Toward low-cost biomanufacturing through in vitro synthetic biology: bottom-up design

2011 ◽  
Vol 21 (47) ◽  
pp. 18877 ◽  
Author(s):  
Y.-H. Percival Zhang ◽  
Suwan Myung ◽  
Chun You ◽  
Zhiguang Zhu ◽  
Joseph A. Rollin
Keyword(s):  
Low Cost ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Shue Wang ◽  
Sagardip Majumder ◽  
Nicholas J Emery ◽  
Allen P Liu

Abstract Transcription and translation are two critical processes during eukaryotic gene expression that regulate cellular activities. The development of mammalian cell-free expression (CFE) systems provides a platform for studying these two critical processes in vitro for bottom-up synthetic biology applications such as construction of an artificial cell. Moreover, real-time monitoring of the dynamics of synthesized mRNA and protein is key to characterize and optimize gene circuits before implementing in living cells or in artificial cells. However, there are few tools for measurement of mRNA and protein dynamics in mammalian CFE systems. Here, we developed a locked nucleic acid (LNA) probe for monitoring transcription in a HeLa-based CFE system in real-time. By using this LNA probe in conjunction with a fluorescent reporter protein, we were able to simultaneously monitor mRNA and protein dynamics in bulk reactions and cell-sized single-emulsion droplets. We found rapid production of mRNA transcripts that decreased over time as protein production ensued in bulk reactions. Our results also showed that transcription in cell-sized droplets has different dynamics compared to the transcription in bulk reactions. The use of this LNA probe in conjunction with fluorescent proteins in HeLa-based mammalian CFE system provides a versatile in vitro platform for studying mRNA dynamics for bottom-up synthetic biology applications.


2018 ◽  
Vol 3 (3) ◽  
pp. 186-195 ◽  
Author(s):  
Ting Shi ◽  
Pingping Han ◽  
Chun You ◽  
Yi-Heng P. Job Zhang
Keyword(s):  

2019 ◽  
Author(s):  
Khalid K. Alam ◽  
Jaeyoung K. Jung ◽  
Matthew S. Verosloff ◽  
Phillip R. Clauer ◽  
Jeong Wook Lee ◽  
...  

ABSTRACTSynthetic biology has enabled the development of powerful nucleic acid diagnostic technologies for detecting pathogens and human health biomarkers. Here we expand the reach of synthetic biology-enabled diagnostics by developing a cell-free biosensing platform that usesRNAoutputsensorsactivated by ligandinduction (ROSALIND) to detect harmful contaminants in aqueous samples. ROSALIND consists of three programmable components: highly-processive RNA polymerases, allosteric transcription factors, and synthetic DNA transcription templates. Together, these components allosterically regulate thein vitrotranscription of a fluorescence-activating RNA aptamer: in the absence of a target compound, transcription is blocked, while in its presence a fluorescent signal is produced. We demonstrate that ROSALIND can be configured to detect a range of water contaminants, including antibiotics, toxic small molecules, and metals. Our cell-free biosensing platform, which can be freeze-dried for field deployment, creates a new capability for point-of-use monitoring of molecular species to address growing global crises in water quality and human health.


Author(s):  
Moema S. Santana ◽  
Rute Lopes ◽  
Isabela H. Peron ◽  
Carla R. Cruz ◽  
Ana M. M. Gaspar ◽  
...  

Background: Hepatitis C virus infection is a significant global health burden, which causes acute or chronic hepatitis. The acute hepatitis C is generally asymptomatic and progresses to cure, while persistent infection can progress to chronic liver disease and extrahepatic manifestations. Standard treatment is expensive, poorly tolerated, and has variable sustained virologic responses amongst the different viral genotypes. New therapies involve direct acting antivirals; however, it is also very expensive and may not be accessible for all patients worldwide. In order to provide a complementary approach to the already existing therapies, natural bioactive compounds are investigated as to their several biologic activities, such as direct antiviral properties against hepatitis C, and effects on mitigating chronic progression of the disease, which includes hepatoprotective, antioxidant, anticarcinogenic and anti-inflammatory activities; additionally, these compounds present advantages, as chemical diversity, low cost of production and milder or inexistent side effects. Objective: To present a broad perspective on hepatitis C infection, the chronic disease, and natural compounds with promising anti-HCV activity. Methods: This review consists of a systematic review study about the natural bioactive compounds as a potential therapy for hepatitis C infection. Results: The quest for natural products have yielded compounds with biologic activity, including viral replication inhibition in vitro, demonstrating antiviral activity against hepatitis C. Conclusion: One of the greatest advantages of using natural molecules from plant extracts is the low cost of production, not requiring chemical synthesis, which can lead to less expensive therapies available to low and middle-income countries.


2021 ◽  
Vol 22 (3) ◽  
pp. 1124
Author(s):  
Mafalda Giovanna Reccia ◽  
Floriana Volpicelli ◽  
Eirkiur Benedikz ◽  
Åsa Fex Svenningsen ◽  
Luca Colucci-D’Amato

Neural stem cells represent a powerful tool to study molecules involved in pathophysiology of Nervous System and to discover new drugs. Although they can be cultured and expanded in vitro as a primary culture, their use is hampered by their heterogeneity and by the cost and time needed for their preparation. Here we report that mes-c-myc A1 cells (A1), a neural cell line, is endowed with staminal properties. Undifferentiated/proliferating and differentiated/non-proliferating A1 cells are able to generate neurospheres (Ns) in which gene expression parallels the original differentiation status. In fact, Ns derived from undifferentiated A1 cells express higher levels of Nestin, Kruppel-like factor 4 (Klf4) and glial fibrillary protein (GFAP), markers of stemness, while those obtained from differentiated A1 cells show higher levels of the neuronal marker beta III tubulin. Interestingly, Ns differentiation, by Epidermal Growth Factors (EGF) and Fibroblast Growth Factor 2 (bFGF) withdrawal, generates oligodendrocytes at high-yield as shown by the expression of markers, Galactosylceramidase (Gal-C) Neuron-Glial antigen 2 (NG2), Receptor-Interacting Protein (RIP) and Myelin Basic Protein (MBP). Finally, upon co-culture, Ns-A1-derived oligodendrocytes cause a redistribution of contactin-associated protein (Caspr/paranodin) protein on neuronal cells, as primary oligodendrocytes cultures, suggesting that they are able to form compact myelin. Thus, Ns-A1-derived oligodendrocytes may represent a time-saving and low-cost tool to study the pathophysiology of oligodendrocytes and to test new drugs.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Evan Amalfitano ◽  
Margot Karlikow ◽  
Masoud Norouzi ◽  
Katariina Jaenes ◽  
Seray Cicek ◽  
...  

AbstractRecent advances in cell-free synthetic biology have given rise to gene circuit-based sensors with the potential to provide decentralized and low-cost molecular diagnostics. However, it remains a challenge to deliver this sensing capacity into the hands of users in a practical manner. Here, we leverage the glucose meter, one of the most widely available point-of-care sensing devices, to serve as a universal reader for these decentralized diagnostics. We describe a molecular translator that can convert the activation of conventional gene circuit-based sensors into a glucose output that can be read by off-the-shelf glucose meters. We show the development of new glucogenic reporter systems, multiplexed reporter outputs and detection of nucleic acid targets down to the low attomolar range. Using this glucose-meter interface, we demonstrate the detection of a small-molecule analyte; sample-to-result diagnostics for typhoid, paratyphoid A/B; and show the potential for pandemic response with nucleic acid sensors for SARS-CoV-2.


Processes ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 915
Author(s):  
Gözde Dursun ◽  
Muhammad Umer ◽  
Bernd Markert ◽  
Marcus Stoffel

(1) Background: Bioreactors mimic the natural environment of cells and tissues by providing a controlled micro-environment. However, their design is often expensive and complex. Herein, we have introduced the development of a low-cost compression bioreactor which enables the application of different mechanical stimulation regimes to in vitro tissue models and provides the information of applied stress and strain in real-time. (2) Methods: The compression bioreactor is designed using a mini-computer called Raspberry Pi, which is programmed to apply compressive deformation at various strains and frequencies, as well as to measure the force applied to the tissue constructs. Besides this, we have developed a mobile application connected to the bioreactor software to monitor, command, and control experiments via mobile devices. (3) Results: Cell viability results indicate that the newly designed compression bioreactor supports cell cultivation in a sterile environment without any contamination. The developed bioreactor software plots the experimental data of dynamic mechanical loading in a long-term manner, as well as stores them for further data processing. Following in vitro uniaxial compression conditioning of 3D in vitro cartilage models, chondrocyte cell migration was altered positively compared to static cultures. (4) Conclusion: The developed compression bioreactor can support the in vitro tissue model cultivation and monitor the experimental information with a low-cost controlling system and via mobile application. The highly customizable mold inside the cultivation chamber is a significant approach to solve the limited customization capability of the traditional bioreactors. Most importantly, the compression bioreactor prevents operator- and system-dependent variability between experiments by enabling a dynamic culture in a large volume for multiple numbers of in vitro tissue constructs.


Biomedicines ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 16
Author(s):  
Borja Sanz ◽  
Ane Albillos Sanchez ◽  
Bonnie Tangey ◽  
Kerry Gilmore ◽  
Zhilian Yue ◽  
...  

Collagen is a major component of the extracellular matrix (ECM) that modulates cell adhesion, growth, and migration, and has been utilised in tissue engineering applications. However, the common terrestrial sources of collagen carry the risk of zoonotic disease transmission and there are religious barriers to the use of bovine and porcine products in many cultures. Marine based collagens offer an attractive alternative and have so far been under-utilized for use as biomaterials for tissue engineering. Marine collagen can be extracted from fish waste products, therefore industry by-products offer an economical and environmentally sustainable source of collagen. In a handful of studies, marine collagen has successfully been methacrylated to form collagen methacrylate (ColMA). Our work included the extraction, characterization and methacrylation of Red Snapper collagen, optimisation of conditions for neural cell seeding and encapsulation using the unmodified collagen, thermally cross-linked, and the methacrylated collagen with UV-induced cross-linking. Finally, the 3D co-axial printing of neural and skeletal muscle cell cultures as a model for neuromuscular junction (NMJ) formation was investigated. Overall, the results of this study show great potential for a novel NMJ in vitro 3D bioprinted model that, with further development, could provide a low-cost, customizable, scalable and quick-to-print platform for drug screening and to study neuromuscular junction physiology and pathogenesis.


Crystals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 252
Author(s):  
Henni Setia Ningsih ◽  
Leonhard Tannesia ◽  
Hsiang-Ho Chen ◽  
Shao-Ju Shih

Mesoporous beta tricalcium phosphate (β-TCP) has recently attracted significant interest as an artificial bone tissue in orthopedics. However, a scalable process is required to meet future demands. Spray drying is one of the potential synthesis methods owing to its low cost and scalable production. In this study, various mesoporous β-TCP powders were calcined in the range of 800 to 1100 °C, with particle sizes ranging from ~0.3 to ~1.8 μm, specific surface areas from ~16 to ~64 m2/g, and average pore sizes of 3 nm. Except for the 800 °C calcined powder, the other β-TCP powders (calcination temperatures of 900, 1000, and 1100 °C) exhibited no cytotoxicity. These results indicate that spray-dried mesoporous β-TCP powders were obtained. Finally, the corresponding formation mechanisms are discussed.


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