3D Barcodes Research Articles

Duplex-specific nuclease powered 3D DNA walker and quantum dots barcodes for homogeneous electrochemical detection of microRNAs

Multiplex microRNAs (miRNAs) detection is beneficial for early diagnosis and prognosis of cancer. Herein, duplex-specific nuclease (DSN) powered 3D DNA walker and quantum dots (QDs) barcodes were designed for the simultaneous detection of miRNAs in a homogeneous electrochemical sensor. In the proof-of-concept experiment, the effective active area of the as-prepared graphene aerogel-modified carbon paper (CP-GAs) electrode was ∼14.30 times larger than that of the traditional glassy carbon electrode (GCE), endowing the enhanced capability of loading more metal ions for ultrasensitive detection of miRNAs. In addition, DSN-powered target recycling and DNA walking strategy assured the sensitive detection of miRNAs. After the introduction of magnetic beads (MNs) and electrochemical double enrichment strategies, the integration of triple signal amplification methods yielded good detection results. Under optimal conditions, towards simultaneous detection of microRNA-21 (miR-21) and miRNA-155 (miR-155), a linear range of 10−16–10−7 M and a sensitivity of 10 aM (miR-21) and 2.18 aM (miR-155) were achieved, respectively. It was worth mentioning that the prepared sensor can detect miR-155 down to 0.17 aM, which was also extremely advantageous among the sensors reported so far. What's more, through verification, the prepared sensor had good selectivity and reproducibility, and exhibited good detection ability in complex serum environments, showing great potential in early clinical diagnosis and screening.

Quaternionic views of rs-fMRI hierarchical brain activation regions. Discovery of multilevel brain activation region intensities in rs-fMRI video frames

This paper introduces quaternionic views of multi-level brain activation region intensities in resting-state functional magnetic resonance imaging (rs-fMRI) videos. Quaternions make it possible to explore rs-fMRI brain activation regions in a 4D space in which there are varying brain activation intensities in spiralling activation cycles (each with its own intensity). As a result, there is a natural formation of multi-level cycles that form pyramidal vortex shapes with varying diameters. These pyramidal vortexes reflect the fractality (self-similarity) of clusters of similar multilevel brain activation region cycles. Using a computational topology of data approach, we have found that persistent, recurring clusters of spiraling cycles resulting from blood oxygen level dependent (BOLD) signals in triangulated rs-fMRI video frames. Each brain activation region cycle is a cell complex, which is a collection path-connected vertexes that has no end vertex. Measurement of persistence of spiraling vortex shapes in BOLD signal propagation regions is carried out in terms of Betti numbers (counts of distinguished cycle vertexes called generators) that rise and fall over time during spontaneous activity of the brain. A main result given here is that every quaternionic brain activation region vortex has a free group presentation. In addition, we introduce 3D barcodes of brain activation videos that help visualize and quantify the fractality of clusters of multilevel vortexes arising naturally from triangulated brain activation regions in rs-fMRI video frames. We have made freely available downloadable archives of videos that exhibit the resulting clusters of spiraling brain activation cycles.

Three-Dimensional Barcodes with Ultrahigh Encoding Capacities: A Flexible, Accurate, and Reproducible Encoding Strategy for Suspension Arrays

Novel 3D barcodes with an extraordinarily high encoding capacity are developed through a flexible, accurate, and reproducible method. Here, the three dimensions refer to the size, fluorescence emission wavelength, and intensity of the barcodes. As a proof of concept, a 3D barcode library with an encoding capacity of 100 flow cytometry-distinguishable barcodes is achieved successfully by combining the multiscaled host particles with a set of guest nanoparticles owning to their individual different fluorescent intensity via an ingenious host–guest structure, where fluorescein isothiocyanate and a kind of quantum dots are separately loaded inside. Five-plexed tumor marker detection is further implemented, and the results demonstrate the strong feasibility of 3D barcodes in multiplex assays.

DRIE based technology for 3D silicon barcodes fabrication

Microworld barcoding has become a promising tool for cell biology. Individual and subpopulation cell tracking is of great interest to evaluate cell behaviour. Nowadays, many micrometer and even nanometer size silicon structures can be fabricated using microelectronics techniques. In this work we report for first time the development of 3D barcodes based on silicon substrate. The proposed silicon micromachining technology based on deep reactive ion etching (DRIE) allows to obtain micrometer-sized cylindrical structures with vertical etch profile that defines a bit = 1 and non-vertical etch profile that defines a bit = 0. Although this technology will allow more than 15 bits representation, only 4–8 bits are necessary for cell labelling. The results of this work show that DRIE has become a versatile technique to produce high aspect 3D biocompatible silicon-based barcodes structures for cell studies.

DRIE based technology for 3D silicon barcodes fabrication

Barcoding the microworld has become a promising tool for Cell Biology. Individual and subpopulation cell tracking is of great interest to evaluate cell behavoir. Nowadays, many micrometer and even nanometer size silicon 3D structures can be fabricated using microelectronics techniques, i.e., Deep Reactive Ion Etching (DRIE). 3D barcodes reading are less sensitive to the spatial orientation of the code respect to the reader. Therefore, the motivation of this work is to produce small biocompatible barcodes for cell studies that could be freely programmed by controlling the DRIE process parameters.