scholarly journals Testing theoretical minimal genomes using whole-cell models

2020 ◽  
Author(s):  
Joshua Rees-Garbutt ◽  
Jake Rightmyer ◽  
Oliver Chalkley ◽  
Lucia Marucci ◽  
Claire Grierson
Keyword(s):  
In Silico ◽  
Cell Model ◽  
Mycoplasma Genitalium ◽  
Essential Genes ◽  
Cellular Division ◽  
Whole Cell ◽  
Gene Sets ◽  
Dividing Cells ◽  
Species Specific

AbstractThe minimal gene set for life has often been theorised, with at least ten produced for Mycoplasma genitalium (M. genitalium). Due to the difficulty of using M. genitalium in the lab, combined with its long replication time of 12 - 15 hours, none of these theoretical minimal genomes have been tested, even with modern techniques. The publication of the M. genitalium whole-cell model provided the first opportunity to test them, simulating the genome edits in-silico. We simulated eight minimal gene sets from the literature, finding that they produced in-silico cells that did not divide. Using knowledge from previous research, we reintroduced specific essential and low essential genes in-silico; enabling cellular division. This reinforces the need to identify species-specific low essential genes and their interactions. Any genome designs created using the currently incomplete and fragmented gene essentiality information, will very likely require in-vivo reintroductions to correct issues and produce dividing cells.

scholarly journals Designing Minimal Genomes Using Whole-Cell Models

2018 ◽  
Author(s):  
Joshua Rees ◽  
Oliver Chalkley ◽  
Sophie Landon ◽  
Oliver Purcell ◽  
Lucia Marucci ◽  
...  
Keyword(s):  
In Silico ◽  
Genome Engineering ◽  
Cell Model ◽  
Mycoplasma Genitalium ◽  
Computational Design ◽  
Functional Assay ◽  
Proof Of Concept ◽  
Computational Tools ◽  
Whole Cell ◽  
Genome Design

AbstractIn the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept. Minimal genomes are ideal for this purpose as they have a simple functional assay, the cell either replicates or not. We used the first (and currently only published) whole-cell model, for the bacterium Mycoplasma genitalium. Our computational design-simulate-test cycles discovered novel in-silico minimal genomes smaller than JCVI-Syn3.0, a bacteria with, currently, the smallest genome that can be grown in pure culture. In the process, we identified 10 low essentiality genes, 18 high essentiality genes, and produced evidence for at least two Mycoplasma genitalium in-silico minimal genomes. This work brings combined computational and laboratory genome engineering a step closer.

scholarly journals In vivo and in silico determination of essential genes of Campylobacter jejuni

BMC Genomics ◽  
2011 ◽  
Vol 12 (1) ◽  
Author(s):  
Aline Metris ◽  
Mark Reuter ◽  
Duncan JH Gaskin ◽  
Jozsef Baranyi ◽  
Arnoud HM van Vliet
Keyword(s):  
Campylobacter Jejuni ◽  
In Silico ◽  
Essential Genes

scholarly journals Whole yeast model: what and why

2018 ◽  
Author(s):  
Pasquale Palumbo ◽  
Marco Vanoni ◽  
Federico Papa ◽  
Stefano Busti ◽  
Lilia Alberghina
Keyword(s):  
Life Science ◽  
Cell Model ◽  
Model Organism ◽  
Science Research ◽  
Cellular Functions ◽  
Cellular Division ◽  
Whole Cell ◽  
Proposed Model ◽  
Cell Modeling ◽  
Single Input

One of the most challenging fields in Life Science research is to deeply understand how complex cellular functions arise from the interactions of molecules in living cells. Mathematical and computational methods in Systems Biology are fundamental to study the complex molecular interactions within biological systems and to accelerate discoveries. Within this framework, a need exists to integrate different mathematical tools in order to develop quantitative models of entire organisms, i.e. whole-cell models. This note presents a first attempt to show the feasibility of such a task for the budding yeast Saccharomyces cerevisiae, a model organism for eukaryotic cells: the proposed model refers to the main cellular activities like metabolism, growth and cycle in a modular fashion, therefore allowing to treat them separately as single input/output modules, as well as to interconnect them in order to build the backbone of a coarse-grain whole cell model. The model modularity allows to substitute a low granularity module with one with a finer grain, whenever molecular details are required to correctly reproduce specific experiments. Furthermore, by properly setting the cellular division, simulations of cell populations are achieved, able to deal with protein distributions. Whole cell modeling will help understanding logic of cell resilience.

scholarly journals Whole yeast model: what and why

2018 ◽  
Author(s):  
Pasquale Palumbo ◽  
Marco Vanoni ◽  
Federico Papa ◽  
Stefano Busti ◽  
Lilia Alberghina
Keyword(s):  
Life Science ◽  
Cell Model ◽  
Model Organism ◽  
Science Research ◽  
Cellular Functions ◽  
Cellular Division ◽  
Whole Cell ◽  
Proposed Model ◽  
Cell Modeling ◽  
Single Input

One of the most challenging fields in Life Science research is to deeply understand how complex cellular functions arise from the interactions of molecules in living cells. Mathematical and computational methods in Systems Biology are fundamental to study the complex molecular interactions within biological systems and to accelerate discoveries. Within this framework, a need exists to integrate different mathematical tools in order to develop quantitative models of entire organisms, i.e. whole-cell models. This note presents a first attempt to show the feasibility of such a task for the budding yeast Saccharomyces cerevisiae, a model organism for eukaryotic cells: the proposed model refers to the main cellular activities like metabolism, growth and cycle in a modular fashion, therefore allowing to treat them separately as single input/output modules, as well as to interconnect them in order to build the backbone of a coarse-grain whole cell model. The model modularity allows to substitute a low granularity module with one with a finer grain, whenever molecular details are required to correctly reproduce specific experiments. Furthermore, by properly setting the cellular division, simulations of cell populations are achieved, able to deal with protein distributions. Whole cell modeling will help understanding logic of cell resilience.

scholarly journals MCM2 and Carbonic Anhydrase 9 Are Novel Potential Targets for Neuroblastoma Pharmacological Treatment

Biomedicines ◽  
2020 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Patrizia Garbati ◽  
Raffaella Barbieri ◽  
Davide Cangelosi ◽  
Carlo Zanon ◽  
Delfina Costa ◽  
...  
Keyword(s):  
Cell Differentiation ◽  
Carbonic Anhydrase ◽  
Tumor Growth ◽  
Cell Model ◽  
Tumor Growth Rate ◽  
In Vivo Models ◽  
Gene Sets ◽  
Carbonic Anhydrase 9

To overcome the lack of effective pharmacological treatments for high-risk neuroblastoma (HR-NB), the development of novel in vitro and in vivo models that better recapitulate the disease is required. Here, we used an in vitro multiclonal cell model encompassing NB cell differentiation stages, to identify potential novel pharmacological targets. This model allowed us to identify, by low-density RT-PCR arrays, two gene sets, one over-expressed during NB cell differentiation, and the other up-regulated in more malignant cells. Challenging two HR-NB gene expression datasets, we found that these two gene sets are related to high and low survival, respectively. Using mouse NB cisplatin-treated xenografts, we identified two genes within the list associated to the malignant stage (MCM2 and carbonic anhydrase 9), whose expression is positively correlated with tumor growth. Thus, we tested their pharmacological targeting as potential therapeutic strategy. We measured mice survival and tumor growth rate after xenografts of human NB treated with cisplatin in the presence of MCM2/carbonic anhydrase 9 inhibitors (ciprofloxacin and acetazolamide). MCM2 or carbonic anhydrase 9 inhibition significantly increased cisplatin activity, supporting their possible testing for NB therapy.

scholarly journals Toward a Whole Cell Model of Mycoplasma Genitalium

2011 ◽  
Vol 100 (3) ◽  
pp. 32a ◽  
Author(s):  
Jonathan R. Karr ◽  
Jayodita C. Sanghvi ◽  
Jared M. Jacobs ◽  
Markus W. Covert
Keyword(s):  
Cell Model ◽  
Mycoplasma Genitalium ◽  
Whole Cell

scholarly journals A Whole Cell Model of Mycoplasma Genitalium Elucidates Mechanisms of Bacterial Replication

2012 ◽  
Vol 102 (3) ◽  
pp. 731a ◽  
Author(s):  
Jonathan R. Karr ◽  
Jayodita C. Sanghvi ◽  
Jared M. Jacobs ◽  
Derek N. Macklin ◽  
Markus W. Covert
Keyword(s):  
Cell Model ◽  
Mycoplasma Genitalium ◽  
Whole Cell ◽  
Bacterial Replication

scholarly journals ISOLATION OF EPIDERMAL CELL PAIRS FROM AN INSECT, TENEBRIO MOLITOR, FOR DUAL WHOLE-CELL RECORDING OF LARGE-CONDUCTANCE GAP-JUNCTIONAL CHANNELS

1993 ◽  
Vol 178 (1) ◽  
pp. 261-267
Author(s):  
D. Churchill ◽  
S. Caveney
Keyword(s):  
Cell Model ◽  
Cell Voltage ◽  
Epidermal Cells ◽  
Moult Cycle ◽  
Whole Cell ◽  
Cell Recording ◽  
Insect Integument ◽  
Gap Junctional

The segmented insect integument, composed of an epidermal monolayer and its cuticular secretion, is a paradigm for the study of pattern formation during development (Lawrence, 1992). Epidermal activity during development may be coordinated by the transfer of cytoplasmic molecules through cell-cell gap-junctional channels (reviewed in Caveney, 1985). Gap junctions within intact epidermal segments exhibit dynamic changes in their permeability properties during the moult cycle in vivo (Caveney, 1978) and with exposure to the developmental hormone 20-hydroxyecdysone in vitro (Caveney and Blennerhassett, 1980). In addition, the row of epidermal cells at segment borders has distinct permeability properties creating developmental and communication compartments (Warner and Lawrence, 1982; Blennerhassett and Caveney, 1984). This paper documents a method for isolating epidermal cells that are suitable for dual whole-cell voltage-clamp studies of gap-junctional currents. We have identified a large-conductance gap-junctional channel in cell pairs with octanol- reduced junctional currents. This cell model may be useful for examining mechanisms of gap- junctional channel gating during development.

Endogenous hydrogen sulfide sulfhydrates IKKβ at cysteine 179 to control pulmonary artery endothelial cell inflammation

2019 ◽  
Vol 133 (20) ◽  
pp. 2045-2059 ◽  
Author(s):  
Da Zhang ◽  
Xiuli Wang ◽  
Siyao Chen ◽  
Selena Chen ◽  
Wen Yu ◽  
...  
Keyword(s):  
Hydrogen Sulfide ◽  
Endothelial Cell ◽  
Pulmonary Artery ◽  
Cell Model ◽  
Site Directed Mutagenesis ◽  
Critical Event ◽  
Hypertensive Rats ◽  
Pulmonary Artery Endothelial Cell

Abstract Background: Pulmonary artery endothelial cell (PAEC) inflammation is a critical event in the development of pulmonary arterial hypertension (PAH). However, the pathogenesis of PAEC inflammation remains unclear. Methods: Purified recombinant human inhibitor of κB kinase subunit β (IKKβ) protein, human PAECs and monocrotaline-induced pulmonary hypertensive rats were employed in the study. Site-directed mutagenesis, gene knockdown or overexpression were conducted to manipulate the expression or activity of a target protein. Results: We showed that hydrogen sulfide (H2S) inhibited IKKβ activation in the cell model of human PAEC inflammation induced by monocrotaline pyrrole-stimulation or knockdown of cystathionine γ-lyase (CSE), an H2S generating enzyme. Mechanistically, H2S was proved to inhibit IKKβ activity directly via sulfhydrating IKKβ at cysteinyl residue 179 (C179) in purified recombinant IKKβ protein in vitro, whereas thiol reductant dithiothreitol (DTT) reversed H2S-induced IKKβ inactivation. Furthermore, to demonstrate the significance of IKKβ sulfhydration by H2S in the development of PAEC inflammation, we mutated C179 to serine (C179S) in IKKβ. In purified IKKβ protein, C179S mutation of IKKβ abolished H2S-induced IKKβ sulfhydration and the subsequent IKKβ inactivation. In human PAECs, C179S mutation of IKKβ blocked H2S-inhibited IKKβ activation and PAEC inflammatory response. In pulmonary hypertensive rats, C179S mutation of IKKβ abolished the inhibitory effect of H2S on IKKβ activation and pulmonary vascular inflammation and remodeling. Conclusion: Collectively, our in vivo and in vitro findings demonstrated, for the first time, that endogenous H2S directly inactivated IKKβ via sulfhydrating IKKβ at Cys179 to inhibit nuclear factor-κB (NF-κB) pathway activation and thereby control PAEC inflammation in PAH.

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