Pseudomonas: Model Organism, Pathogen, Cell Factory. Edited by Bernd H. A. Rehm. Weinheim (Germany): Wiley‐VCH . $270.00. xxi + 402 p.; ill.; index. 978‐3‐527‐31914‐5. 2008.

2009 ◽  
Vol 84 (2) ◽  
pp. 204-205
Author(s):  
Soeren Molin
Keyword(s):  
Model Organism ◽  
Cell Factory

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 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 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 Aspergillus nidulans: A Potential Resource of the Production of the Native and Heterologous Enzymes for Industrial Applications

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Amit Kumar
Keyword(s):  
Aspergillus Nidulans ◽  
Low Cost ◽  
Model Organism ◽  
Alcohol Oxidase ◽  
Industrial Applications ◽  
Genetically Engineered ◽  
Cell Factory ◽  
Industrial Enzymes ◽  
Fungal Cell ◽  
Potential Resource

Aspergillus nidulans is a filamentous fungus that is a potential resource for industrial enzymes. It is a versatile fungal cell factory that can synthesize various industrial enzymes such as cellulases, β-glucosidases, hemicellulases, laccases, lipases, proteases, β-galactosidases, tannases, keratinase, cutinases, and aryl alcohol oxidase. A. nidulans has shown the potential to utilize low-cost substrates such as wheat bran, rice straw, sugarcane bagasse, rice bran, coir pith, black gram residue, and chicken feathers to produce enzymes cost-effectively. A. nidulans has also been known as a model organism for the production of heterologous enzymes. Several studies reported genetically engineered strains of A. nidulans for the production of different enzymes. Native as well as heterologous enzymes of A. nidulans have been employed for various industrial processes.

scholarly journals Genome sequencing of the neotype strain CBS 554.65 reveals the MAT1-2 locus of Aspergillus niger

2021 ◽  
Author(s):  
Valeria Ellena ◽  
Sjoerd J. Seekles ◽  
Arthur F.J. Ram ◽  
Matthias G. Steiger
Keyword(s):  
Aspergillus Niger ◽  
Genome Sequence ◽  
Model Organism ◽  
Nuclear Genome ◽  
Fungal Species ◽  
Cell Factory ◽  
Dna Assembly ◽  
High Quality ◽  
Genetic Organization ◽  
Wide Range

Abstract Background Aspergillus niger is a ubiquitous filamentous fungus widely employed as a cell factory thanks to its abilities to produce a wide range of organic acids and enzymes. Due to its economic importance and its role as model organism to study fungal fermentation, its genome was one of the first Aspergillus genomes to be sequenced in 2007. Nowadays, the genome sequences of at least five other A. niger strains are available. These, however, do not include the neotype strain CBS 554.65. Results In this study, the genome of CBS 554.65 was sequenced with PacBio. A high-quality nuclear genome sequence consisting of 17 contigs with a N50 value of 4.07 Mbp was obtained. The sequencing covered all the 8 centromeric regions of the chromosomes. In addition, a complete circular mitochondrial DNA assembly was obtained. In silico analyses revealed the presence of a MAT1-2-1 gene in this genome, contrary to the so far sequenced A. niger strains, which all contain a MAT1-1-1 gene. An alignment at the MAT locus showed a different position of the MAT1-1-1 gene of ATCC 1015 compared to the MAT1-2-1 gene of CBS 554.65, relative to the surrounding genes. In addition, 24 other sequenced isolates of A. niger showed a 1:1 ratio of MAT1-1 and MAT1-2 loci. While the genetic organization of the MAT1-2 locus of CBS 554.65 is similar to what is found in other aspergilli, the genetic organization of the MAT1-1 locus is flipped in all sequenced strains. Conclusions This study, besides providing a high-quality genome sequence of an important A. niger strain, suggests the occurrence of genetic flipping or switching events at the MAT1-1 locus of A. niger. These results provide new insights in the mating system of A. niger and could contribute to the investigation and potential discovery of sexuality of this so far asexual fungal species.

scholarly journals The FNR-type regulator GoxR of the obligatory aerobic acetic acid bacterium Gluconobacter oxydans affects expression of genes involved in respiration and redox metabolism

2021 ◽  
Author(s):  
Stefanie Schweikert ◽  
Angela Kranz ◽  
Toshiharu Yakushi ◽  
Andrei Filipchyk ◽  
Tino Polen ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Oxygen Sensor ◽  
Target Genes ◽  
Model Organism ◽  
Gluconobacter Oxydans ◽  
Acetic Acid Bacterium ◽  
Cell Factory ◽  
Dependent Manner ◽  
Expression Of Genes

Gene expression in the obligately aerobic acetic acid bacterium Gluconobacter oxydans responds to oxygen limitation, but the regulators involved are unknown. In this study, we analyzed a transcriptional regulator named GoxR (GOX0974), which is the only member of the FNR family in this species. Evidence was obtained that GoxR contains an iron-sulfur cluster, suggesting that GoxR functions as an oxygen sensor similar to FNR. The direct target genes of GoxR were determined by combining several approaches including a transcriptome comparison of a ΔgoxR mutant with the wild type and detection of in vivo GoxR binding sites by ChAP-Seq. Prominent targets were the cioAB genes encoding a cytochrome bd oxidase with low O2 affinity, which were repressed by GoxR, and the pnt operon, which was activated by GoxR. The pnt operon encodes a transhydrogenase (pntA1A2B), an NADH-dependent oxidoreductase (GOX0313), and another oxidoreductase (GOX0314). Evidence was obtained for GoxR being active despite a high dissolved oxygen concentration in the medium. We suggest a model in which the very high respiration rates of G. oxydans due to the periplasmic oxidations cause an oxygen-limited cytoplasm and insufficient reoxidation of NAD(P)H in the respiratory chain, leading to an inhibited cytoplasmic carbohydrate degradation. GoxR-triggered induction of the pnt operon enhances fast interconversion of NADPH and NADH by the transhydrogenase and NADH reoxidation by the GOX0313 oxidoreductase via reduction of acetaldehyde formed by pyruvate decarboxylase to ethanol. In fact, small amounts of ethanol were formed by G. oxydans under oxygen-restricted conditions in a GoxR-dependent manner. IMPORTANCE Gluconobacter oxydans serves as cell factory for oxidative biotransformations based on membrane-bound dehydrogenases and as model organism for elucidating the metabolism of acetic acid bacteria. Surprisingly, to our knowledge none of the more than 100 transcriptional regulators encoded in the genome of G. oxydans has been studied experimentally up to now. In this work, we analyzed the function of a regulator named GoxR, which belongs to the FNR family. Members of this family serve as oxygen sensors by means of an oxygen-sensitive [4Fe-4S] cluster and typically regulate genes important for growth under anoxic conditions by anaerobic respiration or fermentation. Because G. oxydans has an obligatory aerobic respiratory mode of energy metabolism, it was tempting to elucidate the target genes regulated by GoxR. Our results show that GoxR affects the expression of genes that support the interconversion of NADPH and NADH and NADH reoxidation by reduction of acetaldehyde to ethanol.

scholarly journals Big data in yeast systems biology

2019 ◽  
Vol 19 (7) ◽  
Author(s):  
Rosemary Yu ◽  
Jens Nielsen
Keyword(s):  
Gene Expression ◽  
Big Data ◽  
Systems Biology ◽  
Model Organism ◽  
Cell Factory ◽  
Yeast Saccharomyces Cerevisiae ◽  
Complex Interactions ◽  
Biological Insight ◽  
Big Data Technologies ◽  
Gene Expression Dynamics

ABSTRACT Systems biology uses computational and mathematical modeling to study complex interactions in a biological system. The yeast Saccharomyces cerevisiae, which has served as both an important model organism and cell factory, has pioneered both the early development of such models and modeling concepts, and the more recent integration of multi-omics big data in these models to elucidate fundamental principles of biology. Here, we review the advancement of big data technologies to gain biological insight in three aspects of yeast systems biology: gene expression dynamics, cellular metabolism and the regulation network between gene expression and metabolism. The role of big data and complementary modeling approaches, including the expansion of genome-scale metabolic models and machine learning methodologies, are discussed as key drivers in the rapid advancement of yeast systems biology.

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