Assessing characteristics of RNA amplification methods for single cell RNA sequencing.

BACKGROUND: Recently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of single cell methods and the factors governing their performance are still poorly known. RESULTS: Here, we conducted a large-scale control experiment to assess the transfer function of three scRNA-seq methods and factors modulating the function. All three methods detected greater than 70% of the expected number of genes and had a 50% probability of detecting genes with abundance greater than 2 to 4 molecules. Despite the small number of molecules, sequencing depth significantly affected gene detection. While biases in detection and quantification were qualitatively similar across methods, the degree of bias differed, consistent with differences in molecular protocol. Measurement reliability increased with expression level for all methods and we conservatively estimate measurements to be quantitative at an expression level greater than ~5-10 molecules. CONCLUSIONS: Based on these extensive control studies, we propose that RNA-seq of single cells has come of age, yielding quantitative biological information.

Enhance the light-harvesting capability of the ITO-free inverted small molecule solar cell by ZnO nanorods.

The ITO-free inverted SMPV1:PC71BM solar cells with an Al doped ZnO (AZO) transparent electrodes are fabricated. The AZO thin film prepared by pulsed laser deposition (PLD) technique exhibits high transmission (>85%) and low sheet resistance (~30 Ω/sq) and the power conversion efficiency (PCE) of devices based on AZO electrode can reach around 4%. To further enhance the light harvesting of the absorption layer of solar cells, ZnO nanorods interlayer is grown on the AZO layer before the deposition the active layer. The absorption spectrums of devices under various conditions are also simulated by RCWA method to identify the optical saturation length of the ZnO nanorods. The PCE of ITO-free inverted small molecule solar cell improved with ZnO nanorods can reach 6.6%.

The DcpS inhibitor RG3039 improves motor function in SMA mice.

Spinal muscular atrophy (SMA) is caused by mutations of the survival motor neuron 1 (SMN1) gene, retention of the survival motor neuron 2 (SMN2) gene and insufficient expression of full-length survival motor neuron (SMN) protein. Quinazolines increase SMN2 promoter activity and inhibit the ribonucleic acid scavenger enzyme DcpS. The quinazoline derivative RG3039 has advanced to early phase clinical trials. In preparation for efficacy studies in SMA patients, we investigated the effects of RG3039 in severe SMA mice. Here, we show that RG3039 distributed to central nervous system tissues where it robustly inhibited DcpS enzyme activity, but minimally activated SMN expression or the assembly of small nuclear ribonucleoproteins. Nonetheless, treated SMA mice showed a dose-dependent increase in survival, weight and motor function. This was associated with improved motor neuron somal and neuromuscular junction synaptic innervation and function and increased muscle size. RG3039 also enhanced survival of conditional SMA mice in which SMN had been genetically restored to motor neurons. As this systemically delivered drug may have therapeutic benefits that extend beyond motor neurons, it could act additively with SMN-restoring therapies delivered directly to the central nervous system such as antisense oligonucleotides or gene therapy.

Characterization of behavioral and neuromuscular junction phenotypes in a novel allelic series of SMA mouse models.

A number of mouse models for spinal muscular atrophy (SMA) have been genetically engineered to recapitulate the severity of human SMA by using a targeted null mutation at the mouse Smn1 locus coupled with the transgenic addition of varying copy numbers of human SMN2 genes. Although this approach has been useful in modeling severe SMA and very mild SMA, a mouse model of the intermediate form of the disease would provide an additional research tool amenable for drug discovery. In addition, many of the previously engineered SMA strains are multi-allelic by design, containing a combination of transgenes and targeted mutations in the homozygous state, making further genetic manipulation difficult. A new genetic engineering approach was developed whereby variable numbers of SMN2 sequences were incorporated directly into the murine Smn1 locus. Using combinations of these alleles, we generated an allelic series of SMA mouse strains harboring no, one, two, three, four, five, six or eight copies of SMN2. We report here the characterization of SMA mutants in this series that displayed a range in disease severity from embryonic lethal to viable with mild neuromuscular deficits.

Plasmonic ITO-free polymer solar cell.

The aluminum and sliver multilayered nano-grating structure is fabricated by laser interference lithography and the intervals between nanoslits is filled with modified PEDOT:PSS. The grating structured transparent electrode functions as the anti-reflection layer which not only decreases the reflected light but also increases the absorption of the active layer. The performances of P3HT:PC61BM solar cells are studied experimentally and theoretically in detail. The field intensities of the transverse magnetic (TM) and transverse electrical (TE) waves distributed in the active layer are simulated by rigorous coupled wave analysis (RCWA). The power conversion efficiency of the plasmonic ITO-free polymer solar cell can reach 3.64% which is higher than ITO based polymer solar cell with efficiency of 3.45%.

Design and fabrication of birefringent nano-grating structure for circularly polarized light emission.

Three different nano-grating structures are designed as phase retarders that can transform linearly polarized light to circularly polarized emission for the wavelengths of 488 nm, 532 nm and 632.8 nm, respectively. Gold based nano-grating structures with various periods are fabricated by utilizing laser interference lithography. The ellipticity of all circularly polarized emission can reach around 90% such that the structure has great potential in the applications of three-dimensional (3D) display. The effects of the slit width and metal thickness modulations are simulated by rigorous coupled wave analysis (RCWA) method. Besides, the field intensity and phase of the transmitted TM and TE waves are also simulated to understand their polarization characteristics.

Complexin facilitates exocytosis and synchronizes vesicle release in two secretory model systems.

Complexins (Cplxs) are small, SNARE-associated proteins believed to regulate fast, calcium-triggered exocytosis. However, studies have pointed to either an inhibitory and/or facilitatory role in exocytosis, and the role of Cplxs in synchronizing exocytosis is relatively unexplored. Here, we compare the function of two types of complexin, Cplx 1 and 2, in two model systems of calcium-dependent exocytosis. In mouse neuromuscular junctions (NMJs), we find that lack of Cplx 1 significantly reduces and desynchronizes calcium-triggered synaptic transmission; furthermore, high-frequency stimulation elicits synaptic facilitation, instead of normal synaptic depression, and the degree of facilitation is highly sensitive to the amount of cytoplasmic calcium buffering. In Cplx 2-null adrenal chromaffin cells, we also find decreased and desynchronized evoked release, and identify a significant reduction in the vesicle pool close to the calcium channels (immediately releasable pool, IRP). Viral transduction with either Cplx 1 or 2 rescues both the size of the evoked response and the synchronicity of release, and it restores the IRP size. Our findings in two model systems are mutually compatible and indicate a role of Cplx 1 and 2 in facilitating vesicle priming, and also lead to the new hypothesis that Cplxs may synchronize vesicle release by promoting coupling between secretory vesicles and calcium channels.

Simple and efficient defect-tailored fiber-based UV-VIS broadband white light generation.

We propose and demonstrate a facile approach for ultraviolet-visible broadband generation from a sapphire crystal core-borosilicate glass cladding hybrid fiber using a laser-heated pedestal growth technique. Considerable formation of F- and F(2)-type color emitters is effectively facilitated by Ti(4+) ions and Al(3+) vacancies, retaining efficient luminescence and high crystallinity of the sapphire core. These color centers intensify the ultraviolet, blue, and green emissions at 370, 450, and 540 nm, whereas the 650-nm red emission is contributed by Cr(3+) in the octahedral sites of the corundum structure. Over 1-mW white light with an optical-to-optical efficiency of up to nearly 5% and 1931 Commission International de l'Eclairage chromaticity coordinate of (0.287, 0.333) is achieved under 325-nm excitation.

Investigating contactless high frequency ultrasound microbeam stimulation for determination of invasion potential of breast cancer cells.

In this article, we investigate the application of contactless high frequency ultrasound microbeam stimulation (HFUMS) for determining the invasion potential of breast cancer cells. In breast cancer patients, the finding of tumor metastasis significantly worsens the clinical prognosis. Thus, early determination of the potential of a tumor for invasion and metastasis would significantly impact decisions about aggressiveness of cancer treatment. Recent work suggests that invasive breast cancer cells (MDA-MB-231), but not weakly invasive breast cancer cells (MCF-7, SKBR3, and BT-474), display a number of neuronal characteristics, including expression of voltage-gated sodium channels. Since sodium channels are often co-expressed with calcium channels, this prompted us to test whether single-cell stimulation by a highly focused ultrasound microbeam would trigger Ca(2+) elevation, especially in highly invasive breast cancer cells. To calibrate the diameter of the microbeam ultrasound produced by a 200-MHz single element LiNbO3 transducer, we focused the beam on a wire target and performed a pulse-echo test. The width of the beam was ∼17 µm, appropriate for single cell stimulation. Membrane-permeant fluorescent Ca(2+) indicators were utilized to monitor Ca(2+) changes in the cells due to HFUMS. The cell response index (CRI), which is a composite parameter reflecting both Ca(2+) elevation and the fraction of responding cells elicited by HFUMS, was much greater in highly invasive breast cancer cells than in the weakly invasive breast cancer cells. The CRI of MDA-MB-231 cells depended on peak-to-peak amplitude of the voltage driving the transducer. These results suggest that HFUMS may serve as a novel tool to determine the invasion potential of breast cancer cells, and with further refinement may offer a rapid test for invasiveness of tumor biopsies in situ.

On-Chip Monolithically Integrated Ultraviolet Low-Threshold Plasmonic Metal-Semiconductor Heterojunction Nanolasers.

The metal-semiconductor heterojunction is imperative for the realization of electrically driven nanolasers for chip-level platforms. Progress in developing such nanolasers has hitherto rarely been realized, however, because of their complexity in heterojunction fabrication and the need to use noble metals that are incompatible with microelectronic manufacturing. Most plasmonic nanolasers lase either above a high threshold (101 -103 MW cm-2 ) or at a cryogenic temperature, and lasing is possible only after they are removed from the substrate to avoid the large ohmic loss and the low modal reflectivity, making monolithic fabrication impossible. Here, for the first time, record-low-threshold, room-temperature ultraviolet (UV) lasing of plasmon-coupled core-shell nanowires that are directly grown on silicon is demonstrated. The naturally formed core-shell metal-semiconductor heterostructure of the nanowires leads to a 100-fold improvement in growth density over previous results. This unprecedentedly high nanowire density creates intense plasmonic resonance, which is outcoupled to the resonant Fabry-Pérot microcavity. By boosting the emission strength by a factor of 100, the hybrid photonic-plasmonic system successfully facilitates a record-low laser threshold of 12 kW cm-2 with a spontaneous emission coupling factor as high as ≈0.32 in the 340-360 nm range. Such architecture is simple and cost-competitive for future UV sources in silicon integration.

Detecting mouse squamous cell carcinoma from submicron full-field optical coherence tomography images by deep learning.

The standard medical practice for cancer diagnosis requires histopathology, which is an invasive and time-consuming procedure. Optical coherence tomography (OCT) is an alternative that is relatively fast, noninvasive, and able to capture three-dimensional structures of epithelial tissue. Unlike most previous OCT systems, which cannot capture crucial cellular-level information for squamous cell carcinoma (SCC) diagnosis, the full-field OCT (FF-OCT) technology used in this paper is able to produce images at sub-micron resolution and thereby facilitates the development of a deep learning algorithm for SCC detection. Experimental results show that the SCC detection algorithm can achieve a classification accuracy of 80% for mouse skin. Using the sub-micron FF-OCT imaging system, the proposed SCC detection algorithm has the potential for in-vivo applications.

Classification of squamous cell carcinoma from FF-OCT images: Data selection and progressive model construction.

We investigate the speed and performance of squamous cell carcinoma (SCC) classification from full-field optical coherence tomography (FF-OCT) images based on the convolutional neural network (CNN). Due to the unique characteristics of SCC features, the high variety of CNN, and the high volume of our 3D FF-OCT dataset, progressive model construction is a time-consuming process. To address the issue, we develop a training strategy for data selection that makes model training 16 times faster by exploiting the dependency between images and the knowledge of SCC feature distribution. The speedup makes progressive model construction computationally feasible. Our approach further refines the regularization, channel attention, and optimization mechanism of SCC classifier and improves the accuracy of SCC classification to 87.12% at the image level and 90.10% at the tomogram level. The results are obtained by testing the proposed approach on an FF-OCT dataset with over one million mouse skin images.

Ultralow-Threshold Continuous-Wave Room-Temperature Crystal-Fiber/Nanoperovskite Hybrid Lasers for All-Optical Photonic Integration.

Continuous-wave (CW) room-temperature (RT) laser operation with low energy consumption is an ultimate goal for electrically driven lasers. A monolithically integrated perovskite laser in a chip-level fiber scheme is ideal. However, because of the well-recognized air and thermal instabilities of perovskites, laser action in a perovskite has mostly been limited to either pulsed or cryogenic-temperature operations. Most CW laser operations at RT have had poor durability. Here, crystal fibers that have robust and high-heat-load nature are shown to be the key to enabling the first demonstration of ultralow-threshold CW RT laser action in a compact, monolithic, and inexpensive crystal fiber/nanoperovskite hybrid architecture that is directly pumped with a 405 nm diode laser. Purcell-enhanced light-matter coupling between the atomically smooth fiber microcavity and the perovskite nanocrystallites gain medium enables a high Q (≈1500) and a high ß (0.31). This 762 nm laser outperforms previously reported structures with a record-low threshold of 132 nW and an optical-to-optical slope conversion efficiency of 2.93%, and it delivers a stable output for CW and RT operation. These results represent a significant advancement toward monolithic all-optical integration.

Yb:MoO3/Ag/MoO3 Multilayer Transparent Top Cathode for Top-Emitting Green Quantum Dot Light-Emitting Diodes.

In this study, we report on the application of a dielectric/ultra-thin metal/dielectric (DMD) multilayer consisting of ytterbium (Yb)-doped molybdenum oxide (MoO3)/silver (Ag)/MoO3 stacked as the transparent cathode in top-emitting green quantum dot light-emitting diodes (QLED). By optimizing the Yb doping ratio, we have highly improved the electron injection ability from 0.01 to 0.35. In addition, the dielectric/ultra-thin metal/dielectric (DMD) cathode also shows a low sheet resistance of only 12.2 Ω/sq, which is superior to the resistance of the commercially-available indium tin oxide (ITO) electrode (~15 Ω/sq). The DMD multilayer exhibits a maximum transmittance of 75% and an average transmittance of 70% over the visible range of 400-700 nm. The optimized DMD-based G-QLED has a smaller current leakage at low driving voltage. The optimized DMD-based G-QLED enhances the current density than that of G-QLED with indium zinc oxide (IZO) as a cathode. The fabricated DMD-based G-QLED shows a low turn-on voltage of 2.2 V, a high current efficiency of 38 cd/A, and external quantum efficiency of 9.8. These findings support the fabricated DMD multilayer as a promising cathode for transparent top-emitting diodes.

Robust RNA-Seq of aRNA-amplified single cell material collected by patch clamp.

Most single cell RNA sequencing protocols start with single cells dispersed from intact tissue. High-throughput processing of the separated cells is enabled using microfluidics platforms. However, dissociation of tissue results in loss of information about cell location and morphology and potentially alters the transcriptome. An alternative approach for collecting RNA from single cells is to re-purpose the electrophysiological technique of patch clamp recording. A hollow patch pipette is attached to individual cells, enabling the recording of electrical activity, after which the cytoplasm may be extracted for single cell RNA-Seq ("Patch-Seq"). Since the tissue is not disaggregated, the location of cells is readily determined, and the morphology of the cells is maintained, making possible the correlation of single cell transcriptomes with cell location, morphology and electrophysiology. Recent Patch-Seq studies utilizes PCR amplification to increase amount of nucleic acid material to the level required for current sequencing technologies. PCR is prone to create biased libraries - especially with the extremely high degrees of exponential amplification required for single cell amounts of RNA. We compared a PCR-based approach with linear amplifications and demonstrate that aRNA amplification (in vitro transcription, IVT) is more sensitive and robust for single cell RNA collected by a patch clamp pipette.

Oxidative stress promotes autophagic cell death in human neuroblastoma cells with ectopic transfer of mitochondrial PPP2R2B (Bbeta2).

BACKGROUND: The multifunctional protein phosphatase 2A (PP2A) is a heterotrimeric serine/threonine protein phosphatase composed of a scaffolding, catalytic and regulatory subunits. By modifying various downstream signal transducers, the aberrant expression of the brain-targeted regulatory subunit PPP2R2B is associated with the onset of a panel of neuronal disorders. The alternatively splicing of PPP2R2B encodes two regulatory subunit isoforms that determine cellular distribution of the neuron-specific holoenzyme to mitochondria (Bbeta2) and cytoplasm (Bbeta1), respectively. RESULTS: Human neuroblastoma cells were transfected with PPP2R2B constructs encoding the complete sequences of Bbeta2 and Bbeta1, respectively. The colonies with antibiotic resistance were selected as stable cell lines. Both ectopic Bbeta1 and Bbeta2 clones exhibited characteristics of autophagy. To test how cells respond to reactive oxygen species generators, the cells were treated with either hydrogen peroxide or t-butyl hydroperoxide and Bbeta2 clones induced cell death. Suppression of autophagy using either RNA interference of the essential autophagy gene or pharmacological inhibitor rescued cell death caused by oxidative stress. CONCLUSIONS: Cells with ectopically expressed mitochondria-targeted regulatory subunit PPP2R2B of the holoenzyme PP2A were shown predisposed to autophagy and oxidative stress induced cell death that is related to apoptosis. The results promised a model for studying the mechanism and function of aberrant PPP2R2B expression in neuronal cells. The work provided a new target for understanding and prevention of neuropathogenesis.

Influence of Annealing Temperature on Weak-Cavity Top-Emission Red Quantum Dot Light Emitting Diode.

In this report, we show that the annealing temperature in QDs/Mg-doped ZnO film plays a very important role in determining QLEDs performance. Measurements of capacitance and single carrier device reveal that the change of the device efficiency with different annealing temperatures is related to the balance of both electron and hole injection. A comparison of annealing temperatures shows that the best performance is demonstrated with 150 °C-annealing temperature. With the improved charge injection and charge balance, a maximum current efficiency of 24.81 cd/A and external quantum efficiency (EQE) of 20.09% are achievable in our red top-emission QLEDs with weak microcavity structure.

White-Light Photosensors Based on Ag Nanoparticle-Reduced Graphene Oxide Hybrid Materials.

The unique and outstanding electrical and optical properties of graphene make it a potential material to be used in the construction of high-performance photosensors. However, the fabrication process of a graphene photosensor is usually complicated and the size of the device also is restricted to micrometer scale. In this work, we report large-area photosensors based on reduced graphene oxide (rGO) implemented with Ag nanoparticles (AgNPs) via a simple and cost-effective method. To further optimize the performance of photosensors, the absorbance and distribution of the electrical field intensity of graphene with AgNPs was simulated using the finite-difference time-domain (FDTD) method through use of the surface plasmon resonance effect. Based on the simulated results, we constructed photosensors using rGO with 60⁻80 nm AgNPs and analyzed the characteristics at room temperature under white-light illumination for outdoor environment applications. The on/off ratio of the photosensor with AgNPs was improved from 1.166 to 9.699 at the bias voltage of -1.5 V, which was compared as a sample without AgNPs. The proposed photosensor affords a new strategy to construct cost-effective and large-area graphene films which raises opportunities in the field of next-generation optoelectronic devices operated in an outdoor environment.

Well-aligned Vertically Oriented ZnO Nanorod Arrays and their Application in Inverted Small Molecule Solar Cells.

This manuscript describes how to design and fabricate efficient inverted solar cells, which are based on a two-dimensional conjugated small molecule (SMPV1) and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM), by utilizing ZnO nanorods (NRs) grown on a high quality Al-doped ZnO (AZO) seed layer. The inverted SMPV1:PC71BM solar cells with ZnO NRs that grew on both a sputtered and sol-gel processed AZO seed layer are fabricated. Compared with the AZO thin film prepared by the sol-gel method, the sputtered AZO thin film exhibits better crystallization and lower surface roughness, according to X-ray diffraction (XRD) and atomic force microscope (AFM) measurements. The orientation of the ZnO NRs grown on a sputtered AZO seed layer shows better vertical alignment, which is beneficial for the deposition of the subsequent active layer, forming better surface morphologies. Generally, the surface morphology of the active layer mainly dominates the fill factor (FF) of the devices. Consequently, the well-aligned ZnO NRs can be used to improve the carrier collection of the active layer and to increase the FF of the solar cells. Moreover, as an anti-reflection structure, it can also be utilized to enhance the light harvesting of the absorption layer, with the power conversion efficiency (PCE) of solar cells reaching 6.01%, higher than the sol-gel based solar cells with an efficiency of 4.74%.

Zika Virus Infects Intermediate Progenitor Cells and Post-mitotic Committed Neurons in Human Fetal Brain Tissues.

Zika virus (ZIKV) infection is associated with microcephaly in fetuses, but the pathogenesis of ZIKV-related microcephaly is not well understood. Here we show that ZIKV infects the subventricular zone in human fetal brain tissues and that the tissue tropism broadens with the progression of gestation. Our research demonstrates also that intermediate progenitor cells (IPCs) are the main target cells for ZIKV. Post-mitotic committed neurons become susceptible to ZIKV infection as well at later stages of gestation. Furthermore, activation of microglial cells, DNA fragmentation, and apoptosis of infected or uninfected cells could be found in ZIKV-infected brain tissues. Our studies identify IPCs as the main target cells for ZIKV. They also suggest that immune activation after ZIKV infection may play an important role in the pathogenesis of ZIKV-related microcephaly.