1
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Guo J, Wang P, Li Y, Liu Y, Ye Y, Chen Y, Kankala RK, Tong F. Advances in hybridized nanoarchitectures for improved oro-dental health. J Nanobiotechnology 2024; 22:469. [PMID: 39113060 PMCID: PMC11305065 DOI: 10.1186/s12951-024-02680-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/01/2024] [Indexed: 08/11/2024] Open
Abstract
On a global note, oral health plays a critical role in improving the overall human health. In this vein, dental-related issues with dentin exposure often facilitate the risk of developing various oral-related diseases in gums and teeth. Several oral-based ailments include gums-associated (gingivitis or periodontitis), tooth-based (dental caries, root infection, enamel erosion, and edentulous or total tooth loss), as well as miscellaneous diseases in the buccal or oral cavity (bad breath, mouth sores, and oral cancer). Although established conventional treatment modalities have been available to improve oral health, these therapeutic options suffer from several limitations, such as fail to eradicate bacterial biofilms, deprived regeneration of dental pulp cells, and poor remineralization of teeth, resulting in dental emergencies. To this end, the advent of nanotechnology has resulted in the development of various innovative nanoarchitectured composites from diverse sources. This review presents a comprehensive overview of different nanoarchitectured composites for improving overall oral health. Initially, we emphasize various oral-related diseases, providing detailed pathological circumstances and their effects on human health along with deficiencies of the conventional therapeutic modalities. Further, the importance of various nanostructured components is emphasized, highlighting their predominant actions in solving crucial dental issues, such as anti-bacterial, remineralization, and tissue regeneration abilities. In addition to an emphasis on the synthesis of different nanostructures, various nano-therapeutic solutions from diverse sources are discussed, including natural (plant, animal, and marine)-based components and other synthetic (organic- and inorganic-) architectures, as well as their composites for improving oral health. Finally, we summarize the article with an interesting outlook on overcoming the challenges of translating these innovative platforms to clinics.
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Affiliation(s)
- Jun Guo
- School of Stomatology, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China.
- Jiangxi Province Key Laboratory of Oral Biomedicine, Nanchang, 330006, People's Republic of China.
- Jiangxi Province Clinical Research Center for Oral Diseases, Nanchang, 330006, People's Republic of China.
| | - Pei Wang
- School of Stomatology, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
- Jiangxi Province Key Laboratory of Oral Biomedicine, Nanchang, 330006, People's Republic of China
- Jiangxi Province Clinical Research Center for Oral Diseases, Nanchang, 330006, People's Republic of China
| | - Yuyao Li
- School of Stomatology, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
- Jiangxi Province Key Laboratory of Oral Biomedicine, Nanchang, 330006, People's Republic of China
- Jiangxi Province Clinical Research Center for Oral Diseases, Nanchang, 330006, People's Republic of China
| | - Yifan Liu
- School of Stomatology, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
- Jiangxi Province Key Laboratory of Oral Biomedicine, Nanchang, 330006, People's Republic of China
- Jiangxi Province Clinical Research Center for Oral Diseases, Nanchang, 330006, People's Republic of China
| | - Yingtong Ye
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen, 361021, People's Republic of China
| | - Yi Chen
- School of Stomatology, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China
- Jiangxi Province Key Laboratory of Oral Biomedicine, Nanchang, 330006, People's Republic of China
- Jiangxi Province Clinical Research Center for Oral Diseases, Nanchang, 330006, People's Republic of China
| | - Ranjith Kumar Kankala
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen, 361021, People's Republic of China.
| | - Fei Tong
- School of Stomatology, Jiangxi Medical College, Nanchang University, Nanchang, 330006, People's Republic of China.
- Jiangxi Province Key Laboratory of Oral Biomedicine, Nanchang, 330006, People's Republic of China.
- Jiangxi Province Clinical Research Center for Oral Diseases, Nanchang, 330006, People's Republic of China.
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2
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Zedler JAZ, Schirmacher AM, Russo DA, Hodgson L, Gundersen E, Matthes A, Frank S, Verkade P, Jensen PE. Self-Assembly of Nanofilaments in Cyanobacteria for Protein Co-localization. ACS NANO 2023; 17:25279-25290. [PMID: 38065569 PMCID: PMC10754207 DOI: 10.1021/acsnano.3c08600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 12/27/2023]
Abstract
Cyanobacteria offer great potential as alternative biotechnological hosts due to their photoautotrophic capacities. However, in comparison to established heterotrophic hosts, several key aspects, such as product titers, are still lagging behind. Nanobiotechnology is an emerging field with great potential to improve existing hosts, but so far, it has barely been explored in microbial photosynthetic systems. Here, we report the establishment of large proteinaceous nanofilaments in the unicellular model cyanobacterium Synechocystis sp. PCC 6803 and the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973. Transmission electron microscopy and electron tomography demonstrated that expression of pduA*, encoding a modified bacterial microcompartment shell protein, led to the generation of bundles of longitudinally aligned nanofilaments in S. elongatus UTEX 2973 and shorter filamentous structures in Synechocystis sp. PCC 6803. Comparative proteomics showed that PduA* was at least 50 times more abundant than the second most abundant protein in the cell and that nanofilament assembly had only a minor impact on cellular metabolism. Finally, as a proof-of-concept for co-localization with the filaments, we targeted a fluorescent reporter protein, mCitrine, to PduA* by fusion with an encapsulation peptide that natively interacts with PduA. The establishment of nanofilaments in cyanobacterial cells is an important step toward cellular organization of heterologous pathways and the establishment of cyanobacteria as next-generation hosts.
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Affiliation(s)
- Julie A. Z. Zedler
- Synthetic
Biology of Photosynthetic Organisms, Matthias Schleiden Institute
for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Alexandra M. Schirmacher
- Synthetic
Biology of Photosynthetic Organisms, Matthias Schleiden Institute
for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - David A. Russo
- Bioorganic
Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Lorna Hodgson
- School
of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Emil Gundersen
- Department
of Plant and Environmental Sciences, University
of Copenhagen, 1871 Frederiksberg, Denmark
| | - Annemarie Matthes
- Department
of Plant and Environmental Sciences, University
of Copenhagen, 1871 Frederiksberg, Denmark
| | - Stefanie Frank
- Department
of Biochemical Engineering, University College
London, London, WC1E 6BT, United
Kingdom
| | - Paul Verkade
- School
of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Poul Erik Jensen
- Department
of Food Science, University of Copenhagen, 1958 Frederiksberg, Denmark
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3
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Ichihashi N. What can we learn from the construction of in vitro replication systems? Ann N Y Acad Sci 2019; 1447:144-156. [PMID: 30957237 DOI: 10.1111/nyas.14042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/25/2019] [Accepted: 02/04/2019] [Indexed: 01/08/2023]
Abstract
Replication is a central function of living organisms. Several types of replication systems have been constructed in vitro from various molecules, including peptides, DNA, RNA, and proteins. In this review, I summarize the progress in the construction of replication systems over the past few decades and discuss what we can learn from their construction. I introduce various types of replication systems, supporting the feasibility of the spontaneous appearance of replication early in Earth's history. In the latter part of the review, I focus on parasitic replicators, one of the largest obstacles for sustainable replication. Compartmentalization is discussed as a possible solution.
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Affiliation(s)
- Norikazu Ichihashi
- Graduate School of Arts and Sciences and Komaba Institute for Science, The University of Tokyo, Tokyo, Japan
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4
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Norred SE, Caveney PM, Chauhan G, Collier LK, Collier CP, Abel SM, Simpson ML. Macromolecular Crowding Induces Spatial Correlations That Control Gene Expression Bursting Patterns. ACS Synth Biol 2018; 7:1251-1258. [PMID: 29687993 DOI: 10.1021/acssynbio.8b00139] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent superresolution microscopy studies in E. coli demonstrate that the cytoplasm has highly variable local concentrations where macromolecular crowding plays a central role in establishing membrane-less compartmentalization. This spatial inhomogeneity significantly influences molecular transport and association processes central to gene expression. Yet, little is known about how macromolecular crowding influences gene expression bursting-the episodic process where mRNA and proteins are produced in bursts. Here, we simultaneously measured mRNA and protein reporters in cell-free systems, showing that macromolecular crowding decoupled the well-known relationship between fluctuations in the protein population (noise) and mRNA population statistics. Crowded environments led to a 10-fold increase in protein noise even though there were only modest changes in the mRNA population and fluctuations. Instead, cell-like macromolecular crowding created an inhomogeneous spatial distribution of mRNA ("spatial noise") that led to large variability in the protein production burst size. As a result, the mRNA spatial noise created large temporal fluctuations in the protein population. These results highlight the interplay between macromolecular crowding, spatial inhomogeneities, and the resulting dynamics of gene expression, and provide insights into using these organizational principles in both cell-based and cell-free synthetic biology.
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Affiliation(s)
- S Elizabeth Norred
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee Knoxville and Oak Ridge National Laboratory , Knoxville , Tennessee 37996 , United States
| | - Patrick M Caveney
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee Knoxville and Oak Ridge National Laboratory , Knoxville , Tennessee 37996 , United States
| | - Gaurav Chauhan
- Chemical and Biomolecular Engineering Department , University of Tennessee Knoxville , Knoxville , Tennessee 37996 , United States
| | - Lauren K Collier
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - C Patrick Collier
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
| | - Steven M Abel
- Chemical and Biomolecular Engineering Department , University of Tennessee Knoxville , Knoxville , Tennessee 37996 , United States
| | - Michael L Simpson
- Center for Nanophase Materials Sciences , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37831 , United States
- Bredesen Center for Interdisciplinary Research and Graduate Education , University of Tennessee Knoxville and Oak Ridge National Laboratory , Knoxville , Tennessee 37996 , United States
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5
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Promising applications of synthetic biology – and how to avoid their potential pitfalls. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-658-10988-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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6
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Abstract
Protein noise measurements are increasingly used to elucidate biophysical parameters. Unfortunately noise analyses are often at odds with directly measured parameters. Here we show that these inconsistencies arise from two problematic analytical choices: (i) the assumption that protein translation rate is invariant for different proteins of different abundances, which has inadvertently led to (ii) the assumption that a large constitutive extrinsic noise sets the low noise limit in gene expression. While growing evidence suggests that transcriptional bursting may set the low noise limit, variability in translational bursting has been largely ignored. We show that genome-wide systematic variation in translational efficiency can–and in the case of E. coli does–control the low noise limit in gene expression. Therefore constitutive extrinsic noise is small and only plays a role in the absence of a systematic variation in translational efficiency. These results show the existence of two distinct expression noise patterns: (1) a global noise floor uniformly imposed on all genes by expression bursting; and (2) high noise distributed to only a select group of genes.
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7
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Grochmal A, Prout L, Makin-Taylor R, Prohens R, Tomas S. Modulation of reactivity in the cavity of liposomes promotes the formation of peptide bonds. J Am Chem Soc 2015; 137:12269-75. [PMID: 26356087 DOI: 10.1021/jacs.5b06207] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In living cells, reactions take place in membrane-bound compartments, often in response to changes in the environment. Learning how the reactions are influenced by this compartmentalization will help us gain an optimal understanding of living organisms at the molecular level and, at the same time, will offer vital clues on the behavior of simple compartmentalized systems, such as prebiotic precursors of cells and cell-inspired artificial systems. In this work we show that a reactive building block (an activated amino acid derivative) trapped in the cavity of a liposome is protected against hydrolysis and reacts nearly quantitatively with another building block, which is membrane-permeable and free in solution, to form the dipeptide. By contrast, when the activated amino acid is found outside the liposome, hydrolysis is the prevalent reaction, showing that the cavity of the liposomes promotes the formation of peptide bonds. We attribute this result to the large lipid concentration in small compartments from the point of view of a membrane-impermeable molecule. Based on this result, we show how the outcome of the reaction can be predicted as a function of the size of the compartment. The implications of these results on the behavior of biomolecules in cell compartments, abiogenesis, and the design of artificial cell-inspired systems are considered.
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Affiliation(s)
- Anna Grochmal
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
| | - Luba Prout
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
| | - Robert Makin-Taylor
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
| | - Rafel Prohens
- CIRCE Crystal Engineering , 07121 Palma de Mallorca, Spain.,Unitat de Polimorfisme i Calorimetria, CCiT, Universitat de Barcelona , 08028 Barcelona, Spain
| | - Salvador Tomas
- Institute of Structural and Molecular Biology and Department of Biological Sciences, School of Science, Birkbeck University of London , Malet Street, London WC1E 7HX, U.K
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8
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Barbeyron R, Martin AR, Jean-Jacques Vasseur JJV, Michael Smietana MS. DNA-templated borononucleic acid self assembly: a study of minimal complexity. RSC Adv 2015. [DOI: 10.1039/c5ra20767c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The minimal degree of sequence complexity needed for DNA-templated self-assembly of bifunctional oligonucleotides able to form internucleosidic boronate linkages has been studied.
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Affiliation(s)
- Renaud Barbeyron
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
| | - Anthony R. Martin
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
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9
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10
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Ichihashi N, Yomo T. Positive roles of compartmentalization in internal reactions. Curr Opin Chem Biol 2014; 22:12-7. [PMID: 25032508 DOI: 10.1016/j.cbpa.2014.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 06/09/2014] [Accepted: 06/14/2014] [Indexed: 12/23/2022]
Abstract
Recently, many researchers have attempted to construct artificial cell models using a bottom-up approach in which various biochemical reactions that involve a defined set of molecules are reconstructed in cell-like compartments, such as liposomes and water-in-oil droplets. In many of these studies, the cell-like compartments have acted only as containers for the encapsulated biochemical reactions, whereas other studies have indicated that compartmentalization improves the rates and yields of these reactions. Here, we introduce two ways in which compartmentalization can improve internal reactions: the isolation effect and the condensation effect. These positive effects of compartmentalization might have played an important role in the genesis of the first primitive cell on early Earth.
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Affiliation(s)
- Norikazu Ichihashi
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan; Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan; Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan; Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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11
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Iyer S, Doktycz MJ. Thrombin-mediated transcriptional regulation using DNA aptamers in DNA-based cell-free protein synthesis. ACS Synth Biol 2014; 3:340-6. [PMID: 24059754 DOI: 10.1021/sb4000756] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Realizing the potential of cell-free systems will require development of ligand-sensitive gene promoters that control gene expression in response to a ligand of interest. Here, we describe an approach to designing ligand-sensitive transcriptional control in cell-free systems that is based on the combination of a DNA aptamer that binds thrombin and the T7 bacteriophage promoter. Placement of the aptamer near the T7 promoter, and using a primarily single-stranded template, results in up to a 6-fold change in gene expression in a ligand concentration-dependent manner. We further demonstrate that the sensitivity to thrombin concentration and the fold change in expression can be tuned by altering the position of the aptamer. The results described here pave the way for the use of DNA aptamers to achieve modular regulation of transcription in response to a wide variety of ligands in cell-free systems.
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Affiliation(s)
- Sukanya Iyer
- Graduate
Program
in Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Mitchel J. Doktycz
- Graduate
Program
in Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center for
Nanophase
Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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12
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Iyer S, Karig DK, Norred SE, Simpson ML, Doktycz MJ. Multi-input regulation and logic with T7 promoters in cells and cell-free systems. PLoS One 2013; 8:e78442. [PMID: 24194933 PMCID: PMC3806817 DOI: 10.1371/journal.pone.0078442] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/10/2013] [Indexed: 11/21/2022] Open
Abstract
Engineered gene circuits offer an opportunity to harness biological systems for biotechnological and biomedical applications. However, reliance on native host promoters for the construction of circuit elements, such as logic gates, can make the implementation of predictable, independently functioning circuits difficult. In contrast, T7 promoters offer a simple orthogonal expression system for use in a variety of cellular backgrounds and even in cell-free systems. Here we develop a T7 promoter system that can be regulated by two different transcriptional repressors for the construction of a logic gate that functions in cells and in cell-free systems. We first present LacI repressible T7lacO promoters that are regulated from a distal lac operator site for repression. We next explore the positioning of a tet operator site within the T7lacO framework to create T7 promoters that respond to tet and lac repressors and realize an IMPLIES gate. Finally, we demonstrate that these dual input sensitive promoters function in an E. coli cell-free protein expression system. Our results expand the utility of T7 promoters in cell based as well as cell-free synthetic biology applications.
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Affiliation(s)
- Sukanya Iyer
- Graduate Program in Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - David K. Karig
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - S. Elizabeth Norred
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
| | - Michael L. Simpson
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
| | - Mitchel J. Doktycz
- Graduate Program in Genome Science and Technology, University of Tennessee, Knoxville, Knoxville, Tennessee, United States of America
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
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13
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Sorokin VV, Skladnev DA, Volkov VV, Tereshchenko EY, Mulukin AL, Gal'chenko VF. The pathways of silver nanoparticles formation by Mycobacterium smegmatis. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2013; 452:325-328. [PMID: 24150658 DOI: 10.1134/s0012496613050153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Indexed: 06/02/2023]
Affiliation(s)
- V V Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
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14
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Hoffmann C, Mazari E, Lallet S, Le Borgne R, Marchi V, Gosse C, Gueroui Z. Spatiotemporal control of microtubule nucleation and assembly using magnetic nanoparticles. NATURE NANOTECHNOLOGY 2013; 8:199-205. [PMID: 23334169 DOI: 10.1038/nnano.2012.246] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 12/03/2012] [Indexed: 05/20/2023]
Abstract
Decisions on the fate of cells and their functions are dictated by the spatiotemporal dynamics of molecular signalling networks. However, techniques to examine the dynamics of these intracellular processes remain limited. Here, we show that magnetic nanoparticles conjugated with key regulatory proteins can artificially control, in time and space, the Ran/RCC1 signalling pathway that regulates the cell cytoskeleton. In the presence of a magnetic field, RanGTP proteins conjugated to superparamagnetic nanoparticles can induce microtubule fibres to assemble into asymmetric arrays of polarized fibres in Xenopus laevis egg extracts. The orientation of the fibres is dictated by the direction of the magnetic force. When we locally concentrated nanoparticles conjugated with the upstream guanine nucleotide exchange factor RCC1, the assembly of microtubule fibres could be induced over a greater range of distances than RanGTP particles. The method shows how bioactive nanoparticles can be used to engineer signalling networks and spatial self-organization inside a cell environment.
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Affiliation(s)
- Céline Hoffmann
- Département de Chimie, Ecole Normale Supérieure, UMR 8640 CNRS-ENS-UPMC Pasteur, 24, rue Lhomond, 75005 Paris, France
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15
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Matsuura T, Hosoda K, Kazuta Y, Ichihashi N, Suzuki H, Yomo T. Effects of compartment size on the kinetics of intracompartmental multimeric protein synthesis. ACS Synth Biol 2012; 1:431-7. [PMID: 23651340 DOI: 10.1021/sb300041z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The cell contents are encapsulated within a compartment, the volume of which is a fundamental physical parameter that may affect intracompartmental reactions. However, there have been few studies to elucidate whether and how volume changes alone can affect the reaction kinetics. It is difficult to address these questions in vivo, because forced cell volume changes, e.g., by osmotic inflation/deflation, globally alters the internal state. Here, we prepared artificial cell-like compartments with different volumes but with identical constituents, which is not possible with living cells, and synthesized two tetrameric enzymes, β-glucuronidase (GUS) and β-galactosidase (GAL), by cell-free protein synthesis. Tetrameric GUS but not GAL was synthesized more quickly in smaller compartments. The difference between the two was dependent on the rate-limiting step and the reaction order. The observed acceleration mechanism would be applicable to living cells as multimeric protein synthesis in a microcompartment is ubiquitous in vivo.
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Affiliation(s)
- Tomoaki Matsuura
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka, Japan
| | | | - Yasuaki Kazuta
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Norikazu Ichihashi
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Hiroaki Suzuki
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka, Japan
| | - Tetsuya Yomo
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka, Japan
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16
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Okano T, Matsuura T, Kazuta Y, Suzuki H, Yomo T. Cell-free protein synthesis from a single copy of DNA in a glass microchamber. LAB ON A CHIP 2012; 12:2704-2711. [PMID: 22622196 DOI: 10.1039/c2lc40098g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
To achieve a cell-mimetic reaction environment, we fabricated and tested quartz microchambers for conducting protein synthesis using an in vitro transcription and translation system, the PURE system. By introducing a glass microchamber and blocking the surface of the chamber with amino acids, the concentration of the synthesized marker protein (green fluorescent protein, GFP) was significantly improved compared to that in the poly(dimethylsiloxane) (PDMS) microchamber. The concentration was below the detection limit in the PDMS microchambers, whereas the glass microchambers yielded 700 nM GFP, representing 41% of the bulk reaction. There was no detectable difference when the GFP synthesis was performed in microchambers with sizes ranging from 40 fL to 7 pL, indicating that the present microchamber system can serve as a cell-sized test tube with a variable reaction volume. Finally, we demonstrated that two different proteins, GFP and β-galactosidase, can be expressed from single genes in our experimental setup. Quantized and distinctive signals from proteins synthesized from 0, 1, or 2 copies of genes were obtained. The microchamber presented here can be utilized not only to study the effects of compartment volume on protein synthesis but also for the comprehensive analysis of complex biochemical reactions in cell-mimetic environments.
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Affiliation(s)
- Taiji Okano
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Suita, Osaka, Japan
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Das SK, Liang J, Schmidt M, Laffir F, Marsili E. Biomineralization mechanism of gold by zygomycete fungi Rhizopus oryzae. ACS NANO 2012; 6:6165-73. [PMID: 22708541 DOI: 10.1021/nn301502s] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
In recent years, there has been significant progress in the biological synthesis of nanomaterials. However, the molecular mechanism of gold biomineralization in microorganisms of industrial relevance remains largely unexplored. Here we describe the biosynthesis mechanism of gold nanoparticles (AuNPs) in the fungus Rhizopus oryzae . Reduction of AuCl(4)(-) [Au(III)] to nanoparticulate Au(0) (AuNPs) occurs in both the cell wall and cytoplasmic region of R. oryzae . The average size of the as-synthesized AuNPs is ~15 nm. The biomineralization occurs through adsorption, initial reduction to Au(I), followed by complexation [Au(I) complexes], and final reduction to Au(0). Subtoxic concentrations (up to 130 μM) of AuCl(4)(-) in the growth medium increase growth of R. oryzae and induce two stress response proteins while simultaneously down-regulating two other proteins. The induction increases mycelial growth, protein yield, and AuNP biosynthesis. At higher Au(III) concentrations (>130 μM), both mycelial and protein yield decrease and damages to the cellular ultrastructure are observed, likely due to the toxic effect of Au(III). Protein profile analysis also confirms the gold toxicity on R. oryzae at high concentrations. Sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis shows that two proteins of 45 and 42 kDa participate in gold reduction, while an 80 kDa protein serves as a capping agent in AuNP biosynthesis.
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Affiliation(s)
- Sujoy K Das
- School of Biotechnology, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland.
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Nakano T, Moore MJ, Fang Wei, Vasilakos AV, Jianwei Shuai. Molecular Communication and Networking: Opportunities and Challenges. IEEE Trans Nanobioscience 2012; 11:135-48. [DOI: 10.1109/tnb.2012.2191570] [Citation(s) in RCA: 424] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Oldham P, Hall S, Burton G. Synthetic biology: mapping the scientific landscape. PLoS One 2012; 7:e34368. [PMID: 22539946 PMCID: PMC3335118 DOI: 10.1371/journal.pone.0034368] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Accepted: 02/27/2012] [Indexed: 12/18/2022] Open
Abstract
This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved. Debates under the Convention are likely to focus on a possible moratorium on the field release of synthetic organisms, cells or genomes. Based on the empirical evidence we propose that guidance could be provided to funding agencies to respect the letter and spirit of the Convention on Biological Diversity in making research investments. Building on the recommendations of the United States Presidential Commission for the Study of Bioethical Issues we demonstrate that it is possible to promote independent and transparent monitoring of developments in synthetic biology using modern information tools. In particular, public and policy understanding and engagement with synthetic biology can be enhanced through the use of online interactive tools. As a step forward in this process we make existing data on the scientific literature on synthetic biology available in an online interactive workbook so that researchers, policy makers and civil society can explore the data and draw conclusions for themselves.
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Affiliation(s)
- Paul Oldham
- ESRC Centre for Economic and Social Aspects of Genomics, Lancaster University, Lancaster, United Kingdom.
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20
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Morton-Blake D. An intramembrane ion trap. J Mol Liq 2012. [DOI: 10.1016/j.molliq.2011.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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21
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Programmable bacterial catalysis - designing cells for biosynthesis of value-added compounds. FEBS Lett 2012; 586:2184-90. [DOI: 10.1016/j.febslet.2012.02.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 02/16/2012] [Accepted: 02/20/2012] [Indexed: 12/26/2022]
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22
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Siuti P, Retterer ST, Choi CK, Doktycz MJ. Enzyme reactions in nanoporous, picoliter volume containers. Anal Chem 2011; 84:1092-7. [PMID: 22148720 DOI: 10.1021/ac202726n] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Advancements in nanoscale fabrication allow creation of small-volume reaction containers that can facilitate the screening and characterization of enzymes. A porous, ∼19 pL volume vessel has been used in this work to carry out enzyme reactions under varying substrate concentrations. Assessment of small-molecule and green fluorescent protein diffusion from the vessels indicates that pore sizes on the order of 10 nm can be obtained, allowing capture of proteins and diffusive exchange of small molecules. Glucose oxidase and horseradish peroxidase can be contained in these structures and diffusively fed with a solution containing glucose and the fluorogenic substrate amplex red through the engineered nanoscale pore structure. Fluorescent microscopy was used to monitor the reaction, which was carried out under microfluidic control. Kinetic characteristics of the enzyme (K(m) and V(max)) were evaluated and compared with results from conventional scale reactions. These picoliter, nanoporous containers can facilitate quick determination of enzyme kinetics in microfluidic systems without the requirement of surface tethering and can be used for applications in drug discovery, clinical diagnostics, and high-throughput screening.
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Affiliation(s)
- Piro Siuti
- Graduate School of Genome Science and Technology, University of Tennessee-Oak Ridge National Laboratory, Knoxville, Tennessee 37996, United States
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Karig DK, Iyer S, Simpson ML, Doktycz MJ. Expression optimization and synthetic gene networks in cell-free systems. Nucleic Acids Res 2011; 40:3763-74. [PMID: 22180537 PMCID: PMC3333853 DOI: 10.1093/nar/gkr1191] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Synthetic biology offers great promise to a variety of applications through the forward engineering of biological function. Most efforts in this field have focused on employing living cells, yet cell-free approaches offer simpler and more flexible contexts. Here, we evaluate cell-free regulatory systems based on T7 promoter-driven expression by characterizing variants of TetR and LacI repressible T7 promoters in a cell-free context and examining sequence elements that determine expression efficiency. Using the resulting constructs, we then explore different approaches for composing regulatory systems, leading to the implementation of inducible negative feedback in Escherichia coli extracts and in the minimal PURE system, which consists of purified proteins necessary for transcription and translation. Despite the fact that negative feedback motifs are common and essential to many natural and engineered systems, this simple building block has not previously been implemented in a cell-free context. As a final step, we then demonstrate that the feedback systems developed using our cell-free approach can be implemented in live E. coli as well, illustrating the potential for using cell-free expression to fast track the development of live cell systems in synthetic biology. Our quantitative cell-free component characterizations and demonstration of negative feedback embody important steps on the path to harnessing biological function in a bottom-up fashion.
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Affiliation(s)
- David K Karig
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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Siuti P, Retterer ST, Doktycz MJ. Continuous protein production in nanoporous, picolitre volume containers. LAB ON A CHIP 2011; 11:3523-9. [PMID: 21879140 DOI: 10.1039/c1lc20462a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The synthetic manufacture of functional proteins enables a bottom-up understanding of the workings of biological systems and opens new opportunities for the treatment of disease. Cell-free protein synthesis is a practical approach for enabling such manufacturing, however, it is typically carried out in fairly large volumes, when compared to a natural cell, leading to increases in cost and loss of efficiency. Here we demonstrate continuous cell free protein synthesis in arrays of cellular scale containers that continuously exchange energy and materials with their environment. A multiscale fabrication process allows the monolithic integration of nanoporous silicon containers within an addressable microfluidic network. Synthesis of enhanced green fluorescent protein (eGFP) in the containers continues beyond 24 h and yields more than twice the amount of protein, on a per volume basis, than conventional scale batch reactions. By mimicking the physical volume and controlled flux of a natural cell, the resulting "cell mimic" devices can enable fundamental studies of biological systems as well as serve applications related to the functional screening of proteins and the on-demand production of biologics.
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Affiliation(s)
- Piro Siuti
- Genome, Science and Technology Program, University of Tennessee, Knoxville, TN 37996, USA.
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26
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Cellular decision making and biological noise: from microbes to mammals. Cell 2011; 144:910-25. [PMID: 21414483 DOI: 10.1016/j.cell.2011.01.030] [Citation(s) in RCA: 656] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 12/17/2010] [Accepted: 01/17/2011] [Indexed: 12/24/2022]
Abstract
Cellular decision making is the process whereby cells assume different, functionally important and heritable fates without an associated genetic or environmental difference. Such stochastic cell fate decisions generate nongenetic cellular diversity, which may be critical for metazoan development as well as optimized microbial resource utilization and survival in a fluctuating, frequently stressful environment. Here, we review several examples of cellular decision making from viruses, bacteria, yeast, lower metazoans, and mammals, highlighting the role of regulatory network structure and molecular noise. We propose that cellular decision making is one of at least three key processes underlying development at various scales of biological organization.
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Collier CP, Simpson ML. Micro/nanofabricated environments for synthetic biology. Curr Opin Biotechnol 2011; 22:516-26. [PMID: 21636262 DOI: 10.1016/j.copbio.2011.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/06/2011] [Indexed: 11/17/2022]
Abstract
A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints.
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Affiliation(s)
- C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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28
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Simpson ML, Cummings PT. Fluctuations and correlations in physical and biological nanosystems: the tale is in the tails. ACS NANO 2011; 5:2425-2432. [PMID: 21456547 DOI: 10.1021/nn201011m] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The inherently small system sizes involved imply that, in the absence of large applied fields designed to overwhelm them, fluctuations will play a major role in determining the response and functionality of nanoscale systems. Theoretical advances over the past two decades have provided fresh insight into fluctuations and their role at the nanoscale, even in the presence of arbitrarily large applied external fields. In contrast to traditional engineered systems, Nature's approach to nanotechnology is to embrace and to exploit fluctuations and noise to create adaptable, persistent, optimized functional architectures. We describe some of the mechanisms by which Nature exploits noise, with the goal of applying these lessons to engineered physical and chemical nanosystems. In particular, we emphasize the critical role of the tails of distributions of properties in both physical and biological nanosystems and their impact on system behavior.
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Affiliation(s)
- Michael L Simpson
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6494, USA.
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Karig DK, Siuti P, Dar RD, Retterer ST, Doktycz MJ, Simpson ML. Model for biological communication in a nanofabricated cell-mimic driven by stochastic resonance. NANO COMMUNICATION NETWORKS 2011; 2:39-49. [PMID: 21731597 PMCID: PMC3124924 DOI: 10.1016/j.nancom.2011.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Cells offer natural examples of highly efficient networks of nanomachines. Accordingly, both intracellular and intercellular communication mechanisms in nature are looked to as a source of inspiration and instruction for engineered nanocommunication. Harnessing biological functionality in this manner requires an interdisciplinary approach that integrates systems biology, synthetic biology, and nanofabrication. Here, we present a model system that exemplifies the synergism between these realms of research. We propose a synthetic gene network for operation in a nanofabricated cell mimic array that propagates a biomolecular signal over long distances using the phenomenon of stochastic resonance. Our system consists of a bacterial quorum sensing signal molecule, a bistable genetic switch triggered by this signal, and an array of nanofabricated cell mimic wells that contain the genetic system. An optimal level of noise in the system helps to propagate a time-varying AHL signal over long distances through the array of mimics. This noise level is determined both by the system volume and by the parameters of the genetic network. Our proposed genetically driven stochastic resonance system serves as a testbed for exploring the potential harnessing of gene expression noise to aid in the transmission of a time-varying molecular signal.
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Affiliation(s)
- David K. Karig
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
| | - Piro Siuti
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Graduate Program in Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Roy D. Dar
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996-2010, USA
| | - Scott. T. Retterer
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Mitchel J. Doktycz
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Michael L. Simpson
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Tennessee, USA 37996-2010, USA
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37996-2010, USA
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30
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Cranford S, Buehler MJ. Materiomics: biological protein materials, from nano to macro. Nanotechnol Sci Appl 2010; 3:127-48. [PMID: 24198478 PMCID: PMC3781696 DOI: 10.2147/nsa.s9037] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain the motivation of the field of materiomics, as well as demonstrate the benefits of a materiomic approach in the understanding of biological and natural materials as well as in the design of de novo materials. We discuss recent studies that exemplify the impact of materiomics - discovering Nature's complexity through a materials science approach that merges concepts of material and structure throughout all scales and incorporates feedback loops that facilitate sensing and resulting structural changes at multiple scales. The development and application of materiomics is illustrated for the specific case of protein-based materials, which constitute the building blocks of a variety of biological systems such as tendon, bone, skin, spider silk, cells, and tissue, as well as natural composite material systems (a combination of protein-based and inorganic constituents) such as nacre and mollusk shells, and other natural multiscale systems such as cellulose-based plant and wood materials. An important trait of these materials is that they display distinctive hierarchical structures across multiple scales, where molecular details are exhibited in macroscale mechanical responses. Protein materials are intriguing examples of materials that balance multiple tasks, representing some of the most sustainable material solutions that integrate structure and function despite severe limitations in the quality and quantity of material building blocks. However, up until now, our attempts to analyze and replicate Nature's materials have been hindered by our lack of fundamental understanding of these materials' intricate hierarchical structures, scale-bridging mechanisms, and complex material components that bestow protein-based materials their unique properties. Recent advances in analytical tools and experimental methods allow a holistic view of such a hierarchical biological material system. The integration of these approaches and amalgamation of material properties at all scale levels to develop a complete description of a material system falls within the emerging field of materiomics. Materiomics is the result of the convergence of engineering and materials science with experimental and computational biology in the context of natural and synthetic materials. Through materiomics, fundamental advances in our understanding of structure-property-process relations of biological systems contribute to the mechanistic understanding of certain diseases and facilitate the development of novel biological, biologically inspired, and completely synthetic materials for applications in medicine (biomaterials), nanotechnology, and engineering.
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Affiliation(s)
- Steven Cranford
- Center for Materials Science and Engineering, Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Markus J Buehler
- Center for Materials Science and Engineering, Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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31
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Chen Q, Rausch KG, Schönherr H, Vancso GJ. α-Chymotrypsin-Catalyzed Reaction Confined in Block-Copolymer Vesicles. Chemphyschem 2010; 11:3534-40. [DOI: 10.1002/cphc.201000429] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Dar RD, Karig DK, Cooke JF, Cox CD, Simpson ML. Distribution and regulation of stochasticity and plasticity in Saccharomyces cerevisiae. CHAOS (WOODBURY, N.Y.) 2010; 20:037106. [PMID: 20887072 DOI: 10.1063/1.3486800] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Stochasticity is an inherent feature of complex systems with nanoscale structure. In such systems information is represented by small collections of elements (e.g., a few electrons on a quantum dot), and small variations in the populations of these elements may lead to big uncertainties in the information. Unfortunately, little is known about how to work within this inherently noisy environment to design robust functionality into complex nanoscale systems. Here, we look to the biological cell as an intriguing model system where evolution has mediated the trade-offs between fluctuations and function, and in particular we look at the relationships and trade-offs between stochastic and deterministic responses in the gene expression of budding yeast (Saccharomyces cerevisiae). We find gene regulatory arrangements that control the stochastic and deterministic components of expression, and show that genes that have evolved to respond to stimuli (stress) in the most strongly deterministic way exhibit the most noise in the absence of the stimuli. We show that this relationship is consistent with a bursty two-state model of gene expression, and demonstrate that this regulatory motif generates the most uncertainty in gene expression when there is the greatest uncertainty in the optimal level of gene expression.
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Affiliation(s)
- R D Dar
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, Oak Ridge, Tennessee 37831, USA
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Brown L, McArthur SL, Wright PC, Lewis A, Battaglia G. Polymersome production on a microfluidic platform using pH sensitive block copolymers. LAB ON A CHIP 2010; 10:1922-8. [PMID: 20480087 DOI: 10.1039/c004036c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Development of pH sensitive biocompatible block copolymer polymersomes, which are stable in physiological conditions, is enabling the intracellular delivery of water soluble drugs and proteins. As a result, it is becoming increasingly important to develop robust production methods to enhance the polymersome encapsulation efficiency. One way that this could be achieved is through production in microfluidic devices that potentially offer more favourable conditions for encapsulation. Here a flow focussing microfluidic device is used to induce self-assembly of poly(2-(methacryloyloxy)ethyl phosphorylcholine)-poly(2-(diisopropylamino)ethyl methacrylate) (PMPC-b-PDPA) block copolymer by changing the pH of the flows within the microchannels. The laminar flow conditions within the device result in a pH gradient at either interface of the central flow, where diffusion of hydrogen ions enables the deprotonation of the PDPA block copolymer and results in self-assembly of polymersomes. Dynamic light scattering reveals hydrodynamic diameters in the range of 75-275 nm and double membrane structures visualized using transmission electron microscopy indicate that polymersome nanostructures are being produced. The encapsulation efficiency for Bovine Serum Albumin (BSA) was calculated by measuring the spectroscopic absorbance at 279 nm and indicates that the encapsulation efficiency produced in the microfluidic device is equivalent to the standard in solution production method. Critically, the microfluidic system eliminates the use of organic solvents, which limit biological applications, through the pH induced self-assembly process and offers a continuous production method for intracellular delivery polymersomes.
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Affiliation(s)
- Luke Brown
- ChELSI Institute, Department of Chemical and Process Engineering, University of Sheffield, UK
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Rialle S, Felicori L, Dias-Lopes C, Pérès S, El Atia S, Thierry AR, Amar P, Molina F. BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks. ACTA ACUST UNITED AC 2010; 26:2298-304. [PMID: 20628073 PMCID: PMC2935418 DOI: 10.1093/bioinformatics/btq409] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks. RESULTS We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network. AVAILABILITY AND IMPLEMENTATION BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/.
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Affiliation(s)
- Stéphanie Rialle
- SysDiag UMR 3145 CNRS/Bio-Rad, Modélisation et ingénierie de systèmes complexes biologiques pour le diagnostic, Cap Delta/Parc Euromédecine, Montpellier, France.
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Choi CK, Fowlkes JD, Retterer ST, Siuti P, Iyer S, Doktycz MJ. Surface charge- and space-dependent transport of proteins in crowded environments of nanotailored posts. ACS NANO 2010; 4:3345-55. [PMID: 20515056 PMCID: PMC2892340 DOI: 10.1021/nn901831q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The reaction and diffusion of molecules across barriers and through crowded environments is integral to biological system function and to separation technologies. Ordered, microfabricated post arrays are a promising route to creating synthetic barriers with controlled chemical and physical characteristics. They can be used to create crowded environments, to mimic aspects of cellular membranes, and to serve as engineered replacements of polymer-based separation media. Here, the translational diffusion of fluorescein isothiocyante and various forms of green fluorescent protein (GFP), including "supercharged" variants, are examined in a silicon-based post array environment. The technique of fluorescence recovery after photobleaching (FRAP) is combined with analytical approximations and numerical simulations to assess the relative effects of reaction and diffusion on molecular transport, respectively. FRAP experiments were conducted for 64 different cases where the molecular species, the density of the posts, and the chemical surface charge of the posts were varied. In all cases, the dense packing of the posts hindered the diffusive transport of the fluorescent species. The supercharged GFPs strongly interacted with oppositely charged surfaces. With similar molecular and surface charges, transport is primarily limited by hindered diffusion. For conventional, enhanced GFP in a positively charged surface environment, transport was limited by the coupled action of hindered diffusion and surface interaction with the posts. Quantification of the size-, space-, time-, and charge-dependent translational diffusion in the post array environments can provide insight into natural processes and guide the design and development of selective membrane systems.
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Affiliation(s)
- Chang Kyoung Choi
- Mechanical Engineering-Engineering Mechanics, Michigan Technological University, Houghton, MI 49931-1295
| | - Jason D. Fowlkes
- Center for Nanoscale Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Scott T. Retterer
- Center for Nanoscale Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Piro Siuti
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Graduate Program in Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
| | - Sukanya Iyer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Graduate Program in Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
| | - Mitchel J. Doktycz
- Center for Nanoscale Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
- Graduate Program in Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
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Retterer ST, Siuti P, Choi CK, Thomas DK, Doktycz MJ. Development and fabrication of nanoporous silicon-based bioreactors within a microfluidic chip. LAB ON A CHIP 2010; 10:1174-81. [PMID: 20390137 PMCID: PMC3076636 DOI: 10.1039/b921592a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Multi-scale lithography and cryogenic deep reactive ion etching techniques were used to create ensembles of nanoporous, picolitre volume, reaction vessels within a microfluidic system. The fabrication of these vessels is described and how this process can be used to tailor vessel porosity by controlling the width of slits that constitute the vessel pores is demonstrated. Control of pore size allows the containment of nucleic acids and enzymes that are the foundation of biochemical reaction systems, while allowing smaller reaction constituents to traverse the container membrane and continuously supply the reaction. In this work, a 5.4 kb DNA plasmid was retained within the reaction vessels and labeled under microfluidic control with ethidium bromide as an initial proof-of-principle. Subsequently, a coupled enzyme reaction, in which glucose oxidase (GOX) and horseradish peroxidase (HRP) were contained and fed with a substrate solution of glucose and Amplex Red to produce fluorescent resorufin, was carried out under microfluidic control and monitored using fluorescent microscopy. The fabrication techniques presented are broadly applicable and can be adapted to produce devices in which a variety of high aspect ratio, nanoporous silicon structures can be integrated within a microfluidic network. The devices shown here are amenable to being scaled in number and organized to implement more complex reaction systems for applications in sensing and actuation as well as fundamental studies of biological reaction systems.
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Simpson ML, Cox CD, Allen MS, McCollum JM, Dar RD, Karig DK, Cooke JF. Noise in biological circuits. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2010; 1:214-25. [PMID: 20049792 DOI: 10.1002/wnan.22] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Noise biology focuses on the sources, processing, and biological consequences of the inherent stochastic fluctuations in molecular transitions or interactions that control cellular behavior. These fluctuations are especially pronounced in small systems where the magnitudes of the fluctuations approach or exceed the mean value of the molecular population. Noise biology is an essential component of nanomedicine where the communication of information is across a boundary that separates small synthetic and biological systems that are bound by their size to reside in environments of large fluctuations. Here we review the fundamentals of the computational, analytical, and experimental approaches to noise biology. We review results that show that the competition between the benefits of low noise and those of low population has resulted in the evolution of genetic system architectures that produce an uneven distribution of stochasticity across the molecular components of cells and, in some cases, use noise to drive biological function. We review the exact and approximate approaches to gene circuit noise analysis and simulation, and review many of the key experimental results obtained using flow cytometry and time-lapse fluorescent microscopy. In addition, we consider the probative value of noise with a discussion of using measured noise properties to elucidate the structure and function of the underlying gene circuit. We conclude with a discussion of the frontiers of and significant future challenges for noise biology.
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Ota S, Yoshizawa S, Takeuchi S. Microfluidic Formation of Monodisperse, Cell-Sized, and Unilamellar Vesicles. Angew Chem Int Ed Engl 2009; 48:6533-7. [DOI: 10.1002/anie.200902182] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Ota S, Yoshizawa S, Takeuchi S. Microfluidic Formation of Monodisperse, Cell-Sized, and Unilamellar Vesicles. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200902182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Nallani M, Woestenenk R, de Hoog HPM, van Dongen SFM, Boezeman J, Cornelissen JJLM, Nolte RJM, van Hest JCM. Sorting catalytically active polymersome nanoreactors by flow cytometry. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:1138-1143. [PMID: 19235803 DOI: 10.1002/smll.200801204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Madhavan Nallani
- Institute for Molecules and Materials, Radboud University Nijmegen, The Netherlands
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The role of predictive modelling in rationally re-engineering biological systems. Nat Rev Microbiol 2009; 7:297-305. [PMID: 19252506 DOI: 10.1038/nrmicro2107] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Technologies to synthesize and transplant a complete genome into a cell have opened limitless potential to redesign organisms for complex, specialized tasks. However, large-scale re-engineering of a biological circuit will require systems-level optimization that will come from a deep understanding of operational relationships among all the constituent parts of a cell. The integrated framework necessary for conducting such complex bioengineering requires the convergence of systems and synthetic biology. Here, we review the status of these rapidly developing interdisciplinary fields of biology and provide a perspective on plausible venues for their merger.
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Siuti P, Retterer ST, Choi CK, Fowlkes JD, Doktycz MJ. Cell Free Translation in Engineered Picoliter Volume Containers. ANNUAL ORNL BIOMEDICAL SCIENCE AND ENGINEERING CENTER CONFERENCE. ORNL BIOMEDICAL SCIENCE AND ENGINEERING CENTER CONFERENCE 2009; 2009:1-4. [PMID: 21278819 DOI: 10.1109/bsec.2009.5090477] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Engineers seek to use biological design principles to manipulate information and import new functionality to synthetic devices. Such devices inspired by natural systems could, in turn, play a crucial role in allowing biologists to explore the effects of physical transport and extreme conditions of temperature and pH on reaction systems. For example, engineered reaction containers can be physically and chemically defined to control the flux of molecules of different sizes and charge. The design and testing of such a container is described here. It has a volume of 19pL with defined slits of 200nm. The device successfully contained DNA and protein molecules and is evaluated for carrying out cell-free protein synthesis. The effect of DNA concentration and slit size on protein yield is discussed.
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Affiliation(s)
- Piro Siuti
- Genome, Science and Technology program, University of Tennessee, Knoxville, TN 37996 USA
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Buxboim A, Daube SS, Bar-Ziv R. Ultradense synthetic gene brushes on a chip. NANO LETTERS 2009; 9:909-913. [PMID: 19170553 DOI: 10.1021/nl8039124] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Dense brushes of linear DNA polymers are assembled on a biochip with approximately 30 nm between anchorage points, amounting to a few mega-base-pairs/microm(3). In bulk solution, a barrier incurs to conjugate more than two end-functionalized DNAs. However, such doublets bind the surface with almost equal efficiency to singlets, suggesting that extended brush buildup reduces the barrier. On-chip transcription reveals that doublets are roughly 2-fold inefficient compared to singlets, a manifestation of the interaction of the enzymatic machinery with the dense brush. Synthetic gene brushes made of DNA conjugates provide simple means to regulate expression on a chip.
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Affiliation(s)
- Amnon Buxboim
- Department of Materials and Interfaces and Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
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Wolf SM, Gupta R, Kohlhepp P. Gene therapy oversight: lessons for nanobiotechnology. THE JOURNAL OF LAW, MEDICINE & ETHICS : A JOURNAL OF THE AMERICAN SOCIETY OF LAW, MEDICINE & ETHICS 2009; 37:659-684. [PMID: 20122108 DOI: 10.1111/j.1748-720x.2009.00439.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Oversight of human gene transfer research ("gene therapy") presents an important model with potential application to oversight of nanobiology research on human participants. Gene therapy oversight adds centralized federal review at the National Institutes of Health's Office of Biotechnology Activities and its Recombinant DNA Advisory Committee to standard oversight of human subjects research at the researcher's institution (by the Institutional Review Board and, for some research, the Institutional Biosafety Committee) and at the federal level by the Office for Human Research Protections. The Food and Drug Administration's Center for Biologics Evaluation and Research oversees human gene transfer research in parallel, including approval of protocols and regulation of products. This article traces the evolution of this dual oversight system; describes how the system is already addressing nanobiotechnology in gene transfer: evaluates gene therapy oversight based on public opinion, the literature, and preliminary expert elicitation; and offers lessons of the gene therapy oversight experience for oversight of nanobiotechnology.
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Affiliation(s)
- Susan M Wolf
- Faculty Member in Center for Bioethics at University of Minnesota, USA
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An integrated cell-free metabolic platform for protein production and synthetic biology. Mol Syst Biol 2008; 4:220. [PMID: 18854819 PMCID: PMC2583083 DOI: 10.1038/msb.2008.57] [Citation(s) in RCA: 256] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 08/20/2008] [Indexed: 11/20/2022] Open
Abstract
Cell-free systems offer a unique platform for expanding the capabilities of natural biological systems for useful purposes, i.e. synthetic biology. They reduce complexity, remove structural barriers, and do not require the maintenance of cell viability. Cell-free systems, however, have been limited by their inability to co-activate multiple biochemical networks in a single integrated platform. Here, we report the assessment of biochemical reactions in an Escherichia coli cell-free platform designed to activate natural metabolism, the Cytomim system. We reveal that central catabolism, oxidative phosphorylation, and protein synthesis can be co-activated in a single reaction system. Never before have these complex systems been shown to be simultaneously activated without living cells. The Cytomim system therefore promises to provide the metabolic foundation for diverse ab initio cell-free synthetic biology projects. In addition, we describe an improved Cytomim system with enhanced protein synthesis yields (up to 1200 mg/l in 2 h) and lower costs to facilitate production of protein therapeutics and biochemicals that are difficult to make in vivo because of their toxicity, complexity, or unusual cofactor requirements.
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Courtois F, Olguin LF, Whyte G, Bratton D, Huck WTS, Abell C, Hollfelder F. An integrated device for monitoring time-dependent in vitro expression from single genes in picolitre droplets. Chembiochem 2008; 9:439-46. [PMID: 18232037 DOI: 10.1002/cbic.200700536] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microdroplets have great potential for high-throughput biochemical screening. We report the design of an integrated microfluidic device for droplet formation, incubation and screening. Picolitre water-in-oil droplets can be stored in a reservoir that contains approximately 10(6) droplets. In this reservoir droplets are stable for at least 6 h, which gives an extended timescale for biochemical experiments. We demonstrate the utility of the system by following the in vitro expression of green fluorescent protein. The high efficiency allows protein expression from a single molecule of DNA template, creating "monoclonal droplets" in which genotype and phenotype are combined in one emulsion compartment.
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Affiliation(s)
- Fabienne Courtois
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Lab-on-a-chip in Vitro Compartmentalization Technologies for Protein Studies. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2008; 110:81-114. [DOI: 10.1007/10_2008_098] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
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Karig DK, Simpson ML. Tying new knots in synthetic biology. HFSP JOURNAL 2008; 2:124-8. [PMID: 19404464 DOI: 10.2976/1.2907240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Indexed: 11/19/2022]
Abstract
Recent years have seen the emergence of synthetic biology, which encompasses the engineering of living organisms as well as the implementation of biological behavior in non-living substrates. Many of these engineered systems have harnessed the diverse toolkit of proteins, genes, and cellular processes that nature offers. While these efforts have been fruitful, they have also illustrated the difficulty associated with programming highly complex functions by tapping into cellular processes. Another set of efforts has focused on building circuits, performing computation, and constructing nanoscale machines using nucleic acids. Zhang et al., 2007, Science 318, 1121-1125 and Yin et al., 2008, Nature 451, 318-322 recently demonstrated flexible approaches for the modular construction of such biochemical devices exclusively using DNA. These approaches have exciting implications both for engineering living cells and for mimicking life-like behavior at the nanoscale.
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Affiliation(s)
- David K Karig
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830
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Synthetic gene brushes: a structure-function relationship. Mol Syst Biol 2008; 4:181. [PMID: 18414482 PMCID: PMC2387232 DOI: 10.1038/msb.2008.20] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Accepted: 02/25/2008] [Indexed: 11/09/2022] Open
Abstract
We present the assembly of gene brushes by means of a photolithographic approach that allows us to control the density of end-immobilized linear double-stranded DNA polymers coding for entire genes. For 2 kbp DNAs, the mean distance varies from 300 nm, where DNAs are dilute and assume relaxed conformations, down to 30 nm, where steric repulsion at dense packing forces stretching out. We investigated the gene-to-protein relationship of firefly luciferase under the T7/E.Coli-extract expression system, as well as transcription-only reactions with T7 RNA polymerase, and found both systems to be highly sensitive to brush density, conformation, and orientation. A 'structure-function' picture emerges in which extension of genes induced by moderate packing exposes coding sequences and improves their interaction with the transcription/translation machinery. However, tighter packing impairs the penetration of the machinery into the brush. The response of expression to two-dimensional gene crowding at the nanoscale identifies gene brushes as basic controllable units en route to multicomponent synthetic systems. In turn, these brushes could deepen our understanding of biochemical reactions taking place under confinement and molecular crowding in living cells.
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