Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks

2016 ◽  
pp. 117-146 ◽  
Author(s):  
Gaspar Morgado ◽  
Daniel Gerngross ◽  
Tania M. Roberts ◽  
Sven Panke
Keyword(s):  
Synthetic Biology ◽  
Enzyme Reaction ◽  
Reaction Networks

scholarly journals Programmed mechano-chemical coupling in reaction-diffusion active matter

2021 ◽  
Author(s):  
Anis Senoussi ◽  
Jean-Christophe Galas ◽  
André Estevez-Torres
Keyword(s):  
Enzyme Reaction ◽  
Reaction Diffusion ◽  
Reaction Networks ◽  
Active Matter ◽  
C Elegans ◽  
Polarization Mechanism ◽  
Chemical Coupling ◽  
Pattern Forming ◽  
Key Aspects

AbstractEmbryo morphogenesis involves a complex combination of pattern-forming mechanisms. However, classical in vitro patterning experiments explore only one mechanism at a time, thus missing coupling effects. Here, we conjugate two major pattern-forming mechanisms —reaction-diffusion and active matter— by integrating dissipative DNA/enzyme reaction networks within an active gel composed of cytoskeletal motors and filaments. We show that the strength of the flow generated by the active gel controls the mechano-chemical coupling between the two subsystems. We use this property to engineer the mechanical activation of chemical reaction networks both in time and space, thus mimicking key aspects of the polarization mechanism observed in C. elegans oocytes. We anticipate that reaction-diffusion active matter may be useful to investigate mechano-chemical transduction and to design new materials with life-like properties.

Investigation of the effect of loratadine and calcium ions on oxidoreductase activity of catalase enzyme

2020 ◽  
Vol 16 ◽  
Author(s):  
Edhem Hasković ◽  
Safija Herenda ◽  
Zehra Halilović ◽  
Snežana Unčanin ◽  
Denis Hasković ◽  
...  
Keyword(s):  
Calcium Ions ◽  
Enzyme Reaction ◽  
Analytical Techniques ◽  
Competitive Inhibitor ◽  
Cellular Functions ◽  
Oxidoreductase Activity ◽  
H1 Antihistamines ◽  
Activity Of Enzymes ◽  
The Given

Background: The Spectrophotometric method is one of the most suitable analytical techniques for testing the activity of enzymes under the influence of various factors. Methods: The effect of H1-antihistamines of loratadine and calcium ions on enzyme catalase under in vitro conditions was investigated in this paper. Results and Discussion: It has been shown that loratadine isa partial inhibitor of catalase, but this effect is diminished in the presence of calcium ions. Calcium as well as other cations are important for many biological and cellular functions. The kidneys play a central role in the homeostasis of these ions. The activity of the catalase enzyme under the given conditions, the type of inhibition,and the kinetic parameters of the enzyme reaction were determined. Conclusion: We concluded that loratadine is a partially competitive inhibitor.

scholarly journals Nutricosmetic effects of Asparagus officinalis: a potent matrix metalloproteinase-1 inhibitor

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Suwannee Sriyab ◽  
Nachtharinee Laosirisathian ◽  
Chanun Punyoyai ◽  
Songyot Anuchapreeda ◽  
Singkome Tima ◽  
...  
Keyword(s):  
Matrix Metalloproteinase ◽  
Antioxidant Activities ◽  
Epigallocatechin Gallate ◽  
Enzyme Reaction ◽  
Asparagus Officinalis ◽  
Peripheral Blood Mononuclear ◽  
Antioxidant Power ◽  
Matrix Metalloproteinase 1 ◽  
Ferric Reducing Antioxidant Power

AbstractThis study aimed to investigate the nutricosmetic effect of Asparagus officinalis extracts. The tip and spear of A. officinalis were successively extracted with 95% ethanol. The rutin, phenolic, and flavonoid contents of A. officinalis extracts were investigated. The antioxidant activities were determined by 2,2-azinobis (3-ethylbenzothiazoline-6-sulphonic acid) and a ferric reducing antioxidant power assay. Matrix metalloproteinase-1 (MMP-1), elastase, and hyaluronidase inhibition were determined by in vitro enzyme reaction assay. The cytotoxicity was analyzed on peripheral blood mononuclear cellss. Findings revealed that drying temperature and drying duration had significant effects on the chemical composition and biological activity of A. officinalis extract. A. officinalis tips dried at 50 °C for 24 h contained the (significantly) highest flavonoid and rutin content. The most potent extract was from A. officinalis spears since it possessed the (significantly) highest MMP-1, elastase, and hyaluronidase inhibition rates of 83.4 ± 1.5%, 70.4 ± 4.1%, and 75.2 ± 1.0%, respectively. Interestingly, at the same concentration, the A. officinalis spear extract was more potent in MMP-1 inhibition than oleanolic acid and epigallocatechin gallate, the well-known natural MMP-1 inhibitors. The results show that A. officinalis extract is an attractive source of natural anti-skin-wrinkle ingredients.

scholarly journals In Vitro and In Silico Characterization of an Antimalarial Compound with Antitumor Activity Targeting Human DNA Topoisomerase IB

2021 ◽  
Vol 22 (14) ◽  
pp. 7455
Author(s):  
Bini Chhetri Soren ◽  
Jagadish Babu Dasari ◽  
Alessio Ottaviani ◽  
Beatrice Messina ◽  
Giada Andreotti ◽  
...  
Keyword(s):  
Enzyme Reaction ◽  
Dna Topoisomerase ◽  
Human Dna ◽  
Topoisomerase Ib ◽  
Topological State ◽  
Cleavage Step ◽  
Dynamics Simulations ◽  
In Silico Characterization ◽  
Dna Complex

Human DNA topoisomerase IB controls the topological state of supercoiled DNA through a complex catalytic cycle that consists of cleavage and religation reactions, allowing the progression of fundamental DNA metabolism. The catalytic steps of human DNA topoisomerase IB were analyzed in the presence of a drug, obtained by the open-access drug bank Medicines for Malaria Venture. The experiments indicate that the compound strongly and irreversibly inhibits the cleavage step of the enzyme reaction and reduces the cell viability of three different cancer cell lines. Molecular docking and molecular dynamics simulations suggest that the drug binds to the human DNA topoisomerase IB-DNA complex sitting inside the catalytic site of the enzyme, providing a molecular explanation for the cleavage-inhibition effect. For all these reasons, the aforementioned drug could be a possible lead compound for the development of an efficient anti-tumor molecule targeting human DNA topoisomerase IB.

scholarly journals Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems

2019 ◽  
Vol 2 (2) ◽  
pp. 39 ◽  
Author(s):  
Dohyun Jeong ◽  
Melissa Klocke ◽  
Siddharth Agarwal ◽  
Jeongwon Kim ◽  
Seungdo Choi ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Free Expression ◽  
Dna Nanostructures ◽  
Expression Systems ◽  
Natural Systems ◽  
The Past ◽  
Current Cell ◽  
Recent Developments ◽  
Biological Circuits

Synthetic biology integrates diverse engineering disciplines to create novel biological systems for biomedical and technological applications. The substantial growth of the synthetic biology field in the past decade is poised to transform biotechnology and medicine. To streamline design processes and facilitate debugging of complex synthetic circuits, cell-free synthetic biology approaches has reached broad research communities both in academia and industry. By recapitulating gene expression systems in vitro, cell-free expression systems offer flexibility to explore beyond the confines of living cells and allow networking of synthetic and natural systems. Here, we review the capabilities of the current cell-free platforms, focusing on nucleic acid-based molecular programs and circuit construction. We survey the recent developments including cell-free transcription–translation platforms, DNA nanostructures and circuits, and novel classes of riboregulators. The links to mathematical models and the prospects of cell-free synthetic biology platforms will also be discussed.

scholarly journals Synthetic biology projects in vitro

2006 ◽  
Vol 17 (1) ◽  
pp. 1-6 ◽  
Author(s):  
A. C. Forster ◽  
G. M. Church
Keyword(s):  
Synthetic Biology

scholarly journals Strains, Mechanism, and Perspective:Salmonella-Based Cancer Therapy

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Cheng-Zhi Wang ◽  
Robert A. Kazmierczak ◽  
Abraham Eisenstark
Keyword(s):  
Synthetic Biology ◽  
Tumor Targeting ◽  
Tumor Therapy ◽  
The Other ◽  
Cancer Therapies ◽  
Chemotherapeutic Drugs ◽  
Serovar Typhimurium ◽  
Candidate Strain

Recently, investigation of bacterial-based tumor therapy has regained focus due to progress in molecular, cellular, and microbial biology. Many bacteria such asSalmonella,Listeria,Escherichia, andClostridiumhave proved to have tumor targeting and in some cases even tumor-destroying phenotypes. Furthermore, bacterial clinical treatments for cancer have been improved by combination with other therapeutic methods such as chemotherapeutic drugs and radioactive agents. Synthetic biology techniques have also driven the development of new bacterial-based cancer therapies. However, basic questions about the mechanisms of bacterial-mediated tumor targeting and destruction are still being elucidated. In this review, we focus on three tumor-therapeuticSalmonellamodels, the most intensively studied bacterial genus in this field. One of theseSalmonellamodels is ourSalmonella entericaserovar Typhimurium LT2 derived strain CRC2631, engineered to minimize toxicity but maximize tumor-targeting and destruction effects. The other two are VNP20009 and A1-R. We compare the means by which these therapeutic candidate strain models were selected for study, their tumor targeting and tumor destruction phenotypesin vitroandin vivo, and what is currently known about the mechanisms by which they target and destroy tumors.

scholarly journals The effect of disulfiram on the aldehyde dehydrogenases of sheep liver

1975 ◽  
Vol 151 (2) ◽  
pp. 407-412 ◽  
Author(s):  
T M Kitson
Keyword(s):  
Ph Dependence ◽  
Maximum Velocity ◽  
Enzyme Reaction ◽  
Thiol Group ◽  
Inhibitory Effect ◽  
Mitochondrial Enzyme ◽  
Aldehyde Dehydrogenases ◽  
Sheep Liver ◽  
Rate Profile

1. The effect of disulfiram on the activity of the cytoplasmic and mitochondrial aldehyde dehydrogenases of sheep liver was studied. 2. Disulfiram causes an immediate inhibition of the enzyme reaction. The effect on the cytoplasmic enzyme is much greater than on the mitochondrial enzyme. 3. In both cases, the initial partial inhibition is followed by a gradual irreversible loss of activity. 4. The pH-rate profile of the inactivation of the mitochondrial enzyme by disulfiram and the pH-dependence of the maximum velocity of the enzyme-catalysed reaction are both consistent with the involvement of a thiol group. 5. Excess of 2-mercaptoethanol or GSH abolishes the effect of disulfiram. However, equimolar amounts of either of these reagents and disulfiram cause an effect greater than does disulfiram alone. It was shown that the mixed disulphide, Et2N-CS-SS-CH2-CH2OH, strongly inhibits aldehyde dehydrogenase. 6. The inhibitory effect of diethyldithiocarbamate in vitro is due mainly to contamination by disulfiram.

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