- 标题
- 摘要
- 关键词
- 实验方案
- 产品
-
Designing bacterial chemotactic receptors guided by photonic femtoliter well arrays for quantifiable, label-free measurement of bacterial chemotaxis
摘要： Whole cell bioreporters, such as bacterial cells, can be used for environmental and clinical sensing of specific analytes. However, the current methods implemented to observe such bioreporters in the form of chemotactic responses heavily rely on microscope analysis, fluorescent labels, and hard-to-scale microfluidic devices. Herein, we demonstrate that chemotaxis can be detected within minutes using intrinsic optical measurements of silicon femtoliter well arrays (FMAs). This is done via phase-shift reflectometric interference spectroscopic measurements (PRISM) of the wells, which act as silicon diffraction gratings, enabling label-free, real-time quantification of the number of trapped bacteria cells in the optical readout. By generating unsteady chemical gradients over the wells, we first demonstrate that chemotaxis towards attractants and away from repellents can be easily differentiated based on the signal response of PRISM. The lowest concentration of chemorepellent to elicit an observed bacterial response was 50 mM, while the lowest concentration of chemoattractant to elicit a response was 10 mM. Second, we employed PRISM, in combination with a computational approach, to rapidly scan for and identify a novel synthetic histamine chemoreceptor strain. Consequently, we show that by using a combined computational design approach, together with a quantitative, real-time, and label-free detection method, it is possible to manufacture and characterize novel synthetic chemoreceptors in Escherichia coli (E. coli).
关键词： diffraction,synthetic biology,optical biosensor,chemotaxis,microstructures
更新于2025-09-23 15:23:52
-
Characterization and engineering of photoactivated adenylyl cyclases
摘要： Cyclic nucleoside monophosphates (cNMP) serve as universal second messengers in signal transduction across prokaryotes and eukaryotes. As signaling often relies on transiently formed microdomains of elevated second messenger concentration, means to precisely perturb the spatiotemporal dynamics of cNMPs are uniquely poised for the interrogation of the underlying physiological processes. Optogenetics appears particularly suited as it affords light-dependent, accurate control in time and space of diverse cellular processes. Several sensory photoreceptors function as photoactivated adenylyl cyclases (PAC) and hence serve as light-regulated actuators for the control of intracellular levels of 3′, 5′-cyclic adenosine monophosphate. To characterize PACs and to refine their properties, we devised a test bed for the facile analysis of these photoreceptors. Cyclase activity is monitored in bacterial cells via expression of a fluorescent reporter, and programmable illumination allows the rapid exploration of multiple lighting regimes. We thus probed two PACs responding to blue and red light, respectively, and observed significant dark activity for both. We next engineered derivatives of the red-light-sensitive PAC with altered responses to light, with one variant, denoted DdPAC, showing enhanced response to light. These PAC variants stand to enrich the optogenetic toolkit and thus facilitate the detailed analysis of cNMP metabolism and signaling.
关键词： synthetic biology,phytochrome,sensory photoreceptor,adenylyl cyclase,BLUF,optogenetics
更新于2025-09-23 15:22:29
-
[IEEE 2019 16th China International Forum on Solid State Lighting & 2019 International Forum on Wide Bandgap Semiconductors China (SSLChina: IFWS) - Shenzhen, China (2019.11.25-2019.11.27)] 2019 16th China International Forum on Solid State Lighting & 2019 International Forum on Wide Bandgap Semiconductors China (SSLChina: IFWS) - Review of High Power Phosphor-Converted Light-Emitting Diodes
摘要： The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic design automation tools. The latest version of the standard, SBOL 2.0, enables the annotation of a large variety of biological components (e.g., DNA, RNA, proteins, complexes, small molecules, etc.) and their interactions. SBOL 2.0 also allows researchers to organize components into hierarchical modules, to specify their intended functions, and to link modules to models that describe their behavior mathematically. To support the use of SBOL 2.0, we have developed the libSBOLj 2.0 Java library, which provides an easy to use Application Programming Interface (API) for developers, including manipulation of SBOL constructs, serialization to and from an RDF/XML file format, and migration support in the form of conversion from the prior SBOL 1.1 standard to SBOL 2.0. This letter describes the libSBOLj 2.0 library and key engineering decisions involved in its design.
关键词： software tools,synthetic biology,computational biology,Application programming interfaces,software libraries
更新于2025-09-23 15:19:57
-
A Dual Polarized Magneto-Electric Dipole Antenna Based on Printed Ridge Gap Waveguide Technology
摘要： We review the field of synthetic biology from an analog circuits and analog computation perspective, focusing on circuits that have been built in living cells. This perspective is well suited to pictorially, symbolically, and quantitatively representing the nonlinear, dynamic, and stochastic (noisy) ordinary and partial differential equations that rigorously describe the molecular circuits of synthetic biology. This perspective enables us to construct a canonical analog circuit schematic that helps unify and review the operation of many fundamental circuits that have been built in synthetic biology at the DNA, RNA, protein, and small-molecule levels over nearly two decades. We review 17 circuits in the literature as particular examples of feedforward and feedback analog circuits that arise from special topological cases of the canonical analog circuit schematic. Digital circuit operation of these circuits represents a special case of saturated analog circuit behavior and is automatically incorporated as well. Many issues that have prevented synthetic biology from scaling are naturally represented in analog circuit schematics. Furthermore, the deep similarity between the Boltzmann thermodynamic equations that describe noisy electronic current flow in subthreshold transistors and noisy molecular flux in biochemical reactions has helped map analog circuit motifs in electronics to analog circuit motifs in cells and vice versa via a 'cytomorphic' approach. Thus, a body of knowledge in analog electronic circuit design, analysis, simulation, and implementation may also be useful in the robust and efficient design of molecular circuits in synthetic biology, helping it to scale to more complex circuits in the future.
关键词： feedback,resource consumption,cytomorphic,cellular engineering,biological circuit design,synthetic biology analog computation,Analog circuits,review
更新于2025-09-23 15:19:57
-
[IEEE 2019 IEEE 13th International Conference on Power Electronics and Drive Systems (PEDS) - Toulouse, France (2019.7.9-2019.7.12)] 2019 IEEE 13th International Conference on Power Electronics and Drive Systems (PEDS) - A Novel Fast-Switching SOI LIGBT with Anode Junction Paralleled by a Diode
摘要： Bacterial plasmids employ copy number control systems to ensure that they do not overburden their hosts. Plasmid incompatibility is caused by shared components of copy number control systems, resulting in mutual inhibition of replication. Incompatible plasmids cannot be stably maintained within a host cell. Unilateral incompatibility, in which the plasmid replicons are compatible but one plasmid encodes for the replication inhibitor of the other, leads to rapid displacement of the inhibited plasmid. Thus, we propose that the unilateral incompatibility can be used to eradicate an undesirable plasmid from a population. To investigate this process, we developed deterministic and stochastic models of plasmid dynamics. An analysis of these models provides predictions about the efficacy of plasmid displacement.
关键词： Biological system modeling,genetic engineering,synthetic biology
更新于2025-09-23 15:19:57
-
[IEEE 2018 IEEE 8th International Conference Nanomaterials: Application & Properties (NAP) - Zatoka, Ukraine (2018.9.9-2018.9.14)] 2018 IEEE 8th International Conference Nanomaterials: Application & Properties (NAP) - Silicon Hyperdoped with Selenium by Ion Implantation Followed by Pulsed Laser Annealing
摘要： The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic design automation tools. The latest version of the standard, SBOL 2.0, enables the annotation of a large variety of biological components (e.g., DNA, RNA, proteins, complexes, small molecules, etc.) and their interactions. SBOL 2.0 also allows researchers to organize components into hierarchical modules, to specify their intended functions, and to link modules to models that describe their behavior mathematically. To support the use of SBOL 2.0, we have developed the libSBOLj 2.0 Java library, which provides an easy to use Application Programming Interface (API) for developers, including manipulation of SBOL constructs, serialization to and from an RDF/XML file format, and migration support in the form of conversion from the prior SBOL 1.1 standard to SBOL 2.0. This letter describes the libSBOLj 2.0 library and key engineering decisions involved in its design.
关键词： software tools,synthetic biology,computational biology,Application programming interfaces,software libraries
更新于2025-09-19 17:13:59
-
[IEEE 2019 IEEE CPMT Symposium Japan (ICSJ) - Kyoto, Japan (2019.11.18-2019.11.20)] 2019 IEEE CPMT Symposium Japan (ICSJ) - Effect of Sidewall Roughness on Polymer Waveguide for Optical Interconnects Application
摘要： The Synthetic Biology Open Language (SBOL) is an emerging data standard for representing synthetic biology designs. The goal of SBOL is to improve the reproducibility of these designs and their electronic exchange between researchers and/or genetic design automation tools. The latest version of the standard, SBOL 2.0, enables the annotation of a large variety of biological components (e.g., DNA, RNA, proteins, complexes, small molecules, etc.) and their interactions. SBOL 2.0 also allows researchers to organize components into hierarchical modules, to specify their intended functions, and to link modules to models that describe their behavior mathematically. To support the use of SBOL 2.0, we have developed the libSBOLj 2.0 Java library, which provides an easy to use Application Programming Interface (API) for developers, including manipulation of SBOL constructs, serialization to and from an RDF/XML file format, and migration support in the form of conversion from the prior SBOL 1.1 standard to SBOL 2.0. This letter describes the libSBOLj 2.0 library and key engineering decisions involved in its design.
关键词： software tools,synthetic biology,computational biology,Application programming interfaces,software libraries
更新于2025-09-19 17:13:59
-
Off-colony screening of biosynthetic libraries by rapid laser-enabled mass spectrometry
摘要： Leveraging advances in DNA synthesis and molecular cloning techniques, synthetic biology increasingly makes use of large construct libraries to explore large design spaces. For biosynthetic pathway engineering the ability to screen these libraries for a variety of metabolites of interest is essential. If the metabolite of interest or the metabolic phenotype is not easily measurable, screening soon becomes a major bottleneck involving time-consuming culturing, sample preparation, and extraction. To address this, we demonstrate the use of automated Laser-Assisted Rapid Evaporative Ionisation Mass Spectrometry (LA-REIMS) – a form of ambient laser desorption ionisation mass spectrometry – to perform rapid mass spectrometry analysis direct from agar plate yeast colonies without sample preparation or extraction. We use LA-REIMS to assess production levels of violacein and betulinic acid directly from yeast colonies at a rate of 6 colonies per minute. We then demonstrate the throughput enabled by LA-REIMS by screening over 450 yeast colonies in under 4 hours, while simultaneously generating recoverable glycerol stocks of each colony in real-time. This showcases LA-REIMS as a pre-screening tool to complement downstream quantification methods such as LCMS. Through pre-screening several hundred colonies with LA-REIMS, we successfully isolate and verify a strain with a 2.5-fold improvement in betulinic acid production. Finally, we show that LA-REIMS can detect 20 out of a panel of 27 diverse biological molecules, demonstrating the broad applicability of LA-REIMS to metabolite detection. The rapid and automated nature of LA-REIMS makes this a valuable new technology to complement existing screening technologies currently employed in academic and industrial workflows.
关键词： synthetic biology,metabolic engineering,REIMS,ambient mass spectrometry,high throughput screening
更新于2025-09-19 17:13:59
-
[IEEE 2019 IEEE 46th Photovoltaic Specialists Conference (PVSC) - Chicago, IL, USA (2019.6.16-2019.6.21)] 2019 IEEE 46th Photovoltaic Specialists Conference (PVSC) - Increased Power Output of Thin Film GaAs Solar Cells on Flexible Metal Substrates Using PDMS Microconcentrators
摘要： Bacterial plasmids employ copy number control systems to ensure that they do not overburden their hosts. Plasmid incompatibility is caused by shared components of copy number control systems, resulting in mutual inhibition of replication. Incompatible plasmids cannot be stably maintained within a host cell. Unilateral incompatibility, in which the plasmid replicons are compatible but one plasmid encodes for the replication inhibitor of the other, leads to rapid displacement of the inhibited plasmid. Thus, we propose that the unilateral incompatibility can be used to eradicate an undesirable plasmid from a population. To investigate this process, we developed deterministic and stochastic models of plasmid dynamics. An analysis of these models provides predictions about the efficacy of plasmid displacement.
关键词： Biological system modeling,genetic engineering,synthetic biology
更新于2025-09-19 17:13:59
-
[IEEE 2019 IEEE 46th Photovoltaic Specialists Conference (PVSC) - Chicago, IL, USA (2019.6.16-2019.6.21)] 2019 IEEE 46th Photovoltaic Specialists Conference (PVSC) - Correlation of advanced accelerated stress testing with polyamide-based photovoltaic backsheet field-failures
摘要： Patients have been known to regain consciousness during surgery while still paralyzed by the anesthesia and unable to communicate their distress. Recently, electronic engineers have helped resolve this problem by improving the real-time monitoring of depth of anesthesia. Electronic measurements of the brain’s activity are used for many clinical and research purposes. This is possible because the brain uses electrochemical phenomena in order to process data. Many researchers have taken this to mean that advances in computer science will eventually result in sentient computers. Some con?ate arti?cial consciousness with arti?cial intelligence even though consciousness and intelligence are not positively correlated. Those not trained in neurology, or at least medicine, understandably fail to comprehend what the rich, complex word ‘‘consciousness’’ actually means as a term of art. Human consciousness can only be evaluated with surrogate markers and is a broad and complex spectrum that ranges from minimally conscious to waking consciousness (what the reader is experiencing right now). The necessary conditions for waking consciousness include a brain in just the right electrical, chemical, and thermal states with suf?cient blood pressure. These conditions, in turn, require the brain to have a body that is maintained in the right environment. Hence, waking consciousness is a proper subset of spectrum consciousness and cannot be considered an independent phenomenon capable of being disembodied or sliced off of the spectrum. The Theory of Mind (TOM) from developmental psychology infers that a brain similar to that of humans is a suf?cient condition for spectrum consciousness. But this theory is precluded for computers because a child would not recognize a computer as being a living organism that is just like the child. Although TOM could be applied to an ideal android, there is a classic mathematical theorem from systems science that makes such an android seem infeasible.
关键词： synthetic biology,electroencephalography,arti?cial intelligence,Anesthesia,theory of mind
更新于2025-09-16 10:30:52