factories

Abstract Background In industrial fermentation, pH fluctuation resulted from microbial metabolism influences the strain performance and the final production. The common way to control pH is adding acid or alkali after probe detection, which is not a fine-tuned method and often leads to increased costs and complex downstream processing. Here, we constructed an intelligent pH-sensing and controlling genetic circuits called “Genetic pH Shooting (GPS)” to realize microbial self-regulation of pH. Results In order to achieve the self-regulation of pH, GPS circuits consisting of pH-sensing promoters and acid-/alkali-producing genes were designed and constructed. Designed pH-sensing promoters in the GPS can respond to high or low pHs and generate acidic or alkaline substances, achieving endogenously self-responsive pH adjustments. Base shooting circuit (BSC) and acid shooting circuit (ASC) were constructed and enabled better cell growth under alkaline or acidic conditions, respectively. Furthermore, the genetic circuits including GPS, BSC and ASC were applied to lycopene production with a higher yield without an artificial pH regulation compared with the control under pH values ranging from 5.0 to 9.0. In scale-up fermentations, the lycopene titer in the engineered strain harboring GPS was increased by 137.3% and ammonia usage decreased by 35.6%. Conclusions The pH self-regulation achieved through the GPS circuits is helpful to construct intelligent microbial cell factories and reduce the production costs, which would be much useful in industrial applications.

scholarly journals Enhancement of Astaxanthin Biosynthesis in Oleaginous Yeast Yarrowia lipolytica via Microalgal Pathway

2019 ◽  
Vol 7 (10) ◽  
pp. 472 ◽  
Author(s):  
Larissa Ribeiro Ramos Tramontin ◽  
Kanchana Rueksomtawin Kildegaard ◽  
Suresh Sudarsan ◽  
Irina Borodina
Keyword(s):  
Yarrowia Lipolytica ◽  
Oleaginous Yeast ◽  
Small Scale ◽  
Cell Factory ◽  
Standard Equipment ◽  
Cell Factories ◽  
Dry Cell Weight ◽  
Astaxanthin Production ◽  
Yeast Yarrowia Lipolytica ◽  
Β Carotene

Astaxanthin is a high-value red pigment and antioxidant used by pharmaceutical, cosmetics, and food industries. The astaxanthin produced chemically is costly and is not approved for human consumption due to the presence of by-products. The astaxanthin production by natural microalgae requires large open areas and specialized equipment, the process takes a long time, and results in low titers. Recombinant microbial cell factories can be engineered to produce astaxanthin by fermentation in standard equipment. In this work, an oleaginous yeast Yarrowia lipolytica was engineered to produce astaxanthin at high titers in submerged fermentation. First, a platform strain was created with an optimised pathway towards β-carotene. The platform strain produced 331 ± 66 mg/L of β-carotene in small-scale cultivation, with the cellular content of 2.25% of dry cell weight. Next, the genes encoding β-ketolase and β-hydroxylase of bacterial (Paracoccus sp. and Pantoea ananatis) and algal (Haematococcus pluvialis) origins were introduced into the platform strain in different copy numbers. The resulting strains were screened for astaxanthin production, and the best strain, containing algal β-ketolase and β-hydroxylase, resulted in astaxanthin titer of 44 ± 1 mg/L. The same strain was cultivated in controlled bioreactors, and a titer of 285 ± 19 mg/L of astaxanthin was obtained after seven days of fermentation on complex medium with glucose. Our study shows the potential of Y. lipolytica as the cell factory for astaxanthin production.

scholarly journals Quantitative Imaging and In Situ Concentration Measurements of Quantum Dot Nanomaterials in Variably Saturated Porous Media

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Burcu Uyuşur ◽  
Preston T. Snee ◽  
Chunyan Li ◽  
Christophe J. G. Darnault
Keyword(s):  
Porous Media ◽  
Quantum Dot ◽  
Light Transmission ◽  
Water Saturation ◽  
Uv Light ◽  
Light Exposure ◽  
Fluorescence Method ◽  
Fluorescent Light ◽  
Subsurface Environment

Knowledge of the fate and transport of nanoparticles in the subsurface environment is limited, as techniques to monitor and visualize the transport and distribution of nanoparticles in porous media and measure their in situ concentrations are lacking. To address these issues, we have developed a light transmission and fluorescence method to visualize and measure in situ concentrations of quantum dot (QD) nanoparticles in variably saturated environments. Calibration cells filled with sand as porous medium and various known water saturation levels and QD concentrations were prepared. By measuring the intensity of the light transmitted through porous media exposed to fluorescent light and by measuring the hue of the light emitted by the QDs under UV light exposure, we obtained simultaneously in situ measurements of water saturation and QD nanoparticle concentrations with high spatial and temporal resolutions. Water saturation was directly proportional to the light intensity. A linear relationship was observed between hue-intensity ratio values and QD concentrations for constant water saturation levels. The advantages and limitations of the light transmission and fluorescence method as well as its implications for visualizing and measuring in situ concentrations of QDs nanoparticles in the subsurface environment are discussed.

scholarly journals Leveraging budding yeast Saccharomyces cerevisiae for discovering aging modulation substances for functional food

2019 ◽  
Vol 9 (5) ◽  
pp. 297
Author(s):  
Shaoyu Wang
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Bioactive Compounds ◽  
Functional Food ◽  
Budding Yeast ◽  
Model Organism ◽  
Cellular Systems ◽  
Cell Factory ◽  
Compression Of Morbidity ◽  
Bioactive Substances ◽  
Yeast Saccharomyces Cerevisiae

Background: Discovery of bioactive substances contained in functional food and the mechanism of their aging modulation are imperative steps in developing better, potent and safer functional food for promoting health and compression of morbidity in the aging population.  Budding yeast (Saccharomyces cerevisiae) is invaluable model organism for aging modulation and bioactive compounds discovery. In this paper we have conceptualised a framework for achieving such aim. This framework consists of four components: discovering targets for aging modulation, discovering and validating caloric restriction mimetics, acting as cellular systems for screening natural products or compounds for aging modulation and being a biological factory for producing bioactive compounds according to the roles the yeast systems play. It have been argued that the component of being a biological factory for producing bioactive compounds has much underexplored which also present an opportunity for new active substance discovery and validation for health promotion in functional food industry.Keywords: Aging modulation, budding yeast, functional food, bioactive substances, cell factory

scholarly journals How Do Operational and Design Parameters Effect Biomass Productivity in a Flat-Panel Photo-Bioreactor? A Computational Analysis

Processes ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 1387
Author(s):  
Varun Loomba ◽  
Eric von Lieres ◽  
Gregor Huber
Keyword(s):  
Light Intensity ◽  
Light Exposure ◽  
Incident Light ◽  
Algal Growth ◽  
Biomass Productivity ◽  
Design Parameters ◽  
Operational Parameters ◽  
Incident Light Intensity ◽  
Flat Panel ◽  
Air Inlet

Optimal production of microalgae in photo-bioreactors (PBRs) largely depends on the amount of light intensity received by individual algal cells, which is affected by several operational and design factors. A key question is: which process parameters have the highest potential for the optimization of biomass productivity? This can be analyzed by simulating the complex interplay of PBR design, hydrodynamics, dynamic light exposure, and growth of algal cells. A workflow was established comprising the simulation of hydrodynamics in a flat-panel PBR using computational fluid dynamics, calculation of light irradiation inside the PBR, tracing the light exposure of individual cells over time, and calculation the algal growth and biomass productivity based on this light exposure. Different PBR designs leading to different flow profiles were compared, and operational parameters such as air inlet flowrate, microalgal concentration, and incident light intensity were varied to investigate their effect on PBR productivity. The design of internal structures and lighting had a significant effect on biomass productivity, whereas air inlet flowrate had a minimal effect. Microalgal concentration and incident light intensity controlled the amount of light intensity inside the PBR, thereby significantly affecting the overall productivity. For detailed quantitative insight into these dependencies, better parameterization of algal growth models is required.

scholarly journals The dark side of artificial light

2020 ◽  
Vol 42 (5) ◽  
pp. 32-35
Author(s):  
Jun Yang ◽  
David A Hendrix ◽  
Jadwiga M Giebultowicz
Keyword(s):  
Blue Light ◽  
Light Exposure ◽  
Model Organism ◽  
Dark Side ◽  
Constant Darkness ◽  
Artificial Light ◽  
Light Emitting ◽  
Adverse Health Effects ◽  
Ambient Lighting

Light is necessary for life, but increasing exposure to artificial light may be detrimental to human health. With prevalent use of light-emitting diodes (LEDs) in ambient lighting and electronic devices, humans are increasingly exposed to blue light that appears white due to addition of other colours. Excessive blue light can damage eyes, but it is not known whether daily LED exposure across lifespan may have other adverse health effects. A recent study in short-lived model organism Drosophila melanogaster revealed that cumulative, long-term exposure to blue light impacts brain function, accelerates the aging process and significantly shortens lifespan compared to flies maintained in constant darkness or in white light with blue wavelengths blocked. Increased mortality and brain neurodegeneration was also observed in flies with genetically ablated eyes, demonstrating damage to non-retinal cells. As molecular responses to light are similar in the cells of both fruit flies and humans, these studies suggest that lifelong daily blue light exposure may impair cellular health in humans.

scholarly journals Modular, synthetic chromosomes as new tools for large scale engineering of metabolism

2021 ◽  
Author(s):  
Eline Postma ◽  
Else-Jasmijn Hassing ◽  
Venda Mangkusaputra ◽  
Jordi Geelhoed ◽  
Pilar de la Torre ◽  
...  
Keyword(s):  
Copy Number ◽  
Large Scale ◽  
Metabolic Networks ◽  
De Novo ◽  
Microbial Cell ◽  
Cell Factory ◽  
Microbial Cell Factory ◽  
Microbial Cell Factories ◽  
Cell Factories

The construction of powerful cell factories requires intensive genetic engineering for the addition of new functionalities and the remodeling of native pathways and processes. The present study demonstrates the feasibility of extensive genome reprogramming using modular, specialized de novo-assembled neochromosomes in yeast. The in vivo assembly of linear and circular neochromosomes, carrying 20 native and 21 heterologous genes, enabled the first de novo production in a microbial cell factory of anthocyanins, plant compounds with a broad range pharmacological properties. Turned into exclusive expression platforms for heterologous and essential metabolic routes, the neochromosomes mimic native chromosomes regarding mitotic and genetic stability, copy number, harmlessness for the host and editability by CRISPR/Cas9. This study paves the way for future microbial cell factories with modular genomes in which core metabolic networks, localized on satellite, specialized neochromosomes can be swapped for alternative configurations and serve as landing pads for the addition of functionalities.

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