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Krishnaswamy B, McClean MN. Shining light on molecular communication. PROCEEDINGS OF THE 7TH ACM INTERNATIONAL CONFERENCE ON NANOSCALE COMPUTING AND COMMUNICATION : VIRTUAL CONFERENCE, SEPTEMBER 23-25, 2020 : NANOCOM 2020. ACM INTERNATIONAL CONFERENCE ON NANOSCALE COMPUTING AND COMMUNICATION (7TH : 2020 :... 2020; 2020:11. [PMID: 35425948 PMCID: PMC9006593 DOI: 10.1145/3411295.3411307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecules and combinations of molecules are the natural communication currency of microbes; microbes have evolved and been engineered to sense a variety of compounds, often with exquisite sensitivity. The availability of microbial biosensors, combined with the ability to genetically engineer biological circuits to process information, make microbes attractive bionanomachines for propagating information through molecular communication (MC) networks. However, MC networks built entirely of biological components suffer a number of limitations. They are extremely slow due to processing and propagation delays and must employ simple algorithms due to the still limited computational capabilities of biological circuits. In this work, we propose a hybrid bio-electronic framework which utilizes biological components for sensing but offloads processing and computation to traditional electronic systems and communication infrastructure. This is achieved by using tools from the burgeoning field of optogenetics to trigger biosensing through an optoelectronic interface, alleviating the need for computation and communication in the biological domain.
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Xu P. Branch point control at malonyl-CoA node: A computational framework to uncover the design principles of an ideal genetic-metabolic switch. Metab Eng Commun 2020; 10:e00127. [PMID: 32455112 PMCID: PMC7236061 DOI: 10.1016/j.mec.2020.e00127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 01/10/2023] Open
Abstract
Living organism is an intelligent system coded by hierarchically-organized information to perform precisely-controlled biological functions. Biophysical models are important tools to uncover the design rules underlying complex genetic-metabolic circuit interactions. Based on a previously engineered synthetic malonyl-CoA switch (Xu et al., PNAS, 2014), we have formulated nine differential equations to unravel the design principles underlying an ideal metabolic switch to improve fatty acids production in E. coli. By interrogating the physiologically accessible parameter space, we have determined the optimal controller architecture to configure both the metabolic source pathway and metabolic sink pathway. We determined that low protein degradation rate, medium strength of metabolic inhibitory constant, high metabolic source pathway induction rate, strong binding affinity of the transcriptional activator toward the metabolic source pathway, weak binding affinity of the transcriptional repressor toward the metabolic sink pathway, and a strong cooperative interaction of transcriptional repressor toward metabolic sink pathway benefit the accumulation of the target molecule (fatty acids). The target molecule (fatty acid) production is increased from 50% to 10-folds upon application of the autonomous metabolic switch. With strong metabolic inhibitory constant, the system displays multiple steady states. Stable oscillation of metabolic intermediate is the driving force to allow the system deviate from its equilibrium state and permits bidirectional ON-OFF gene expression control, which autonomously compensates enzyme level for both the metabolic source and metabolic sink pathways. The computational framework may facilitate us to design and engineer predictable genetic-metabolic switches, quest for the optimal controller architecture of the metabolic source/sink pathways, as well as leverage autonomous oscillation as a powerful tool to engineer cell function.
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Affiliation(s)
- Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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53
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Letourneau A, Kegel J, Al-Ramahi J, Yachinich E, Krause HB, Stewart CJ, McClean MN. A Microfluidic Device for Imaging Samples from Microbial Suspension Cultures. MethodsX 2020; 7:100891. [PMID: 32420047 PMCID: PMC7214938 DOI: 10.1016/j.mex.2020.100891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/02/2020] [Indexed: 11/15/2022] Open
Abstract
Traditional methods to assess microbial cells during suspension culture require laborious and frequent manual sampling. Approaches to automate sampling and assessment utilize dedicated, sophisticated equipment and suffer from a lack of temporal resolution and sampling efficiency. In this study we describe a simple microfluidic device that allows microbial cells to be sampled from suspension culture and rapidly slowed and concentrated for single-cell imaging on a standard laboratory microscope. We demonstrate a device that: •slows and concentrates microbial cells, specifically budding yeast, sampled from suspension culture and improves imaging of individual cells by concentrating them in a single focal plane•provides imaging quality and temporal resolution that is capable of monitoring dynamic spatiotemporal processes, such as nuclear localization of a protein•is inexpensive and simple enough to be fabricated and used in laboratories equipped for standard molecular and cellular biology.
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Hartmann J, Krueger D, De Renzis S. Using optogenetics to tackle systems-level questions of multicellular morphogenesis. Curr Opin Cell Biol 2020; 66:19-27. [PMID: 32408249 DOI: 10.1016/j.ceb.2020.04.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/03/2020] [Accepted: 04/06/2020] [Indexed: 01/13/2023]
Abstract
Morphogenesis of multicellular systems is governed by precise spatiotemporal regulation of biochemical reactions and mechanical forces which together with environmental conditions determine the development of complex organisms. Current efforts in the field aim at decoding the system-level principles underlying the regulation of developmental processes. Toward this goal, optogenetics, the science of regulation of protein function with light, is emerging as a powerful new tool to quantitatively perturb protein function in vivo with unprecedented precision in space and time. In this review, we provide an overview of how optogenetics is helping to address system-level questions of multicellular morphogenesis and discuss future directions.
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Affiliation(s)
- Jonas Hartmann
- European Molecular Biology Laboratory (EMBL), Developmental Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
| | - Daniel Krueger
- European Molecular Biology Laboratory (EMBL), Developmental Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Stefano De Renzis
- European Molecular Biology Laboratory (EMBL), Developmental Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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55
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Perkins ML, Benzinger D, Arcak M, Khammash M. Cell-in-the-loop pattern formation with optogenetically emulated cell-to-cell signaling. Nat Commun 2020; 11:1355. [PMID: 32170129 PMCID: PMC7069979 DOI: 10.1038/s41467-020-15166-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 02/11/2020] [Indexed: 12/22/2022] Open
Abstract
Designing and implementing synthetic biological pattern formation remains challenging due to underlying theoretical complexity as well as the difficulty of engineering multicellular networks biochemically. Here, we introduce a cell-in-the-loop approach where living cells interact through in silico signaling, establishing a new testbed to interrogate theoretical principles when internal cell dynamics are incorporated rather than modeled. We present an easy-to-use theoretical test to predict the emergence of contrasting patterns in gene expression among laterally inhibiting cells. Guided by the theory, we experimentally demonstrate spontaneous checkerboard patterning in an optogenetic setup, where cell-to-cell signaling is emulated with light inputs calculated in silico from real-time gene expression measurements. The scheme successfully produces spontaneous, persistent checkerboard patterns for systems of sixteen patches, in quantitative agreement with theoretical predictions. Our research highlights how tools from dynamical systems theory may inform our understanding of patterning, and illustrates the potential of cell-in-the-loop for engineering synthetic multicellular systems.
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Affiliation(s)
- Melinda Liu Perkins
- Department of Electrical Engineering, University of California, Berkeley, CA, USA.
| | - Dirk Benzinger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Murat Arcak
- Department of Electrical Engineering, University of California, Berkeley, CA, USA
| | - Mustafa Khammash
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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56
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An-Adirekkun JM, Stewart CJ, Geller SH, Patel MT, Melendez J, Oakes BL, Noyes MB, McClean MN. A yeast optogenetic toolkit (yOTK) for gene expression control in Saccharomyces cerevisiae. Biotechnol Bioeng 2019; 117:886-893. [PMID: 31788779 DOI: 10.1002/bit.27234] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/07/2019] [Accepted: 11/27/2019] [Indexed: 12/17/2022]
Abstract
Optogenetic tools for controlling gene expression are ideal for tuning synthetic biological networks due to the exquisite spatiotemporal control available with light. Here we develop an optogenetic system for gene expression control integrated with an existing yeast toolkit allowing for rapid, modular assembly of light-controlled circuits in the important chassis organism Saccharomyces cerevisiae. We reconstitute activity of a split synthetic zinc-finger transcription factor (TF) using light-induced dimerization mediated by the proteins CRY2 and CIB1. We optimize function of this split TF and demonstrate the utility of the toolkit workflow by assembling cassettes expressing the TF activation domain and DNA-binding domain at different levels. Utilizing this TF and a synthetic promoter we demonstrate that light intensity and duty cycle can be used to modulate gene expression over the range currently available from natural yeast promoters. This study allows for rapid generation and prototyping of optogenetic circuits to control gene expression in S. cerevisiae.
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Affiliation(s)
| | - Cameron J Stewart
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Stephanie H Geller
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - Michael T Patel
- Lewis-Sigler Institute for Integrated Genomics, Princeton University, Princeton, New Jersey
| | - Justin Melendez
- Lewis-Sigler Institute for Integrated Genomics, Princeton University, Princeton, New Jersey
| | - Benjamin L Oakes
- Lewis-Sigler Institute for Integrated Genomics, Princeton University, Princeton, New Jersey
| | - Marcus B Noyes
- Department of Biochemistry and Molecular Pharmacology and Institute for Systems Genetics, NYU Langone Health, New York, New York
| | - Megan N McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin
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57
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Controlling cell-to-cell variability with synthetic gene circuits. Biochem Soc Trans 2019; 47:1795-1804. [DOI: 10.1042/bst20190295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 02/05/2023]
Abstract
Cell-to-cell variability originating, for example, from the intrinsic stochasticity of gene expression, presents challenges for designing synthetic gene circuits that perform robustly. Conversely, synthetic biology approaches are instrumental in uncovering mechanisms underlying variability in natural systems. With a focus on reducing noise in individual genes, the field has established a broad synthetic toolset. This includes noise control by engineering of transcription and translation mechanisms either individually, or in combination to achieve independent regulation of mean expression and its variability. Synthetic feedback circuits use these components to establish more robust operation in closed-loop, either by drawing on, but also by extending traditional engineering concepts. In this perspective, we argue that major conceptual advances will require new theory of control adapted to biology, extensions from single genes to networks, more systematic considerations of origins of variability other than intrinsic noise, and an exploration of how noise shaping, instead of noise reduction, could establish new synthetic functions or help understanding natural functions.
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58
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Stavreva DA, Garcia DA, Fettweis G, Gudla PR, Zaki GF, Soni V, McGowan A, Williams G, Huynh A, Palangat M, Schiltz RL, Johnson TA, Presman DM, Ferguson ML, Pegoraro G, Upadhyaya A, Hager GL. Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility. Mol Cell 2019; 75:1161-1177.e11. [PMID: 31421980 PMCID: PMC6754282 DOI: 10.1016/j.molcel.2019.06.042] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/07/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022]
Abstract
Genes are transcribed in a discontinuous pattern referred to as RNA bursting, but the mechanisms regulating this process are unclear. Although many physiological signals, including glucocorticoid hormones, are pulsatile, the effects of transient stimulation on bursting are unknown. Here we characterize RNA synthesis from single-copy glucocorticoid receptor (GR)-regulated transcription sites (TSs) under pulsed (ultradian) and constant hormone stimulation. In contrast to constant stimulation, pulsed stimulation induces restricted bursting centered around the hormonal pulse. Moreover, we demonstrate that transcription factor (TF) nuclear mobility determines burst duration, whereas its bound fraction determines burst frequency. Using 3D tracking of TSs, we directly correlate TF binding and RNA synthesis at a specific promoter. Finally, we uncover a striking co-bursting pattern between TSs located at proximal and distal positions in the nucleus. Together, our data reveal a dynamic interplay between TF mobility and RNA bursting that is responsive to stimuli strength, type, modality, and duration.
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Affiliation(s)
- Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA.
| | - David A Garcia
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA; Department of Physics and Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Prabhakar R Gudla
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - George F Zaki
- High Performance Computing Group, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vikas Soni
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Andrew McGowan
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Geneva Williams
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Anh Huynh
- Department of Physics and Graduate Program in Biomolecular Science, Boise State University, Boise, ID 83725, USA
| | - Murali Palangat
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - R Louis Schiltz
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Diego M Presman
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Matthew L Ferguson
- Department of Physics and Graduate Program in Biomolecular Science, Boise State University, Boise, ID 83725, USA
| | - Gianluca Pegoraro
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA
| | - Arpita Upadhyaya
- Department of Physics and Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, 41 Library Drive, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892-5055, USA.
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59
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Sassi H, Nguyen TM, Telek S, Gosset G, Grünberger A, Delvigne F. Segregostat: a novel concept to control phenotypic diversification dynamics on the example of Gram-negative bacteria. Microb Biotechnol 2019; 12:1064-1075. [PMID: 31141840 PMCID: PMC6680609 DOI: 10.1111/1751-7915.13442] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/13/2019] [Indexed: 12/24/2022] Open
Abstract
Controlling and managing the degree of phenotypic diversification of microbial populations is a challenging task. This task not only requires detailed knowledge regarding diversification mechanisms but also advanced technical set-ups for the real-time analyses and control of population behaviour on single-cell level. In this work, set-up, design and operation of the so called segregostat are described which, in contrast to a traditional chemostat, allows the control of phenotypic diversification of microbial populations over time. Two exemplary case studies will be discussed, i.e. phenotypic diversification dynamics of Eschericia coli and Pseudomonas putida based on outer membrane permeabilization, emphasizing the applicability and versatility of the proposed approach. Upon nutrient limitation, cell population tends to diversify into several subpopulations exhibiting distinct phenotypic features (non-permeabilized and permeabilized cells). Online analysis leads to the determination of the ratio between cells in these two states, which in turn triggers the addition of glucose pulses in order to maintain a predefined diversification ratio. These results prove that phenotypic diversification can be controlled by means of defined pulse-frequency modulation within continuously running bioreactor set-ups. This lays the foundation for systematic studies, not only of phenotypic diversification but also for all processes where dynamics single-cell approaches are required, such as synthetic co-culture processes.
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Affiliation(s)
- Hosni Sassi
- Terra Research and Teaching CentreMicrobial Processes and Interactions (MiPI)Gembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
| | - Thai Minh Nguyen
- Terra Research and Teaching CentreMicrobial Processes and Interactions (MiPI)Gembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
| | - Samuel Telek
- Terra Research and Teaching CentreMicrobial Processes and Interactions (MiPI)Gembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y BiocatálisisInstituto de BiotecnologíaUniversidad Nacional Autónoma de MéxicoCuernavaca, MorelosMéxico
| | - Alexander Grünberger
- Multiscale BioengineeringBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Frank Delvigne
- Terra Research and Teaching CentreMicrobial Processes and Interactions (MiPI)Gembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
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60
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Guinn MT, Balázsi G. Noise-reducing optogenetic negative-feedback gene circuits in human cells. Nucleic Acids Res 2019; 47:7703-7714. [PMID: 31269201 PMCID: PMC6698750 DOI: 10.1093/nar/gkz556] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 12/16/2022] Open
Abstract
Gene autorepression is widely present in nature and is also employed in synthetic biology, partly to reduce gene expression noise in cells. Optogenetic systems have recently been developed for controlling gene expression levels in mammalian cells, but most have utilized activator-based proteins, neglecting negative feedback except for in silico control. Here, we engineer optogenetic gene circuits into mammalian cells to achieve noise-reduction for precise gene expression control by genetic, in vitro negative feedback. We build a toolset of these noise-reducing Light-Inducible Tuner (LITer) gene circuits using the TetR repressor fused with a Tet-inhibiting peptide (TIP) or a degradation tag through the light-sensitive LOV2 protein domain. These LITers provide a range of nearly 4-fold gene expression control and up to 5-fold noise reduction from existing optogenetic systems. Moreover, we use the LITer gene circuit architecture to control gene expression of the cancer oncogene KRAS(G12V) and study its downstream effects through phospho-ERK levels and cellular proliferation. Overall, these novel LITer optogenetic platforms should enable precise spatiotemporal perturbations for studying multicellular phenotypes in developmental biology, oncology and other biomedical fields of research.
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Affiliation(s)
- Michael Tyler Guinn
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794, USA
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Medical Scientist Training Program, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794, USA
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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61
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Abstract
Living cells communicate information about physiological conditions by producing signaling molecules in a specific timed manner. Different conditions can result in the same total amount of a signaling molecule, differing only in the pattern of the molecular concentration over time. Such temporally coded information can be completely invisible to even state-of-the-art molecular sensors with high chemical specificity that respond only to the total amount of the signaling molecule. Here, we demonstrate design principles for circuits with temporal specificity, that is, molecular circuits that respond to specific temporal patterns in a molecular concentration. We consider pulsatile patterns in a molecular concentration characterized by three fundamental temporal features: time period, duty fraction, and number of pulses. We develop circuits that respond to each one of these features while being insensitive to the others. We demonstrate our design principles using general chemical reaction networks and with explicit simulations of DNA strand displacement reactions. In this way, our work develops building blocks for temporal pattern recognition through molecular computation.
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Affiliation(s)
- Jackson O’Brien
- The James Franck Institute and Department of Physics, University of Chicago, Chicago, Illinois 60637, United States
| | - Arvind Murugan
- The James Franck Institute and Department of Physics, University of Chicago, Chicago, Illinois 60637, United States
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62
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Cao Z, Grima R. Accuracy of parameter estimation for auto-regulatory transcriptional feedback loops from noisy data. J R Soc Interface 2019; 16:20180967. [PMID: 30940028 PMCID: PMC6505555 DOI: 10.1098/rsif.2018.0967] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bayesian and non-Bayesian moment-based inference methods are commonly used to estimate the parameters defining stochastic models of gene regulatory networks from noisy single cell or population snapshot data. However, a systematic investigation of the accuracy of the predictions of these methods remains missing. Here, we present the results of such a study using synthetic noisy data of a negative auto-regulatory transcriptional feedback loop, one of the most common building blocks of complex gene regulatory networks. We study the error in parameter estimation as a function of (i) number of cells in each sample; (ii) the number of time points; (iii) the highest-order moment of protein fluctuations used for inference; (iv) the moment-closure method used for likelihood approximation. We find that for sample sizes typical of flow cytometry experiments, parameter estimation by maximizing the likelihood is as accurate as using Bayesian methods but with a much reduced computational time. We also show that the choice of moment-closure method is the crucial factor determining the maximum achievable accuracy of moment-based inference methods. Common likelihood approximation methods based on the linear noise approximation or the zero cumulants closure perform poorly for feedback loops with large protein-DNA binding rates or large protein bursts; this is exacerbated for highly heterogeneous cell populations. By contrast, approximating the likelihood using the linear-mapping approximation or conditional derivative matching leads to highly accurate parameter estimates for a wide range of conditions.
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63
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Scott TD, Sweeney K, McClean MN. Biological signal generators: integrating synthetic biology tools and in silico control. ACTA ACUST UNITED AC 2019; 14:58-65. [PMID: 31673669 DOI: 10.1016/j.coisb.2019.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Biological networks sense extracellular stimuli and generate appropriate outputs within the cell that determine cellular response. Biological signal generators are becoming an important tool for understanding how information is transmitted in these networks and controlling network behavior. Signal generators produce well-defined, dynamic, intracellular signals of important network components, such as kinase activity or the concentration of a specific transcription factor. Synthetic biology tools coupled with in silico control have enabled the construction of these sophisticated biological signal generators. Here we review recent advances in biological signal generator construction and their use in systems biology studies. Challenges for constructing signal generators for a wider range of biological networks and generalizing their use are discussed.
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Affiliation(s)
- Taylor D Scott
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1550 Engineering Drive, Madison, Wisconsin 53706 USA
| | - Kieran Sweeney
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1550 Engineering Drive, Madison, Wisconsin 53706 USA
| | - Megan N McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1550 Engineering Drive, Madison, Wisconsin 53706 USA
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64
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Wu L, Wang H, Ouyang Q. Constructing network topologies for multiple signal-encoding functions. BMC SYSTEMS BIOLOGY 2019; 13:6. [PMID: 30634968 PMCID: PMC6330498 DOI: 10.1186/s12918-018-0676-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 12/28/2018] [Indexed: 11/17/2022]
Abstract
Background Cells use signaling protein networks to sense their environment and mediate specific responses. Information about environmental stress is usually encoded in the dynamics of the signaling molecules, and qualitatively distinct dynamics of the same signaling molecule can lead to dramatically different cell fates. Exploring the design principles of networks with multiple signal-encoding functions is important for understanding how distinct dynamic patterns are shaped and integrated by real cellular networks, and for building cells with targeted sensing–response functions via synthetic biology. Results In this paper, we investigate multi-node enzymatic regulatory networks with three signal-encoding functions, i.e., dynamic responses of oscillation, transient activation, and sustained activation upon step stimulation by three different inducers, respectively. Taking into account competition effects of the substrates for the same enzyme in the enzymatic reactions, we searched for robust subnetworks for each signal-encoding function by three-node-network enumeration and then integrated the three subnetworks together via node-merging. The obtained tri-functional networks consisted of four to six nodes, and the core structures of these networks were hybrids of the motifs for the subfunctions. Conclusions The simplest but relatively robust tri-functional networks demonstrated that the three functions were compatible within a simple negative feedback loop. Depending on the network structure, the competition effects of the substrates for the same enzyme within the networks could promote or hamper the target functions, and can create implicit functional motifs. Overall, the networks we obtained could in principle be synthesized to construct dynamic control circuits with multiple target functions. Electronic supplementary material The online version of this article (10.1186/s12918-018-0676-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lili Wu
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Hongli Wang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China. .,Center for Quantitative Biology, Peking University, Beijing, 100871, China.
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China. .,Center for Quantitative Biology, Peking University, Beijing, 100871, China. .,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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