Single-Cell RNA Sequencing in Organ and Cell Transplantation.

Single-cell RNA sequencing is a high-throughput novel method that provides transcriptional profiling of individual cells within biological samples. This method typically uses microfluidics systems to uncover the complex intercellular communication networks and biological pathways buried within highly heterogeneous cell populations in tissues. One important application of this technology sits in the fields of organ and stem cell transplantation, where complications such as graft rejection and other post-transplantation life-threatening issues may occur. In this review, we first focus on research in which single-cell RNA sequencing is used to study the transcriptional profile of transplanted tissues. This technology enables the analysis of the donor and recipient cells and identifies cell types and states associated with transplant complications and pathologies. We also review the use of single-cell RNA sequencing in stem cell implantation. This method enables studying the heterogeneity of normal and pathological stem cells and the heterogeneity in cell populations. With their remarkably rapid pace, the single-cell RNA sequencing methodologies will potentially result in breakthroughs in clinical transplantation in the coming years.

A Novel Framework for Epileptic Seizure Detection Using Electroencephalogram Signals Based on the Bat Feature Selection Algorithm.

The precise electroencephalogram (EEG) signal classification with the highest possible accuracy is a key goal in the brain-computer interface (BCI). Considering the complexity and nonstationary nature of the EEG signals, there is an urgent need for effective feature extraction and data mining techniques. Here, we introduce a novel pipeline based on Bat and genetic algorithms for feature construction and dimension reduction of EEG signals. After wavelet extraction and segmentation, the Bat algorithm identifies the most relevant features. We use these features and a genetic algorithm combined with a neural network method to automatically classify the segments of the epilepsy EEG signals. We also use available classification methods based on k-Nearest Neighbors or naïve Bayes for comparison purposes. The code distinguishes individual signals within various combinations of data obtained from healthy volunteers with open or closed eyes and patients suffering from epilepsy disorders during seizure-free periods or seizure activities. Compared to the previously introduced methods, our proposed framework demonstrates a superior balance of high accuracy and short runtime. The minimum achieved accuracies for balanced and unbalanced classes are 100% and 75.9%, respectively. This approach has the potential for direct applications in clinics, enabling accurate and rapid analysis of the epilepsy EEG signals obtained from patients.

Magnetophoretic circuits: A review of device designs and implementation for precise single-cell manipulation.

Lab-on-a-chip tools have played a pivotal role in advancing modern biology and medicine. A key goal in this field is to precisely transport single particles and cells to specific locations on a chip for quantitative analysis. To address this large and growing need, magnetophoretic circuits have been developed in the last decade to manipulate a large number of single bioparticles in a parallel and highly controlled manner. Inspired by electrical circuits, magnetophoretic circuits are composed of passive and active circuit elements to offer commensurate levels of control and automation for transporting individual bioparticles. These specifications make them unique compared to other technologies in addressing crucial bioanalytical applications and answering fundamental questions buried in highly heterogeneous cell populations. In this comprehensive review, we describe key theoretical considerations for manufacturing and simulating magnetophoretic circuits. We provide a detailed tutorial for operating magnetophoretic devices containing different circuit elements (e.g., conductors, diodes, capacitors, and transistors). Finally, we provide a critical comparison of the utility of these devices to other microchip-based platforms for cellular manipulation, and discuss how they may address unmet needs in single-cell biology and medicine.

Controlled Transport of Magnetic Particles and Cells Using C-Shaped Magnetic Thin Films in Microfluidic Chips.

Single-cell analysis is an emerging discipline that has shown a transformative impact in cell biology in the last decade. Progress in this field requires systems capable of accurately moving the cells and particles in a controlled manner. Here, we present a microfluidic platform equipped with C-shaped magnetic thin films to precisely transport magnetic particles in a tri-axial rotating magnetic field. This innovative system, compared to the other rivals, offers numerous advantages. The magnetic particles repel each other to prevent undesired cluster formation. Many particles move synced with the external rotating magnetic field, which results in highly parallel controlled particle transport. We show that the particle transport in this system is analogous to electron transport and Ohm's law in electrical circuits. The proposed magnetic transport pattern is carefully studied using both simulations and experiments for various parameters, including the magnetic field characteristics, particle size, and gap size in the design. We demonstrate the appropriate transport of both magnetic beads and magnetized living cells. We also show a pilot mRNA-capturing experiment with barcode-carrying magnetic beads. The introduced chip offers fundamental potential applications in the fields of single-cell biology and bioengineering.

Magnetophoretic capacitors for storing single particles and magnetized cells in microfluidic devices.

Precise positioning of magnetic particles and magnetized cells in lab-on-a-chip systems has attracted broad attention. Recently, drawing inspiration from electrical circuits, we have demonstrated a magnetic particle transport platform composed of patterned magnetic thin films in a microfluidic environment, which accurately moves the particles and single cells to specific spots, called capacitors. However, we have made no prior attempts to optimize the capacitor geometry. Here, we carefully analyze various design parameters and their effect on capacitor operation. We run simulations based on finite element methods and stochastic numerical analysis using our semi-analytical model. We then perform the required experiments to study the loading efficiency of capacitors with different geometries for magnetic particles of multiple sizes. Our experimental results agree well with the design criteria we developed based on our simulation results. We also show the capability of designed capacitors in storing the magnetically labeled cells and illustrate using them in a pilot drug screening application. These results are directly applicable to the design of robust platforms capable of transporting and assembling a large number of single particles and single cells in arrays, which are useful in the emerging field of single-cell analysis.

High-throughput precise particle transport at single-particle resolution in a three-dimensional magnetic field for highly sensitive bio-detection.

Precise manipulation of microparticles have fundamental applications in the fields of lab-on-a-chip and biomedical engineering. Here, for the first time, we propose a fully operational microfluidic chip equipped with thin magnetic films composed of straight tracks and bends which precisely transports numerous single-particles in the size range of ~ 2.8-20 µm simultaneously, to certain points, synced with the general external three-axial magnetic field. The uniqueness of this design arises from the introduced vertical bias field that provides a repulsion force between the particles and prevents unwanted particle cluster formation, which is a challenge in devices operating in two-dimensional fields. Furthermore, the chip operates as an accurate sensor and detects low levels of proteins and DNA fragments, being captured by the ligand-functionalized magnetic beads, while lowering the background noise by excluding the unwanted bead pairs seen in the previous works. The image-processing detection method in this work allows detection at the single-pair resolution, increasing the sensitivity. The proposed device offers high-throughput particle transport and ultra-sensitive bio-detection in a highly parallel manner at single-particle resolution. It can also operate as a robust single-cell analysis platform for manipulating magnetized single-cells and assembling them in large arrays, with important applications in biology.

A novel magnetophoretic-based device for magnetometry and separation of single magnetic particles and magnetized cells.

The use of magnetic micro- and nanoparticles in medicine and biology is expanding. One important example is the transport of magnetic microparticles and magnetized cells in lab-on-a-chip systems. The magnetic susceptibility of the particles is a key factor in determining their response to the externally applied magnetic field. Typically, to measure this parameter, their magnetophoretic mobility is studied. However, the particle tracking system for accurately determining the traveled distance in a certain time may be too complicated. Here, we introduce a lithographically fabricated chip composed of an array of thin magnetic micro-disks for evaluating the magnetic susceptibility of numerous individual magnetic particles simultaneously. The proposed novel magnetometer works based on the phase change in the trajectory of microparticles circulating around the disks in a rotating in-plane magnetic field. We explain that the easily detectable transition between the "phase-locked" and the "phase-slipping" regimes and the frequency at which it happens are appropriate parameters for measuring the magnetic susceptibility of the magnetic particles at the single-particle level. We show that this high-throughput (i.e., ∼ten thousand particles on a 1 cm2 area) single-particle magnetometry method has various crucial applications, including i) magnetic characterization of magnetic beads as well as magnetically labeled living cells, ii) determining the magnetization rate of the cells taking up magnetic nanoparticles with respect to time, iii) evaluating the rate of degradation of magnetic nanoparticles in cells over time, iv) detecting the number of target cells in a sample, and v) separating particles based on their size and magnetic susceptibility.

Nanotechnology and Acoustics in Medicine and Biology.

BACKGROUND: Nanotechnology plays an important role in various engineering fields, one of which is acoustics. METHOD: Here, we review the use of nanotechnology in multiple acoustic-based bioapplications, with a focus on recent patents and advances. Nanoparticles, nanorods, nanotubes, and nanofilms used in acoustic devices are discussed. We cover ultrasonic transducers, biosensors, imaging tools, nanomotors, and particle sorters. RESULTS AND CONCLUSION: The way these ideas help in fundamental disciplines such as medicine is shown. We believe the current work is a good collection of advances in the field.

Microfluidic Synthesis, Control, and Sensing of Magnetic Nanoparticles: A Review.

Magnetic nanoparticles have attracted significant attention in various disciplines, including engineering and medicine. Microfluidic chips and lab-on-a-chip devices, with precise control over small volumes of fluids and tiny particles, are appropriate tools for the synthesis, manipulation, and evaluation of nanoparticles. Moreover, the controllability and automation offered by the microfluidic chips in combination with the unique capabilities of the magnetic nanoparticles and their ability to be remotely controlled and detected, have recently provided tremendous advances in biotechnology. In particular, microfluidic chips with magnetic nanoparticles serve as sensitive, high throughput, and portable devices for contactless detecting and manipulating DNAs, RNAs, living cells, and viruses. In this work, we review recent fundamental advances in the field with a focus on biomedical applications. First, we study novel microfluidic-based methods in synthesizing magnetic nanoparticles as well as microparticles encapsulating them. We review both continues-flow and droplet-based microreactors, including the ones based on the cross-flow, co-flow, and flow-focusing methods. Then, we investigate the microfluidic-based methods for manipulating tiny magnetic particles. These manipulation techniques include the ones based on external magnets, embedded micro-coils, and magnetic thin films. Finally, we review techniques invented for the detection and magnetic measurement of magnetic nanoparticles and magnetically labeled bioparticles. We include the advances in anisotropic magnetoresistive, giant magnetoresistive, tunneling magnetoresistive, and magnetorelaxometry sensors. Overall, this review covers a wide range of the field uniquely and provides essential information for designing "lab-on-a-chip" systems for synthesizing magnetic nanoparticles, labeling bioparticles with them, and sorting and detecting them on a single chip.

Synchronous control of magnetic particles and magnetized cells in a tri-axial magnetic field.

Precise manipulation of single particles is one of the main goals in the lab-on-a-chip field. Here, we present a microfluidic platform with "T" and "I" shaped magnetic tracks on the substrate to transport magnetic particles and magnetized cells in a tri-axial time-varying magnetic field. The driving magnetic field is composed of a vertical field bias and an in-plane rotating field component, with the advantage of lowering the attraction tendency and cluster formation between the particles compared to the traditional magnetophoretic circuits. We demonstrate three fundamental achievements. First, all the particle movements are synced with the external rotating field to achieve precise control over individual particles. Second, single-particle and single living cell transport in a controlled fashion is achieved for a large number of them in parallel, without the need for a complicated control system to send signals to individual particles. We carefully study the proposed design and introduce proper operating parameters. Finally, in addition to moving the particles along straight tracks, transporting them using a ∼60° bend is demonstrated. The proposed chip has direct applications in the fields of lab-on-a-chip, single-cell biology, and drug screening, where precise control over single particles is needed.

Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis.

Single-cell RNA sequencing is a powerful tool to study developmental biology but does not preserve spatial information about tissue morphology and cellular interactions. Here, we combine single-cell and spatial transcriptomics with algorithms for data integration to study the development of the chicken heart from the early to late four-chambered heart stage. We create a census of the diverse cellular lineages in developing hearts, their spatial organization, and their interactions during development. Spatial mapping of differentiation transitions in cardiac lineages defines transcriptional differences between epithelial and mesenchymal cells within the epicardial lineage. Using spatially resolved expression analysis, we identify anatomically restricted expression programs, including expression of genes implicated in congenital heart disease. Last, we discover a persistent enrichment of the small, secreted peptide, thymosin beta-4, throughout coronary vascular development. Overall, our study identifies an intricate interplay between cellular differentiation and morphogenesis.

Recent Patents and Advances on Nanotechnologies against Coronavirus.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is one of the seven known coronaviruses infecting humans; HKU1, 229E, NL63, OC43, Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and SARS-CoV-2, the last three of which can cause severe symptoms in patients. COVID-19, previously known as 2019 novel coronavirus, caused by SARS-CoV-2, was first reported in Wuhan, China, in late 2019, and quickly resulted in a major epidemic across the world. Although the origin of SARS-CoV-2 is not clear yet, genome sequencing results suggest that this is the third reported spillover of an animal coronavirus to humans, from 2002. The development of detection, therapeutic, and prevention strategies for COVID-19 is a fundamental task towards curing infected people and competing with the pandemic. Because of their similarities, scientists believe that treatment/ detection methods similar to what were used against the illnesses caused by SARS-CoV or MERS-CoV may be effective for curing/detecting COVID-19. Here, we review the recent nanotechnology techniques used for treating and testing SARS-CoV, MERS-CoV, and SARS-CoV-2, and potential therapeutic options for curing COVID-19. This patent summarizes the recent findings of advances on Nanotechnologies against Coronavirus.

Poly(oligo(ethylene glycol) methyl ether methacrylate) Brushes on High-κ Metal Oxide Dielectric Surfaces for Bioelectrical Environments.

Advances in electronics and life sciences have generated interest in "lab-on-a-chip" systems utilizing complementary metal oxide semiconductor (CMOS) circuitry for low-power, portable, and cost-effective biosensing platforms. Here, we present a simple and reliable approach for coating "high-κ" metal oxide dielectric materials with "non-fouling" (protein- and cell-resistant) poly(oligo(ethylene glycol) methyl ether methacrylate (POEGMA) polymer brushes as biointerfacial coatings to improve their relevance for biosensing applications utilizing advanced electronic components. By using a surface-initiated "grafting from" strategy, POEGMA films were reliably grown on each material, as confirmed by ellipsometric measurements and X-ray photoelectron spectroscopy (XPS) analysis. The electrical behavior of these POEGMA films was also studied to determine the potential impact on surrounding electronic devices, yielding information on relative permittivity and breakdown field for POEGMA in both dry and hydrated states. We show that the incorporation of POEGMA coatings significantly reduced levels of nonspecific protein adsorption compared to uncoated high-κ dielectric oxide surfaces as shown by protein resistance assays. These attributes, combined with the robust dielectric properties of POEGMA brushes on high-κ surfaces open the way to incorporate this protein and cell resistant polymer interface into CMOS devices for biomolecular detection in a complex liquid milieu.

Nanotechnology and Nanopore Sequencing.

DNA sequencing is one of the crucially important tasks in the fields of genetics and cellular biology, which is benefiting from nanotechnology. DNA carries genetic information and sequencing it in a quick way helps researchers in achieving essential goals, including personalized medicine. Solid state nanopores potentially can offer more durability, in sequencing biomolecules, over the proteinbased nanopores. In recent years, various ideas are introduced towards the goal of fast and low cost sequencing. In this review article recent advances presented in journal articles as well as patents in this field, including sequencing methods, membrane materials and their fabrication techniques, drilling methods, and biomolecule translocation speed control ideas are investigated.

Magnetophoretic transistors in a tri-axial magnetic field.

The ability to direct and sort individual biological and non-biological particles into spatially addressable locations is fundamentally important to the emerging field of single cell biology. Towards this goal, we demonstrate a new class of magnetophoretic transistors, which can switch single magnetically labeled cells and magnetic beads between different paths in a microfluidic chamber. Compared with prior work on magnetophoretic transistors driven by a two-dimensional in-plane rotating field, the addition of a vertical magnetic field bias provides significant advantages in preventing the formation of particle clumps and in better replicating the operating principles of circuits in general. However, the three-dimensional driving field requires a complete redesign of the magnetic track geometry and switching electrodes. We have solved this problem by developing several types of transistor geometries which can switch particles between two different tracks by either presenting a local energy barrier or by repelling magnetic objects away from a given track, hereby denoted as "barrier" and "repulsion" transistors, respectively. For both types of transistors, we observe complete switching of magnetic objects with currents of ∼40 mA, which is consistent over a range of particle sizes (8-15 µm). The switching efficiency was also tested at various magnetic field strengths (50-90 Oe) and driving frequencies (0.1-0.6 Hz); however, we again found that the device performance only weakly depended on these parameters. These findings support the use of these novel transistor geometries to form circuit architectures in which cells can be placed in defined locations and retrieved on demand.

Magnetophoretic Conductors and Diodes in a 3D Magnetic Field.

We demonstrate magnetophoretic conductor tracks that can transport single magnetized beads and magnetically labeled single cells in a 3-dimensional time-varying magnetic field. The vertical field bias, in addition to the in-plane rotating field, has the advantage of reducing the attraction between particles, which inhibits the formation of particle clusters. However, the inclusion of a vertical field requires the re-design of magnetic track geometries which can transport magnetized objects across the substrate. Following insights from magnetic bubble technology, we found that successful magnetic conductor geometries defined in soft magnetic materials must be composed of alternating sections of positive and negative curvature. In addition to the previously studied magnetic tracks taken from the magnetic bubble literature, a drop-shape pattern was found to be even more adept at transporting small magnetic beads and single cells. Symmetric patterns are shown to achieve bi-directional conduction, whereas asymmetric patterns achieve unidirectional conduction. These designs represent the electrical circuit corollaries of the conductor and diode, respectively. Finally, we demonstrate biological applications in transporting single cells and in the size based separation of magnetic particles.

Dynamic trajectory analysis of superparamagnetic beads driven by on-chip micromagnets.

We investigate the non-linear dynamics of superparamagnetic beads moving around the periphery of patterned magnetic disks in the presence of an in-plane rotating magnetic field. Three different dynamical regimes are observed in experiments, including (1) phase-locked motion at low driving frequencies, (2) phase-slipping motion above the first critical frequency fc1, and (3) phase-insulated motion above the second critical frequency fc2. Experiments with Janus particles were used to confirm that the beads move by sliding rather than rolling. The rest of the experiments were conducted on spherical, isotropic magnetic beads, in which automated particle position tracking algorithms were used to analyze the bead dynamics. Experimental results in the phase-locked and phase-slipping regimes correlate well with numerical simulations. Additional assumptions are required to predict the onset of the phase-insulated regime, in which the beads are trapped in closed orbits; however, the origin of the phase-insulated state appears to result from local magnetization defects. These results indicate that these three dynamical states are universal properties of bead motion in non-uniform oscillators.

Characterizing the Switching Thresholds of Magnetophoretic Transistors.

The switching thresholds of magnetophoretic transistors for sorting cells in microfluidic environments are characterized. The transistor operating conditions require short 20-30 mA pulses of electrical current. By demonstrating both attractive and repulsive transistor modes, a single transistor architecture is used to implement the full write cycle for importing and exporting single cells in specified array sites.

Recent patents and advances on applications of magnetic nanoparticles and thin films in cell manipulation.

Cell manipulation is instrumental in most biological applications. One of the most promising methods in handling cells and other biological particles is the magnetic manipulation technique. In this technique, magnetic nanoparticles are employed to magnetize cells. Such cells then can be manipulated, sorted, or separated by applying an external magnetic field. In this work, first recent works and patents on the synthesis methods used for producing magnetic nanoparticles are investigated. These methods include co-precipitation, solvothermal, electrical wire explosion, microemulsion, laser pyrolysis, spray pyrolysis and carbon reduction. Then recent patents and articles on surface modification and functionalization of magnetic nanoparticles using polymers, dithiocarbamate, superparamagnetic shells, antibodies, graphene shells, and fluorescent materials are reviewed. Finally, different techniques on magnetic cell manipulation, such as direct attaching of magnetic particles to cells, employing intercellular markers or extra support molecules, as well as magnetic thin films, microfluidic channels and magnetic beads, are studied.

Magnetophoretic circuits for digital control of single particles and cells.

The ability to manipulate small fluid droplets, colloidal particles and single cells with the precision and parallelization of modern-day computer hardware has profound applications for biochemical detection, gene sequencing, chemical synthesis and highly parallel analysis of single cells. Drawing inspiration from general circuit theory and magnetic bubble technology, here we demonstrate a class of integrated circuits for executing sequential and parallel, timed operations on an ensemble of single particles and cells. The integrated circuits are constructed from lithographically defined, overlaid patterns of magnetic film and current lines. The magnetic patterns passively control particles similar to electrical conductors, diodes and capacitors. The current lines actively switch particles between different tracks similar to gated electrical transistors. When combined into arrays and driven by a rotating magnetic field clock, these integrated circuits have general multiplexing properties and enable the precise control of magnetizable objects.