scholarly journals Establishing a Cell-Free Transcription–Translation Platform for Cutibacterium acnes to Prototype Engineered Metabolic and Synthetic Biology

2021 ◽  
Author(s):  
María-José Fábrega ◽  
Nastassia Knödlseder ◽  
Guillermo Nevot ◽  
Marta Sanvicente ◽  
Lorena Toloza ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Cutibacterium Acnes ◽  
A Cell

scholarly journals A Microbial Screening in Silico Method for the Fitness Step Evaluation in Evolutionary Algorithms

2020 ◽  
Vol 10 (11) ◽  
pp. 3936
Author(s):  
A. Gargantilla Becerra ◽  
R. Lahoz-Beltra
Keyword(s):  
Synthetic Biology ◽  
In Silico ◽  
Optimization Problems ◽  
Evaluation Function ◽  
Laboratory Methods ◽  
Bacterial Colony ◽  
Fitness Value ◽  
General Rules ◽  
A Cell ◽  
Microbial Screening

One of the most delicate stages of an evolutionary algorithm is the evaluation of the goodness of the solutions by some procedure providing a fitness value. However, although there are general rules, it is not always easy to find an appropriate evaluation function for a given problem. In the biological realm, today, there is a variety of experimental methods under the name of microbial screening to identify and select bacteria from their traits, as well as to obtain their fitness. In this paper, we show how given an optimization problem, a colony of synthetic bacteria or bacterial agents is able to evaluate the fitness of candidate solutions by building an evaluation function. The evaluation function is obtained simulating, in silico, a bacterial colony conducting the laboratory methods used in microbiology, biotechnology and synthetic biology to measure microbial fitness. Once the evaluation function is built, it is included in the code of the genetic algorithm as part of the fitness routine. The practical use of this approach is illustrated in two classic optimization problems. In silico routines have been programmed in Gro, a cell programming language oriented to synthetic biology, and can easily be customized to many other optimization problems.

scholarly journals A new improved and extended version of the multicell bacterial simulator gro

2016 ◽  
Author(s):  
Martín Gutiérrez ◽  
Paula Gregorio-Godoy ◽  
Guillermo Pérez del Pulgar ◽  
Luis Muñoz ◽  
Sandra Sáez ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Timed Automata ◽  
Cell Communication ◽  
Colony Growth ◽  
Communication Process ◽  
Intercellular Signaling ◽  
Dividing Cells ◽  
A Cell ◽  
Local Cell ◽  
Cell Cell

Abstractgro is a cell programming language developed in Klavins Lab for simulating colony growth and cell-cell communication. It is used as a synthetic biology prototyping tool for simulating multicellular biocircuits. In this work, we present several extensions made to gro that improve the performance of the simulator, make it easier to use and provide new functionalities. The new version of gro is between one and two orders of magnitude faster than the original version. It is able to grow microbial colonies with up to 105 cells in less than 20 minutes. A new library, CellEngine, accelerates the resolution of spatial physical interactions between growing and dividing cells by implementing a new shoving algorithm. A genetic library, CellPro, based on Probabilistic Timed Automata, simulates gene expression dynamics using simplified and easy to compute digital proteins. We also propose a more convenient language specification layer, ProSpec, based on the idea that proteins drive cell behavior. CellNutrient, another library, implements Monod-based growth and nutrient uptake functionalities. The intercellular signaling management was improved and extended in a library called CellSignals. Finally, bacterial conjugation, another local cell-cell communication process, was added to the simulator. To show the versatility and potential outreach of this version of gro, we provide studies and novel examples ranging from synthetic biology to evolutionary microbiology. We believe that the upgrades implemented for gro have made it into a powerful and fast prototyping tool capable of simulating a large variety of systems and synthetic biology designs.

scholarly journals Synthetic biology: How best to build a cell

Nature ◽  
2014 ◽  
Vol 509 (7499) ◽  
pp. 155-157 ◽  
Keyword(s):  
Synthetic Biology ◽  
A Cell

Encapsulation of the cytoskeleton: towards mimicking the mechanics of a cell

Soft Matter ◽  
2019 ◽  
Vol 15 (42) ◽  
pp. 8425-8436 ◽  
Author(s):  
Yashar Bashirzadeh ◽  
Allen P. Liu
Keyword(s):  
Synthetic Biology ◽  
Cell Shape ◽  
Effective Control ◽  
Bottom Up ◽  
A Cell ◽  
Cell Shape Changes ◽  
Shape Changes

The cytoskeleton of a cell controls all the aspects of cell shape changes. Such conserved and effective control over the mechanics of the cell makes the cytoskeletal components great candidates for bottom-up synthetic biology studies.

Cellular responses to proteostasis perturbations reveal non-optimal feedback in chaperone networks

2017 ◽  
Author(s):  
Asmita Ghosh ◽  
Abhilash Gangadharan ◽  
Sarada Das ◽  
Monika Verma ◽  
Latika Matai ◽  
...  
Keyword(s):  
Quality Control ◽  
Protein Folding ◽  
Synthetic Biology ◽  
Cellular Response ◽  
Protein Quality ◽  
Transcriptional Response ◽  
Cellular Responses ◽  
Over Expression ◽  
Single Deletion ◽  
A Cell

AbstractThe proteostasis network (PN) comprises a plethora of proteins that are dedicated to aid in protein folding; some with over-lapping functions. Despite this, there are multiple pathophysiological states associated with depletion of chaperones. This is counter-intuitive assuming cells have the ability to re-program transcriptional outputs in accordance with its proteostasic limitations. To this effect, we have used S. cerevisiae to understand the route a cell takes as a response when challenged with different proteostasis impairments. Using 14 single deletion strains of genes of Protein Quality Control (PQC) system, we quantify their proteostasis impairment and the transcriptional response. In most cases cellular response was incapable of restoring proteostasis. The response did not activate proteostasis components or pathways that could complement the function of the missing PQC gene. Over-expression of alternate machineries, could restore part of the proteostasis defect in deletion strains. We posit that epistasis guided synthetic biology approaches may be helpful in realizing the true potential of the cellular chaperone machinery.

scholarly journals A curcumin direct protein (DiPro) biosensor for cell-free prototyping

2021 ◽  
Author(s):  
Agata Lesniewska ◽  
Guy Griffin ◽  
Paul K Freemont ◽  
Karen M Polizzi ◽  
Simon J Moore
Keyword(s):  
Synthetic Biology ◽  
Small Molecules ◽  
Detection System ◽  
Reaction Parameters ◽  
Enhanced Fluorescence ◽  
Liquid Handling ◽  
A Cell ◽  
Double Bond Reductase ◽  
Fine Tune ◽  
Synthetic Biology Approach

In synthetic biology, biosensors are routinely coupled to a gene expression cascade for detecting small molecules and physical signals. We posit that an alternative direct protein (DiPro) biosensor mechanism, could provide a new opportunity for rapid detection of specific chemicals. Herein, we reveal a fluorescent curcumin DiPro biosensor, based on the Escherichia coli double bond reductase (EcCurA) as a detection system. We characterise the curcumin DiPro biosensor and propose enhanced fluorescence is generated through π-π stacking between protein and ligand. Using a cell-free synthetic biology approach, we use the DiPro biosensor to fine-tune 10 reaction parameters (cofactor, substrate, and enzyme levels), assisted through acoustic liquid handling robotics. Overall, we increase curcumin DiPro biosensor fluorescence by 80-fold. We propose a generic DiPro biosensor fluorescence mechanism that can be further exploited for a wider range of chemicals that share intrinsic fluorescence and have a suitable binding protein.

Effect of Niacin on Mitochondria of Allium Cepa Root Cells

1967 ◽  
Vol 25 ◽  
pp. 78-79
Author(s):  
M. Arif Hayat
Keyword(s):  
Nicotinamide Adenine Dinucleotide ◽  
Hydrogen Transfer ◽  
Nicotinamide Adenine Dinucleotide Phosphate ◽  
Nicotinamide Adenine ◽  
Root Tips ◽  
Root Cells ◽  
Transfer Processes ◽  
Standard Procedures ◽  
A Cell ◽  
Critical Interest

Although it is recognized that niacin (pyridine-3-carboxylic acid), incorporated as the amide in nicotinamide adenine dinucleotide (NAD) or in nicotinamide adenine dinucleotide phosphate (NADP), is a cofactor in hydrogen transfer in numerous enzyme reactions in all organisms studied, virtually no information is available on the effect of this vitamin on a cell at the submicroscopic level. Since mitochondria act as sites for many hydrogen transfer processes, the possible response of mitochondria to niacin treatment is, therefore, of critical interest.Onion bulbs were placed on vials filled with double distilled water in the dark at 25°C. After two days the bulbs and newly developed root system were transferred to vials containing 0.1% niacin. Root tips were collected at ¼, ½, 1, 2, 4, and 8 hr. intervals after treatment. The tissues were fixed in glutaraldehyde-OsO4 as well as in 2% KMnO4 according to standard procedures. In both cases, the tissues were dehydrated in an acetone series and embedded in Reynolds' lead citrate for 3-10 minutes.

Ultrastructure of melanocyte-keratinocyte interactions and pigment transfer in vitro

1978 ◽  
Vol 36 (2) ◽  
pp. 650-651
Author(s):  
Raul I. Garcia ◽  
Evelyn A. Flynn ◽  
George Szabo
Keyword(s):  
Direct Injection ◽  
Skin Pigmentation ◽  
Freeze Fracture ◽  
Pigment Granule ◽  
Time Lapse ◽  
Ultrastructural Level ◽  
Lanthanum Tracer ◽  
A Cell

Skin pigmentation in mammals involves the interaction of epidermal melanocytes and keratinocytes in the structural and functional unit known as the Epidermal Melanin Unit. Melanocytes(M) synthesize melanin within specialized membrane-bound organelles, the melanosome or pigment granule. These are subsequently transferred by way of M dendrites to keratinocytes(K) by a mechanism still to be clearly defined. Three different, though not necessarily mutually exclusive, mechanisms of melanosome transfer have been proposed: cytophagocytosis by K of M dendrite tips containing melanosomes, direct injection of melanosomes into the K cytoplasm through a cell-to-cell pore or communicating channel formed by localized fusion of M and K cell membranes, release of melanosomes into the extracellular space(ECS) by exocytosis followed by K uptake using conventional phagocytosis. Variability in methods of transfer has been noted both in vivo and in vitro and there is evidence in support of each transfer mechanism. We Have previously studied M-K interactions in vitro using time-lapse cinemicrography and in vivo at the ultrastructural level using lanthanum tracer and freeze-fracture.

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