Browse
Submit Data
Databases
API
Help

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Digital switching in a biosensor circuit via programmable timing of gene availability.

ABSTRACT: Transient delivery of gene circuits is required in many potential applications of synthetic biology, yet the pre-steady-state processes that dominate this delivery route pose major challenges for robust circuit deployment. Here we show that site-specific recombinases can rectify undesired effects by programmable timing of gene availability in multigene circuits. We exemplify the concept with a proportional sensor for endogenous microRNA (miRNA) and show a marked reduction in its ground state leakage due to desynchronization of the circuit's repressor components and their repression target. The new sensors display a dynamic range of up to 1,000-fold compared to 20-fold in the standard configuration. We applied the approach to classify cell types on the basis of miRNA expression profile and measured >200-fold output differential between positively and negatively identified cells. We also showed major improvements in specificity with cytotoxic output. Our study opens new venues in gene circuit design via judicious temporal control of circuits' genetic makeup.

SUBMITTER: Lapique N

PROVIDER: S-EPMC4232471 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Programmable light-driven swimming actuators via wavelength signal switching.

Project description:[Figure: see text].

| S-EPMC8442936 | biostudies-literature

Direct Transmission of Digital Message via Programmable Coding Metasurface.

Project description:In modern wireless communications, digital information is firstly converted to analog signal by a digital-analog convertor, which is then mixed to high-frequency microwave to be transmitted through a series of devices including modulator, mixer, amplifier, filter, and antenna and is finally received by terminals via a reversed process. Although the wireless communication systems have evolved significantly over the past thirty years, the basic architecture has not been challenged. Here, we propose a method to transmit digital information directly via programmable coding metasurface. Since the coding metasurface is composed of '0' and '1' digital units with opposite phase responses, the digital information can be directly modulated to the metasurface with certain coding sequences and sent to space under the illumination of feeding antenna. The information, being modulated in radiation patterns of the metasurface, can be correctly received by multiple receivers distributed in different locations. This method provides a completely new architecture for wireless communications without using complicated digital-analog convertor and a series of active/passive microwave devices. We build up a prototype to validate the new architecture experimentally, which may find promising applications where information security is highly demanded.

| S-EPMC6750087 | biostudies-literature

Programmable Dynamics of Exchange-Biased Domain Wall via Spin-Current-Induced Antiferromagnet Switching.

Project description:Magnetic domain wall (DW) motion in perpendicularly magnetized materials is drawing increased attention due to the prospect of new type of information storage devices, such as racetrack memory. To augment the functionalities of DW motion-based devices, it is essential to improve controllability over the DW motion. Other than electric current, which is known to induce unidirectional shifting of a train of DWs, an application of in-plane magnetic field also enables the control of DW dynamics by rotating the DW magnetization and consequently modulating the inherited chiral DW structure. Applying an external bias field, however, is not a viable approach for the miniaturization of the devices as the external field acts globally. Here, the programmable exchange-coupled DW motion in the antiferromagnet (AFM)/ferromagnet (FM) system is demonstrated, where the role of an external in-plane field is replaced by the exchange bias field from AFM layer, enabling the external field-free modulations of DW motions. Interestingly, the direction of the exchange bias field can also be reconfigured by simply injecting spin currents through the device, enabling electrical and programmable operations of the device. Furthermore, the result inspires a prototype DW motion-based device based on the AFM/FM heterostructure, that could be easily integrated in logic devices.

| S-EPMC8425944 | biostudies-literature

A readily programmable, fully reversible shape-switching material.

Project description:Liquid crystalline (LC) elastomers (LCEs) enable large-scale reversible shape changes in polymeric materials; however, they require intensive, irreversible programming approaches in order to facilitate controllable actuation. We have implemented photoinduced dynamic covalent chemistry (DCC) that chemically anneals the LCE toward an applied equilibrium only when and where the light-activated DCC is on. By using light as the stimulus that enables programming, the dynamic bond exchange is orthogonal to LC phase behavior, enabling the LCE to be annealed in any LC phase or in the isotropic phase with various manifestations of this capability explored here. In a photopolymerizable LCE network, we report the synthesis, characterization, and exploitation of readily shape-programmable DCC-functional LCEs to create predictable, complex, and fully reversible shape changes, thus enabling the literal square peg to fit into a round hole.

| S-EPMC6108565 | biostudies-literature

Hybridization chain reaction circuit-based electrochemiluminescent biosensor for SARS-cov-2 RdRp gene assay.

Project description:In this work, we designed an ECL ratiometric biosensor with a three-stranded Y-type DNA (Y-DNA) probe and induced a hybridization chain reaction (HCR) for the highly sensitive detection of SARS-CoV-2 nucleic acid. The important component of this system is the self-assembled Y-Shaped probe based on three nucleic acids. Y1, Y2, and Y3 can be linked by complementary base pairing to Hairpin1 (H1), Hairpin2 (H2), and Ru modified DNA (Ru1), respectively. H1 and H2 can trigger the HCR reaction when activated by the SARS-CoV-2 RdRp gene and the 5' end of Ru1. The 5' end of Ru1 is modified with the Ru complex, which can produce a strong electrochemiluminescence luminescence signal at 620 nm under an applied voltage. Through the amplification of Y-DNA-induced HCR reaction, Ru1 on the electrode surface gradually increased, the ECL signal at 460 nm was gradually quenched, and the signal at 620 nm was steadily generated. The SARS-CoV-2 RdRp gene can be quantified according to the degree of decrease of ECL signal at 460 nm and the increase of ECL signal at 620 nm. Combining the two signal amplification strategies, this ratiometric ECL biosensor can accurately and efficiently detect the target gene with a detection limit of 59 aM.

| S-EPMC8730713 | biostudies-literature

Multichannel digital heteronuclear magnetic resonance biosensor.

Project description:Low-field, mobile NMR systems are increasingly used across diverse fields, including medical diagnostics, food quality control, and forensics. The throughput and functionality of these systems, however, are limited due to their conventional single-channel detection: one NMR probe exclusively uses an NMR console at any given time. Under this design, multi-channel detection could only be accomplished by either serially accessing individual probes or stacking up multiple copies of NMR electronics; this approach still retains limitations such as long assay times and increased system complexity. Here we present a new scalable architecture, HERMES (hetero-nuclear resonance multichannel electronic system), for versatile, high-throughput NMR analyses. HERMES exploits the concept of software-defined radio by virtualizing NMR electronics in the digital domain. This strategy i) creates multiple NMR consoles without adding extra hardware; ii) acquires signals from multiple NMR channels in parallel; and iii) operates in wide frequency ranges. All of these functions could be realized on-demand in a single compact device. We interfaced HERMES with an array of NMR probes; the combined system simultaneously measured NMR relaxation from multiple samples and resolved spectra of hetero-nuclear spins (1H, 19F, 13C). For potential diagnostic uses, we applied the system to detect dengue fever and molecularly profile cancer cells through multi-channel protein assays. HERMES holds promise as a powerful analytical tool that enables rapid, reconfigurable, and parallel detection.

| S-EPMC6483068 | biostudies-literature

Digital acoustofluidics enables contactless and programmable liquid handling.

Project description:For decades, scientists have pursued the goal of performing automated reactions in a compact fluid processor with minimal human intervention. Most advanced fluidic handling technologies (e.g., microfluidic chips and micro-well plates) lack fluid rewritability, and the associated benefits of multi-path routing and re-programmability, due to surface-adsorption-induced contamination on contacting structures. This limits their processing speed and the complexity of reaction test matrices. We present a contactless droplet transport and processing technique called digital acoustofluidics which dynamically manipulates droplets with volumes from 1?nL to 100?µL along any planar axis via acoustic-streaming-induced hydrodynamic traps, all in a contamination-free (lower than 10-10% diffusion into the fluorinated carrier oil layer) and biocompatible (99.2% cell viability) manner. Hence, digital acoustofluidics can execute reactions on overlapping, non-contaminated, fluidic paths and can scale to perform massive interaction matrices within a single device.

| S-EPMC6062562 | biostudies-literature

Plant Growth Environments with Programmable Relative Humidity and Homogeneous Nutrient Availability.

Project description:We describe the design, characterization, and use of "programmable", sterile growth environments for individual (or small sets of) plants. The specific relative humidities and nutrient availability experienced by the plant is established (RH between 15% and 95%; nutrient concentration as desired) during the setup of the growth environment, which takes about 5 minutes and <1$ in disposable cost. These systems maintain these environmental parameters constant for at least 14 days with minimal intervention (one minute every two days). The design is composed entirely of off-the-shelf components (e.g., LEGO® bricks) and is characterized by (i) a separation of root and shoot environment (which is physiologically relevant and facilitates imposing specific conditions on the root system, e.g., darkness), (ii) the development of the root system on a flat surface, where the root enjoys constant contact with nutrient solution and air, (iii) a compatibility with root phenotyping. We demonstrate phenotyping by characterizing root systems of Brassica rapa plants growing in different relative humidities (55%, 75%, and 95%). While most phenotypes were found to be sensitive to these environmental changes, a phenotype tightly associated with root system topology-the size distribution of the areas encircled by roots-appeared to be remarkably and counterintuitively insensitive to humidity changes. These setups combine many of the advantages of hydroponics conditions (e.g., root phenotyping, complete control over nutrient composition, scalability) and soil conditions (e.g., aeration of roots, shading of roots), while being comparable in cost and setup time to Magenta® boxes.

| S-EPMC4909320 | biostudies-literature

A neural circuit model for human sensorimotor timing.

Project description:Humans and animals can effortlessly coordinate their movements with external stimuli. This capacity indicates that sensory inputs can rapidly and flexibly reconfigure the ongoing dynamics in the neural circuits that control movements. Here, we develop a circuit-level model that coordinates movement times with expected and unexpected temporal events. The model consists of two interacting modules, a motor planning module that controls movement times and a sensory anticipation module that anticipates external events. Both modules harbor a reservoir of latent dynamics, and their interaction forms a control system whose output is adjusted adaptively to minimize timing errors. We show that the model's output matches human behavior in a range of tasks including time interval production, periodic production, synchronization/continuation, and Bayesian time interval reproduction. These results demonstrate how recurrent interactions in a simple and modular neural circuit could create the dynamics needed to control timing behavior.

| S-EPMC7414125 | biostudies-literature

Implementing digital computing with DNA-based switching circuits.

Project description:DNA strand displacement reactions (SDRs) provide a set of intelligent toolboxes for developing molecular computation. Whereas SDR-based logic gate circuits have achieved a high level of complexity, the scale-up for practical achievable computational tasks remains a hurdle. Switching circuits that were originally proposed by Shannon in 1938 and nowadays widely used in telecommunication represent an alternative and efficient means to realize fast-speed and high-bandwidth communication. Here we develop SDR-based DNA switching circuits (DSCs) for implementing digital computing. Using a routing strategy on a programmable DNA switch canvas, we show that arbitrary Boolean functions can be represented by DSCs and implemented with molecular switches with high computing speed. We further demonstrate the implementation of full-adder and square-rooting functions using DSCs, which only uses down to 1/4 DNA strands as compared with a dual-rail logic expression-based design. We expect that DSCs provide a design paradigm for digital computation with biomolecules.

| S-EPMC6949259 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data