1
|
Zhang Z, Li F, Duan Z, Shi C, Wang X, Zhu F, Xue W. OPTICS: An interactive online platform for photosensory and bio-functional proteins in optogenetic systems. Comput Biol Med 2024; 178:108687. [PMID: 38870722 DOI: 10.1016/j.compbiomed.2024.108687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/25/2024] [Accepted: 06/01/2024] [Indexed: 06/15/2024]
Abstract
High-precise modulation of bio-functional proteins related to signaling is crucial in life sciences and human health. The cutting-edge technology of optogenetics, which combines optical method with genetically encoded protein expression, pioneered new pathways for the control of cellular bio-functional proteins (CPs) using optogenetic tools (OTs) in spatial and temporal. Over the past decade, hundreds of optogenetic systems (OSs) have been developed for various applications from living cells to freely moving organisms. However, no database has been constructed to comprehensively provide the valuable information of OSs yet. In this work, a new database named OPTICS (an interactive online platform for photosensory and bio-functional proteins in optogenetic systems) is introduced. Our OPTICS is unique in (i) systematically describing diverse OSs from the perspective of photoreceptor-based classification and mechanism of action, (ii) featuring the detailed biophysical properties and functional data of OSs, (iii) providing the interaction between OT and CP for each OS referring to distinct applications in research, diagnosis, and therapy, and (iv) enabling a light response property-based search against all OSs in the database. Since the information on OSs is essential for rapid and predictable design of optogenetic controls, the comprehensive data provided in OPTICS lay a solid foundation for the future development of novel OSs. OPTICS is freely accessible without login requirement at https://idrblab.org/optics/.
Collapse
Affiliation(s)
- Zhao Zhang
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Zixin Duan
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, China
| | - Chaoqun Shi
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, China
| | - Xiaona Wang
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing, 401331, China.
| |
Collapse
|
2
|
McMillen P, Levin M. Collective intelligence: A unifying concept for integrating biology across scales and substrates. Commun Biol 2024; 7:378. [PMID: 38548821 PMCID: PMC10978875 DOI: 10.1038/s42003-024-06037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
A defining feature of biology is the use of a multiscale architecture, ranging from molecular networks to cells, tissues, organs, whole bodies, and swarms. Crucially however, biology is not only nested structurally, but also functionally: each level is able to solve problems in distinct problem spaces, such as physiological, morphological, and behavioral state space. Percolating adaptive functionality from one level of competent subunits to a higher functional level of organization requires collective dynamics: multiple components must work together to achieve specific outcomes. Here we overview a number of biological examples at different scales which highlight the ability of cellular material to make decisions that implement cooperation toward specific homeodynamic endpoints, and implement collective intelligence by solving problems at the cell, tissue, and whole-organism levels. We explore the hypothesis that collective intelligence is not only the province of groups of animals, and that an important symmetry exists between the behavioral science of swarms and the competencies of cells and other biological systems at different scales. We then briefly outline the implications of this approach, and the possible impact of tools from the field of diverse intelligence for regenerative medicine and synthetic bioengineering.
Collapse
Affiliation(s)
- Patrick McMillen
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Michael Levin
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
| |
Collapse
|
3
|
Lagasse E, Levin M. Future medicine: from molecular pathways to the collective intelligence of the body. Trends Mol Med 2023; 29:687-710. [PMID: 37481382 PMCID: PMC10527237 DOI: 10.1016/j.molmed.2023.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/24/2023]
Abstract
The remarkable anatomical homeostasis exhibited by complex living organisms suggests that they are inherently reprogrammable information-processing systems that offer numerous interfaces to their physiological and anatomical problem-solving capacities. We briefly review data suggesting that the multiscale competency of living forms affords a new path for biomedicine that exploits the innate collective intelligence of tissues and organs. The concept of tissue-level allostatic goal-directedness is already bearing fruit in clinical practice. We sketch a roadmap towards 'somatic psychiatry' by using advances in bioelectricity and behavioral neuroscience to design methods that induce self-repair of structure and function. Relaxing the assumption that cellular control mechanisms are static, exploiting powerful concepts from cybernetics, behavioral science, and developmental biology may spark definitive solutions to current biomedical challenges.
Collapse
Affiliation(s)
- Eric Lagasse
- McGowan Institute for Regenerative Medicine and Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
| |
Collapse
|
4
|
Pio-Lopez L, Kuchling F, Tung A, Pezzulo G, Levin M. Active inference, morphogenesis, and computational psychiatry. Front Comput Neurosci 2022; 16:988977. [PMID: 36507307 PMCID: PMC9731232 DOI: 10.3389/fncom.2022.988977] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/17/2022] [Indexed: 11/26/2022] Open
Abstract
Active inference is a leading theory in neuroscience that provides a simple and neuro-biologically plausible account of how action and perception are coupled in producing (Bayes) optimal behavior; and has been recently used to explain a variety of psychopathological conditions. In parallel, morphogenesis has been described as the behavior of a (non-neural) cellular collective intelligence solving problems in anatomical morphospace. In this article, we establish a link between the domains of cell biology and neuroscience, by analyzing disorders of morphogenesis as disorders of (active) inference. The aim of this article is three-fold. We want to: (i) reveal a connection between disorders of morphogenesis and disorders of active inference as apparent in psychopathological conditions; (ii) show how disorders of morphogenesis can be simulated using active inference; (iii) suggest that active inference can shed light on developmental defects or aberrant morphogenetic processes, seen as disorders of information processing, and perhaps suggesting novel intervention and repair strategies. We present four simulations illustrating application of these ideas to cellular behavior during morphogenesis. Three of the simulations show that the same forms of aberrant active inference (e.g., deficits of sensory attenuation and low sensory precision) that have been used to explain psychopathological conditions (e.g., schizophrenia and autism) also produce familiar disorders of development and morphogenesis when implemented at the level of the collective behavior of a group of cells. The fourth simulation involves two cells with too high precision, in which we show that the reduction of concentration signaling and sensitivity to the signals of other cells treats the development defect. Finally, we present the results of an experimental test of one of the model's predictions in early Xenopus laevis embryos: thioridazine (a dopamine antagonist that may reduce sensory precision in biological systems) induced developmental (anatomical) defects as predicted. The use of conceptual and empirical tools from neuroscience to understand the morphogenetic behavior of pre-neural agents offers the possibility of new approaches in regenerative medicine and evolutionary developmental biology.
Collapse
Affiliation(s)
- Léo Pio-Lopez
- Allen Discovery Center, Tufts University, Medford, MA, United States
| | - Franz Kuchling
- Allen Discovery Center, Tufts University, Medford, MA, United States
| | - Angela Tung
- Allen Discovery Center, Tufts University, Medford, MA, United States
| | - Giovanni Pezzulo
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, United States,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States,*Correspondence: Michael Levin
| |
Collapse
|
5
|
Harris MJ, Fuyal M, James JR. Quantifying persistence in the T-cell signaling network using an optically controllable antigen receptor. Mol Syst Biol 2021; 17:e10091. [PMID: 33988299 PMCID: PMC8120804 DOI: 10.15252/msb.202010091] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/17/2022] Open
Abstract
T cells discriminate between healthy and infected cells with remarkable sensitivity when mounting an immune response, which is hypothesized to depend on T cells combining stimuli from multiple antigen-presenting cell interactions into a more potent response. To quantify the capacity for T cells to accomplish this, we have developed an antigen receptor that is optically tunable within cell conjugates, providing control over the duration, and intensity of intracellular T-cell signaling. We observe limited persistence within the T-cell intracellular network on disruption of receptor input, with signals dissipating entirely in ~15 min, and directly show sustained proximal receptor signaling is required to maintain gene transcription. T cells thus primarily accumulate the outputs of gene expression rather than integrate discrete intracellular signals. Engineering optical control in a clinically relevant chimeric antigen receptor (CAR), we show that this limited signal persistence can be exploited to increase CAR-T cell activation threefold using pulsatile stimulation. Our results are likely to apply more generally to the signaling dynamics of other cellular networks.
Collapse
Affiliation(s)
- Michael J Harris
- Molecular Immunity UnitDepartment of MedicineMRC‐LMBUniversity of CambridgeCambridgeUK
| | - Muna Fuyal
- Division of Biomedical SciencesWarwick Medical SchoolUniversity of WarwickCoventryUK
| | - John R James
- Molecular Immunity UnitDepartment of MedicineMRC‐LMBUniversity of CambridgeCambridgeUK
- Division of Biomedical SciencesWarwick Medical SchoolUniversity of WarwickCoventryUK
| |
Collapse
|
6
|
Mumford TR, Roth L, Bugaj LJ. Reverse and Forward Engineering Multicellular Structures with Optogenetics. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2020; 16:61-71. [PMID: 33718689 PMCID: PMC7945718 DOI: 10.1016/j.cobme.2020.100250] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding how cells self-organize into functional higher-order structures is of great interest, both towards deciphering animal development, as well as for our ability to predictably build custom tissues to meet research and therapeutic needs. The proper organization of cells across length-scales results from interconnected and dynamic networks of molecules and cells. Optogenetic probes provide dynamic and tunable control over molecular events within cells, and thus represent a powerful approach to both dissect and control collective cell behaviors. Here we emphasize the breadth of the optogenetic toolkit and discuss how these methods have already been used to reverse-engineer the design rules of developing organisms. We also offer our perspective on the rich potential for optogenetics to power forward-engineering of tissue assembly towards the generation of bespoke tissues with user-defined properties.
Collapse
Affiliation(s)
- Thomas R. Mumford
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lee Roth
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| | - Lukasz J. Bugaj
- University of Pennsylvania, Department of Bioengineering, 240 Skirkanich Hall, 210 South 33 Street, Philadelphia, Pennsylvania, 19104, United States
| |
Collapse
|
7
|
Resonance energy transfer sensitises and monitors in situ switching of LOV2-based optogenetic actuators. Nat Commun 2020; 11:5107. [PMID: 33037199 PMCID: PMC7547724 DOI: 10.1038/s41467-020-18816-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/08/2020] [Indexed: 11/16/2022] Open
Abstract
Engineered light-dependent switches provide uniquely powerful opportunities to investigate and control cell regulatory mechanisms. Existing tools offer high spatiotemporal resolution, reversibility and repeatability. Cellular optogenetics applications remain limited with diffusible targets as the response of the actuator is difficult to independently validate. Blue light levels commonly needed for actuation can be cytotoxic, precluding long-term experiments. We describe a simple approach overcoming these obstacles. Resonance energy transfer can be used to constitutively or dynamically modulate actuation sensitivity. This simultaneously offers on-line monitoring of light-dependent switching and precise quantification of activation-relaxation properties in intact living cells. Applying this approach to different LOV2-based switches reveals that flanking sequences can lead to relaxation times up to 11-fold faster than anticipated. In situ–measured parameter values guide the design of target-inhibiting actuation trains with minimal blue-light exposure, and context-based optimisation can increase sensitivity and experimental throughput a further 10-fold without loss of temporal precision. Cellular optogenetics applications are limited by difficulties in quantification and blue light toxicity. Here the authors design LOV2-based switches that use resonance energy transfer to overcome these concerns.
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
An Optogenetic Method to Study Signal Transduction in Intestinal Stem Cell Homeostasis. J Mol Biol 2020; 432:3159-3176. [DOI: 10.1016/j.jmb.2020.03.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/09/2020] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
|
10
|
Levin M, Selberg J, Rolandi M. Endogenous Bioelectrics in Development, Cancer, and Regeneration: Drugs and Bioelectronic Devices as Electroceuticals for Regenerative Medicine. iScience 2019; 22:519-533. [PMID: 31837520 PMCID: PMC6920204 DOI: 10.1016/j.isci.2019.11.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/15/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
A major frontier in the post-genomic era is the investigation of the control of coordinated growth and three-dimensional form. Dynamic remodeling of complex organs in regulative embryogenesis, regeneration, and cancer reveals that cells and tissues make decisions that implement complex anatomical outcomes. It is now essential to understand not only the genetics that specifies cellular hardware but also the physiological software that implements tissue-level plasticity and robust morphogenesis. Here, we review recent discoveries about the endogenous mechanisms of bioelectrical communication among non-neural cells that enables them to cooperate in vivo. We discuss important advances in bioelectronics, as well as computational and pharmacological tools that are enabling the taming of biophysical controls toward applications in regenerative medicine and synthetic bioengineering.
Collapse
Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA.
| | - John Selberg
- Electrical and Computer Engineering Department, University of California, Santa Cruz, CA 95064, USA
| | - Marco Rolandi
- Electrical and Computer Engineering Department, University of California, Santa Cruz, CA 95064, USA
| |
Collapse
|
11
|
Levin M. The Computational Boundary of a "Self": Developmental Bioelectricity Drives Multicellularity and Scale-Free Cognition. Front Psychol 2019; 10:2688. [PMID: 31920779 PMCID: PMC6923654 DOI: 10.3389/fpsyg.2019.02688] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/14/2019] [Indexed: 12/12/2022] Open
Abstract
All epistemic agents physically consist of parts that must somehow comprise an integrated cognitive self. Biological individuals consist of subunits (organs, cells, and molecular networks) that are themselves complex and competent in their own native contexts. How do coherent biological Individuals result from the activity of smaller sub-agents? To understand the evolution and function of metazoan creatures' bodies and minds, it is essential to conceptually explore the origin of multicellularity and the scaling of the basal cognition of individual cells into a coherent larger organism. In this article, I synthesize ideas in cognitive science, evolutionary biology, and developmental physiology toward a hypothesis about the origin of Individuality: "Scale-Free Cognition." I propose a fundamental definition of an Individual based on the ability to pursue goals at an appropriate level of scale and organization and suggest a formalism for defining and comparing the cognitive capacities of highly diverse types of agents. Any Self is demarcated by a computational surface - the spatio-temporal boundary of events that it can measure, model, and try to affect. This surface sets a functional boundary - a cognitive "light cone" which defines the scale and limits of its cognition. I hypothesize that higher level goal-directed activity and agency, resulting in larger cognitive boundaries, evolve from the primal homeostatic drive of living things to reduce stress - the difference between current conditions and life-optimal conditions. The mechanisms of developmental bioelectricity - the ability of all cells to form electrical networks that process information - suggest a plausible set of gradual evolutionary steps that naturally lead from physiological homeostasis in single cells to memory, prediction, and ultimately complex cognitive agents, via scale-up of the basic drive of infotaxis. Recent data on the molecular mechanisms of pre-neural bioelectricity suggest a model of how increasingly sophisticated cognitive functions emerge smoothly from cell-cell communication used to guide embryogenesis and regeneration. This set of hypotheses provides a novel perspective on numerous phenomena, such as cancer, and makes several unique, testable predictions for interdisciplinary research that have implications not only for evolutionary developmental biology but also for biomedicine and perhaps artificial intelligence and exobiology.
Collapse
Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
| |
Collapse
|
12
|
Klorig DC, Alberto GE, Smith T, Godwin DW. Optogenetically-Induced Population Discharge Threshold as a Sensitive Measure of Network Excitability. eNeuro 2019; 6:ENEURO.0229-18.2019. [PMID: 31619450 PMCID: PMC6838688 DOI: 10.1523/eneuro.0229-18.2019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/06/2019] [Accepted: 09/27/2019] [Indexed: 12/21/2022] Open
Abstract
Network excitability is governed by synaptic efficacy, intrinsic excitability, and the circuitry in which these factors are expressed. The complex interplay between these factors determines how circuits function and, at the extreme, their susceptibility to seizure. We have developed a sensitive, quantitative estimate of network excitability in freely behaving mice using a novel optogenetic intensity-response procedure. Synchronous activation of deep sublayer CA1 pyramidal cells produces abnormal network-wide epileptiform population discharges (PDs) that are nearly indistinguishable from spontaneously-occurring interictal spikes (IISs). By systematically varying light intensity, and therefore the magnitude of the optogenetically-mediated current, we generated intensity-response curves using the probability of PD as the dependent variable. Manipulations known to increase excitability, such as sub-convulsive doses (20 mg/kg) of the chemoconvulsant pentylenetetrazol (PTZ), produced a leftward shift in the curve compared to baseline. The anti-epileptic drug levetiracetam (LEV; 40 mk/kg), in combination with PTZ, produced a rightward shift. Optogenetically-induced PD threshold (oPDT) baselines were stable over time, suggesting the metric is appropriate for within-subject experimental designs with multiple pharmacological manipulations.
Collapse
Affiliation(s)
- D C Klorig
- Department of Neurobiology and Anatomy
- Neuroscience Program
| | - G E Alberto
- Department of Neurobiology and Anatomy
- Neuroscience Program
| | - T Smith
- Department of Neurobiology and Anatomy
| | - D W Godwin
- Department of Neurobiology and Anatomy
- Neuroscience Program
- Department of Physiology and Pharmacology, Wake Forest University, Winston-Salem, NC
| |
Collapse
|
13
|
Sweeney K, Moreno Morales N, Burmeister Z, Nimunkar AJ, McClean MN. Easy calibration of the Light Plate Apparatus for optogenetic experiments. MethodsX 2019; 6:1480-1488. [PMID: 31293905 PMCID: PMC6594922 DOI: 10.1016/j.mex.2019.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 06/11/2019] [Indexed: 11/16/2022] Open
Abstract
Optogenetic systems use genetically-encoded light-sensitive proteins to control and study cellular processes. As the number and quality of these systems grows, there is an increasing need for user-friendly and flexible hardware to provide programmed illumination to cultures of cells. One platform which satisfies this need for a variety of optogenetic systems and organisms is the Light Plate Apparatus (LPA), which delivers a controlled light dose to each well of a 24-well plate. Experimental reproducibility requires appropriate calibration to produce accurate light doses within individual wells of the LPA and between LPAs. In this study, we present an easy and accurate method for calibrating the LPA. In particular, we: •developed a 3D printed adaptor and MATLAB code to allow rapid measurement of irradiance produced by the LPA and subsequent calibration•provide appropriate code and methodology for generating a standard curve for each LPA•demonstrate the utility and accuracy of this method between users and LPAs.
Collapse
Affiliation(s)
| | | | | | | | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, United States
| |
Collapse
|
14
|
Morphogenesis as Bayesian inference: A variational approach to pattern formation and control in complex biological systems. Phys Life Rev 2019; 33:88-108. [PMID: 31320316 DOI: 10.1016/j.plrev.2019.06.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 12/11/2022]
Abstract
Recent advances in molecular biology such as gene editing [1], bioelectric recording and manipulation [2] and live cell microscopy using fluorescent reporters [3], [4] - especially with the advent of light-controlled protein activation through optogenetics [5] - have provided the tools to measure and manipulate molecular signaling pathways with unprecedented spatiotemporal precision. This has produced ever increasing detail about the molecular mechanisms underlying development and regeneration in biological organisms. However, an overarching concept - that can predict the emergence of form and the robust maintenance of complex anatomy - is largely missing in the field. Classic (i.e., dynamic systems and analytical mechanics) approaches such as least action principles are difficult to use when characterizing open, far-from equilibrium systems that predominate in Biology. Similar issues arise in neuroscience when trying to understand neuronal dynamics from first principles. In this (neurobiology) setting, a variational free energy principle has emerged based upon a formulation of self-organization in terms of (active) Bayesian inference. The free energy principle has recently been applied to biological self-organization beyond the neurosciences [6], [7]. For biological processes that underwrite development or regeneration, the Bayesian inference framework treats cells as information processing agents, where the driving force behind morphogenesis is the maximization of a cell's model evidence. This is realized by the appropriate expression of receptors and other signals that correspond to the cell's internal (i.e., generative) model of what type of receptors and other signals it should express. The emerging field of the free energy principle in pattern formation provides an essential quantitative formalism for understanding cellular decision-making in the context of embryogenesis, regeneration, and cancer suppression. In this paper, we derive the mathematics behind Bayesian inference - as understood in this framework - and use simulations to show that the formalism can reproduce experimental, top-down manipulations of complex morphogenesis. First, we illustrate this 'first principle' approach to morphogenesis through simulated alterations of anterior-posterior axial polarity (i.e., the induction of two heads or two tails) as in planarian regeneration. Then, we consider aberrant signaling and functional behavior of a single cell within a cellular ensemble - as a first step in carcinogenesis as false 'beliefs' about what a cell should 'sense' and 'do'. We further show that simple modifications of the inference process can cause - and rescue - mis-patterning of developmental and regenerative events without changing the implicit generative model of a cell as specified, for example, by its DNA. This formalism offers a new road map for understanding developmental change in evolution and for designing new interventions in regenerative medicine settings.
Collapse
|
15
|
Manicka S, Levin M. The Cognitive Lens: a primer on conceptual tools for analysing information processing in developmental and regenerative morphogenesis. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180369. [PMID: 31006373 PMCID: PMC6553590 DOI: 10.1098/rstb.2018.0369] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2018] [Indexed: 12/31/2022] Open
Abstract
Brains exhibit plasticity, multi-scale integration of information, computation and memory, having evolved by specialization of non-neural cells that already possessed many of the same molecular components and functions. The emerging field of basal cognition provides many examples of decision-making throughout a wide range of non-neural systems. How can biological information processing across scales of size and complexity be quantitatively characterized and exploited in biomedical settings? We use pattern regulation as a context in which to introduce the Cognitive Lens-a strategy using well-established concepts from cognitive and computer science to complement mechanistic investigation in biology. To facilitate the assimilation and application of these approaches across biology, we review tools from various quantitative disciplines, including dynamical systems, information theory and least-action principles. We propose that these tools can be extended beyond neural settings to predict and control systems-level outcomes, and to understand biological patterning as a form of primitive cognition. We hypothesize that a cognitive-level information-processing view of the functions of living systems can complement reductive perspectives, improving efficient top-down control of organism-level outcomes. Exploration of the deep parallels across diverse quantitative paradigms will drive integrative advances in evolutionary biology, regenerative medicine, synthetic bioengineering, cognitive neuroscience and artificial intelligence. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.
Collapse
Affiliation(s)
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA
| |
Collapse
|
16
|
Zi Z. Molecular Engineering of the TGF-β Signaling Pathway. J Mol Biol 2019; 431:2644-2654. [PMID: 31121181 DOI: 10.1016/j.jmb.2019.05.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/05/2019] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
Transforming growth factor beta (TGF-β) is an important growth factor that plays essential roles in regulating tissue development and homeostasis. Dysfunction of TGF-β signaling is a hallmark of many human diseases. Therefore, targeting TGF-β signaling presents broad therapeutic potential. Since the discovery of the TGF-β ligand, a collection of engineered signaling proteins have been developed to probe and manipulate TGF-β signaling responses. In this review, we highlight recent progress in the engineering of TGF-β signaling for different applications and discuss how molecular engineering approaches can advance our understanding of this important pathway. In addition, we provide a future outlook on the opportunities and challenges in the engineering of the TGF-β signaling pathway from a quantitative perspective.
Collapse
Affiliation(s)
- Zhike Zi
- Otto-Warburg Laboratory, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
| |
Collapse
|
17
|
Levin M, Pietak AM, Bischof J. Planarian regeneration as a model of anatomical homeostasis: Recent progress in biophysical and computational approaches. Semin Cell Dev Biol 2019; 87:125-144. [PMID: 29635019 PMCID: PMC6234102 DOI: 10.1016/j.semcdb.2018.04.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 12/22/2022]
Abstract
Planarian behavior, physiology, and pattern control offer profound lessons for regenerative medicine, evolutionary biology, morphogenetic engineering, robotics, and unconventional computation. Despite recent advances in the molecular genetics of stem cell differentiation, this model organism's remarkable anatomical homeostasis provokes us with truly fundamental puzzles about the origin of large-scale shape and its relationship to the genome. In this review article, we first highlight several deep mysteries about planarian regeneration in the context of the current paradigm in this field. We then review recent progress in understanding of the physiological control of an endogenous, bioelectric pattern memory that guides regeneration, and how modulating this memory can permanently alter the flatworm's target morphology. Finally, we focus on computational approaches that complement reductive pathway analysis with synthetic, systems-level understanding of morphological decision-making. We analyze existing models of planarian pattern control and highlight recent successes and remaining knowledge gaps in this interdisciplinary frontier field.
Collapse
Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, United States; Biology Department, Tufts University, Medford, MA 02155, United States.
| | - Alexis M Pietak
- Allen Discovery Center at Tufts University, Medford, MA 02155, United States
| | - Johanna Bischof
- Allen Discovery Center at Tufts University, Medford, MA 02155, United States; Biology Department, Tufts University, Medford, MA 02155, United States
| |
Collapse
|
18
|
Kamm RD, Bashir R, Arora N, Dar RD, Gillette MU, Griffith LG, Kemp ML, Kinlaw K, Levin M, Martin AC, McDevitt TC, Nerem RM, Powers MJ, Saif TA, Sharpe J, Takayama S, Takeuchi S, Weiss R, Ye K, Yevick HG, Zaman MH. Perspective: The promise of multi-cellular engineered living systems. APL Bioeng 2018; 2:040901. [PMID: 31069321 PMCID: PMC6481725 DOI: 10.1063/1.5038337] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/18/2018] [Indexed: 12/31/2022] Open
Abstract
Recent technological breakthroughs in our ability to derive and differentiate induced pluripotent stem cells, organoid biology, organ-on-chip assays, and 3-D bioprinting have all contributed to a heightened interest in the design, assembly, and manufacture of living systems with a broad range of potential uses. This white paper summarizes the state of the emerging field of "multi-cellular engineered living systems," which are composed of interacting cell populations. Recent accomplishments are described, focusing on current and potential applications, as well as barriers to future advances, and the outlook for longer term benefits and potential ethical issues that need to be considered.
Collapse
Affiliation(s)
- Roger D. Kamm
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Rashid Bashir
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | - Natasha Arora
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Roy D. Dar
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | | | - Linda G. Griffith
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Melissa L. Kemp
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | | | | | - Adam C. Martin
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | | | - Robert M. Nerem
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Mark J. Powers
- Thermo Fisher Scientific, Frederick, Maryland 21704, USA
| | - Taher A. Saif
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61820, USA
| | - James Sharpe
- EMBL Barcelona, European Molecular Biology Laboratory, Barcelona 08003, Spain
| | | | | | - Ron Weiss
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | - Kaiming Ye
- Binghamton University, Binghamton, New York 13902, USA
| | - Hannah G. Yevick
- Massachusetts Institute of Technology, Boston, Massachusetts 02139, USA
| | | |
Collapse
|
19
|
Bugaj LJ, Sabnis AJ, Mitchell A, Garbarino JE, Toettcher JE, Bivona TG, Lim WA. Cancer mutations and targeted drugs can disrupt dynamic signal encoding by the Ras-Erk pathway. Science 2018; 361:361/6405/eaao3048. [PMID: 30166458 DOI: 10.1126/science.aao3048] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 07/16/2018] [Indexed: 12/16/2022]
Abstract
The Ras-Erk (extracellular signal-regulated kinase) pathway encodes information in its dynamics; the duration and frequency of Erk activity can specify distinct cell fates. To enable dynamic encoding, temporal information must be accurately transmitted from the plasma membrane to the nucleus. We used optogenetic profiling to show that both oncogenic B-Raf mutations and B-Raf inhibitors can cause corruption of this transmission, so that short pulses of input Ras activity are distorted into abnormally long Erk outputs. These changes can reshape downstream transcription and cell fates, resulting in improper decisions to proliferate. These findings illustrate how altered dynamic signal transmission properties, and not just constitutively increased signaling, can contribute to cell proliferation and perhaps cancer, and how optogenetic profiling can dissect mechanisms of signaling dysfunction in disease.
Collapse
Affiliation(s)
- L J Bugaj
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - A J Sabnis
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - A Mitchell
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - J E Garbarino
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - J E Toettcher
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - T G Bivona
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - W A Lim
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA.,Center for Systems and Synthetic Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
20
|
Zhou X, Wang J, Chen J, Qi Y, Di Nan, Jin L, Qian X, Wang X, Chen Q, Liu X, Xu Y. Optogenetic control of epithelial-mesenchymal transition in cancer cells. Sci Rep 2018; 8:14098. [PMID: 30237527 PMCID: PMC6147862 DOI: 10.1038/s41598-018-32539-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 08/21/2018] [Indexed: 12/20/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is one of the most important mechanisms in the initiation and promotion of cancer cell metastasis. The phosphoinositide 3-kinase (PI3K) signaling pathway has been demonstrated to be involved in TGF-β induced EMT, but the complicated TGF-β signaling network makes it challenging to dissect the important role of PI3K on regulation of EMT process. Here, we applied optogenetic controlled PI3K module (named ‘Opto-PI3K’), which based on CRY2 and the N-terminal of CIB1 (CIBN), to rapidly and reversibly control the endogenous PI3K activity in cancer cells with light. By precisely modulating the kinetics of PI3K activation, we found that E-cadherin is an important downstream target of PI3K signaling. Compared with TGF-β treatment, Opto-PI3K had more potent effect in down-regulation of E-cadherin expression, which was demonstrated to be regulated in a light dose-dependent manner. Surprisingly, sustained PI3K activation induced partial EMT state in A549 cells that is highly reversible. Furthermore, we demonstrated that Opto-PI3K only partially mimicked TGF-β effects on promotion of cell migration in vitro. These results reveal the importance of PI3K signaling in TGF-β induced EMT, suggesting other TGF-β regulated signaling pathways are necessary for the full and irreversible promotion of EMT in cancer cells. In addition, our study implicates the great promise of optogenetics in cancer research for mapping input-output relationships in oncogenic pathways.
Collapse
Affiliation(s)
- Xiaoxu Zhou
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China
| | - Jian Wang
- Department of Respiratory Oncology, The 117th Hospital of PLA, Hangzhou, 310013, China
| | - Junye Chen
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China.,Department of Hepatobiliary and Pancreatic Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310009, China
| | - Yuankai Qi
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China
| | - Di Nan
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China
| | - Luhong Jin
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China
| | - Xiaohan Qian
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China
| | - Xinyi Wang
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China
| | - Qingyong Chen
- Department of Respiratory Oncology, The 117th Hospital of PLA, Hangzhou, 310013, China.
| | - Xu Liu
- Department of Optical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou, 310027, China
| | - Yingke Xu
- Department of Biomedical Engineering, Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China. .,Department of Endocrinology, The Affiliated Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
| |
Collapse
|
21
|
Mathews J, Levin M. The body electric 2.0: recent advances in developmental bioelectricity for regenerative and synthetic bioengineering. Curr Opin Biotechnol 2018; 52:134-144. [PMID: 29684787 PMCID: PMC10464502 DOI: 10.1016/j.copbio.2018.03.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/23/2018] [Indexed: 12/18/2022]
Abstract
Breakthroughs in biomedicine and synthetic bioengineering require predictive, rational control over anatomical structure and function. Recent successes in manipulating cellular and molecular hardware have not been matched by progress in understanding the patterning software implemented during embryogenesis and regeneration. A fundamental capability gap is driving desired changes in growth and form to address birth defects and traumatic injury. Here we review new tools, results, and conceptual advances in an exciting emerging field: endogenous non-neural bioelectric signaling, which enables cellular collectives to make global decisions and implement large-scale pattern homeostasis. Spatially distributed electric circuits regulate gene expression, organ morphogenesis, and body-wide axial patterning. Developmental bioelectricity facilitates the interface to organ-level modular control points that direct patterning in vivo. Cracking the bioelectric code will enable transformative progress in bioengineering and regenerative medicine.
Collapse
Affiliation(s)
- Juanita Mathews
- Biology Department, and Allen Discovery Center at Tufts University, Medford, MA 02155, United States
| | - Michael Levin
- Biology Department, and Allen Discovery Center at Tufts University, Medford, MA 02155, United States.
| |
Collapse
|
22
|
Benedetti L, Barentine AES, Messa M, Wheeler H, Bewersdorf J, De Camilli P. Light-activated protein interaction with high spatial subcellular confinement. Proc Natl Acad Sci U S A 2018; 115:E2238-E2245. [PMID: 29463750 PMCID: PMC5877946 DOI: 10.1073/pnas.1713845115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Methods to acutely manipulate protein interactions at the subcellular level are powerful tools in cell biology. Several blue-light-dependent optical dimerization tools have been developed. In these systems one protein component of the dimer (the bait) is directed to a specific subcellular location, while the other component (the prey) is fused to the protein of interest. Upon illumination, binding of the prey to the bait results in its subcellular redistribution. Here, we compared and quantified the extent of light-dependent dimer occurrence in small, subcellular volumes controlled by three such tools: Cry2/CIB1, iLID, and Magnets. We show that both the location of the photoreceptor protein(s) in the dimer pair and its (their) switch-off kinetics determine the subcellular volume where dimer formation occurs and the amount of protein recruited in the illuminated volume. Efficient spatial confinement of dimer to the area of illumination is achieved when the photosensitive component of the dimerization pair is tethered to the membrane of intracellular compartments and when on and off kinetics are extremely fast, as achieved with iLID or Magnets. Magnets and the iLID variants with the fastest switch-off kinetics induce and maintain protein dimerization in the smallest volume, although this comes at the expense of the total amount of dimer. These findings highlight the distinct features of different optical dimerization systems and will be useful guides in the choice of tools for specific applications.
Collapse
Affiliation(s)
- Lorena Benedetti
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Andrew E S Barentine
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520
| | - Mirko Messa
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Heather Wheeler
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510
- Nanobiology Institute, Yale University, West Haven, CT 06516
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510;
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06510
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510
| |
Collapse
|
23
|
Li Y, Lee M, Kim N, Wu G, Deng D, Kim JM, Liu X, Heo WD, Zi Z. Spatiotemporal Control of TGF-β Signaling with Light. ACS Synth Biol 2018; 7:443-451. [PMID: 29241005 DOI: 10.1021/acssynbio.7b00225] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells employ signaling pathways to make decisions in response to changes in their immediate environment. Transforming growth factor beta (TGF-β) is an important growth factor that regulates many cellular functions in development and disease. Although the molecular mechanisms of TGF-β signaling have been well studied, our understanding of this pathway is limited by the lack of tools that allow the control of TGF-β signaling with high spatiotemporal resolution. Here, we developed an optogenetic system (optoTGFBRs) that enables the precise control of TGF-β signaling in time and space. Using the optoTGFBRs system, we show that TGF-β signaling can be selectively and sequentially activated in single cells through the modulation of the pattern of light stimulations. By simultaneously monitoring the subcellular localization of TGF-β receptor and Smad2 proteins, we characterized the dynamics of TGF-β signaling in response to different patterns of blue light stimulations. The spatial and temporal precision of light control will make the optoTGFBRs system as a powerful tool for quantitative analyses of TGF-β signaling at the single cell level.
Collapse
Affiliation(s)
- Yuchao Li
- Otto-Warburg
Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Minji Lee
- Department
of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Nury Kim
- Center
for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Guoyu Wu
- Otto-Warburg
Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Difan Deng
- Otto-Warburg
Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Jin Man Kim
- Department
of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Xuedong Liu
- Department
of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309-0596, United States
| | - Won Do Heo
- Department
of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Center
for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
- KAIST
Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Zhike Zi
- Otto-Warburg
Laboratory, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| |
Collapse
|
24
|
Levin M, Martyniuk CJ. The bioelectric code: An ancient computational medium for dynamic control of growth and form. Biosystems 2018; 164:76-93. [PMID: 28855098 PMCID: PMC10464596 DOI: 10.1016/j.biosystems.2017.08.009] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/20/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022]
Abstract
What determines large-scale anatomy? DNA does not directly specify geometrical arrangements of tissues and organs, and a process of encoding and decoding for morphogenesis is required. Moreover, many species can regenerate and remodel their structure despite drastic injury. The ability to obtain the correct target morphology from a diversity of initial conditions reveals that the morphogenetic code implements a rich system of pattern-homeostatic processes. Here, we describe an important mechanism by which cellular networks implement pattern regulation and plasticity: bioelectricity. All cells, not only nerves and muscles, produce and sense electrical signals; in vivo, these processes form bioelectric circuits that harness individual cell behaviors toward specific anatomical endpoints. We review emerging progress in reading and re-writing anatomical information encoded in bioelectrical states, and discuss the approaches to this problem from the perspectives of information theory, dynamical systems, and computational neuroscience. Cracking the bioelectric code will enable much-improved control over biological patterning, advancing basic evolutionary developmental biology as well as enabling numerous applications in regenerative medicine and synthetic bioengineering.
Collapse
Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Biology Department, Tufts University, 200 Boston Avenue, Suite 4600 Medford, MA 02155, USA.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| |
Collapse
|
25
|
Pezzulo G, Levin M. Embodying Markov blankets: Comment on "Answering Schrödinger's question: A free-energy formulation" by Maxwell James Désormeau Ramstead et al. Phys Life Rev 2017; 24:32-36. [PMID: 29191410 DOI: 10.1016/j.plrev.2017.11.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Giovanni Pezzulo
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy.
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, United States
| |
Collapse
|
26
|
Arocena M, Rajnicek AM, Collinson JM. Requirement of Pax6 for the integration of guidance cues in cell migration. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170625. [PMID: 29134074 PMCID: PMC5666257 DOI: 10.1098/rsos.170625] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/05/2017] [Indexed: 05/19/2023]
Abstract
The intricate patterns of cell migration that are found throughout development are generated through a vast array of guidance cues. Responding integratively to distinct, often conflicting, migratory signals is probably crucial for cells to reach their correct destination. Pax6 is a master transcription factor with key roles in neural development that include the control of cell migration. In this study, we have investigated the ability of cells derived from cortical neurospheres from wild-type (WT) and Pax6-/- mouse embryos to integrate diverging guidance cues. We used two different cues, either separately or in combination: substratum nanogrooves to induce contact guidance, and electric fields (EFs) to induce electrotaxis. In the absence of an EF, both WT and Pax6-/- cells aligned and migrated parallel to grooves, and on a flat substrate both showed marked electrotaxis towards the cathode. When an EF was applied in a perpendicular orientation to grooves, WT cells responded significantly to both cues, migrating in highly oblique trajectories in the general direction of the cathode. However, Pax6-/- cells had an impaired response to both cues simultaneously. Our results demonstrate that these neurosphere derived cells have the capacity to integrate diverging guidance cues, which requires Pax6 function.
Collapse
Affiliation(s)
- Miguel Arocena
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
- Facultad de Ciencias, UDELAR, Montevideo, Uruguay
- Authors for correspondence: Miguel Arocena e-mail:
| | - Ann M. Rajnicek
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Jon Martin Collinson
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
- Authors for correspondence: Jon Martin Collinson e-mail:
| |
Collapse
|
27
|
Arocena M, Rajnicek AM, Collinson JM. Requirement of Pax6 for the integration of guidance cues in cell migration. ROYAL SOCIETY OPEN SCIENCE 2017. [PMID: 29134074 DOI: 10.5061/dryad.53512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The intricate patterns of cell migration that are found throughout development are generated through a vast array of guidance cues. Responding integratively to distinct, often conflicting, migratory signals is probably crucial for cells to reach their correct destination. Pax6 is a master transcription factor with key roles in neural development that include the control of cell migration. In this study, we have investigated the ability of cells derived from cortical neurospheres from wild-type (WT) and Pax6-/- mouse embryos to integrate diverging guidance cues. We used two different cues, either separately or in combination: substratum nanogrooves to induce contact guidance, and electric fields (EFs) to induce electrotaxis. In the absence of an EF, both WT and Pax6-/- cells aligned and migrated parallel to grooves, and on a flat substrate both showed marked electrotaxis towards the cathode. When an EF was applied in a perpendicular orientation to grooves, WT cells responded significantly to both cues, migrating in highly oblique trajectories in the general direction of the cathode. However, Pax6-/- cells had an impaired response to both cues simultaneously. Our results demonstrate that these neurosphere derived cells have the capacity to integrate diverging guidance cues, which requires Pax6 function.
Collapse
Affiliation(s)
- Miguel Arocena
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
- Facultad de Ciencias, UDELAR, Montevideo, Uruguay
| | - Ann M Rajnicek
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | | |
Collapse
|
28
|
Moore D, Walker SI, Levin M. Cancer as a disorder of patterning information: computational and biophysical perspectives on the cancer problem. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2017. [DOI: 10.1088/2057-1739/aa8548] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|