Single-Cell Transcriptomics Reveals a Heterogeneous Cellular Response to BK Virus Infection.

BK virus (BKV) is a human polyomavirus that is generally harmless but can cause devastating disease in immunosuppressed individuals. BKV infection of renal cells is a common problem for kidney transplant patients undergoing immunosuppressive therapy. In cultured primary human renal proximal tubule epithelial (RPTE) cells, BKV undergoes a productive infection. The BKV-encoded large T antigen (LT) induces cell cycle entry, resulting in the upregulation of numerous genes associated with cell proliferation. Consistently, microarray and transcriptome sequencing (RNA-seq) experiments performed on bulk infected cell populations identified several proliferation-related pathways that are upregulated by BKV. These studies revealed few genes that are downregulated. In this study, we analyzed viral and cellular transcripts in single mock- or BKV-infected cells. We found that the levels of viral mRNAs vary widely among infected cells, resulting in different levels of LT and viral capsid protein expression. Cells expressing the highest levels of viral transcripts account for approximately 20% of the culture and have a gene expression pattern that is distinct from that of cells expressing lower levels of viral mRNAs. Surprisingly, cells expressing low levels of viral mRNA do not progress with time to high expression, suggesting that the two cellular responses are determined prior to or shortly following infection. Finally, comparison of cellular gene expression patterns of cells expressing high levels of viral mRNA with those of mock-infected cells or cells expressing low levels of viral mRNA revealed previously unidentified pathways that are downregulated by BKV. Among these are pathways associated with drug metabolism and detoxification, tumor necrosis factor (TNF) signaling, energy metabolism, and translation.IMPORTANCE The outcome of viral infection is determined by the ability of the virus to redirect cellular systems toward progeny production countered by the ability of the cell to block these viral actions. Thus, an infected culture consists of thousands of cells, each fighting its own individual battle. Bulk measurements, such as PCR or RNA-seq, measure the average of these individual responses to infection. Single-cell transcriptomics provides a window to the one-on-one battle between BKV and each cell. Our studies reveal that only a minority of infected cells are overwhelmed by the virus and produce large amounts of BKV mRNAs and proteins, while the infection appears to be restricted in the remaining cells. Correlation of viral transcript levels with cellular gene expression patterns reveals pathways manipulated by BKV that may play a role in limiting infection.

Linear triglycerol-based fluorosurfactants show high potential for droplet-microfluidics-based biochemical assays.

Fluorosurfactants have expanded the landscape of high-value biochemical assays in microfluidic droplets, but little is known about how the spatial geometries and polarity of the head group contribute to the performance of fluorosurfactants. To decouple this, we design, synthesize, and characterize two linear and two dendritic glycerol- or tris-based surfactants with a common perfluoropolyether tail. To reveal the influence of spatial geometry, we choose inter-droplet cargo transport as a stringent test case. Using surfactants with linear di- and triglycerol, we show that the inter-droplet cargo transport is minimal compared with their dendritic counterparts. When we encapsulated a less-leaky sodium fluorescent dye into the droplets, quantitatively, we find that the mean fluorescence intensity of the PFPE-dTG stabilized PBS-only droplets after 72 h was ∼3 times that of the signal detected in PBS-only droplets stabilized by PFPE-lTG. We also demonstrate that the post-functionalization of PFPE-lTG having a linear geometry and four hydroxy groups enables the 'from-Droplet' fishing of the biotin-streptavidin protein complex without the trade-off between fishing efficiency and droplet stability. Thus, our approach to design user-friendly surfactants reveals the aspects of spatial geometry and facile tunability of the polar head groups that have not been captured or exploited before.

Controlled growth of atomically thin In2Se3 flakes by van der Waals epitaxy.

The controlled production of high-quality atomically thin III-VI semiconductors poses a challenge for practical applications in electronics, optoelectronics, and energy science. Here, we exploit a controlled synthesis of single- and few-layer In2Se3 flakes on different substrates, such as graphene and mica, by van der Waals epitaxy. The thickness, orientation, nucleation site, and crystal phase of In2Se3 flakes were well-controlled by tuning the growth condition. The obtained In2Se3 flakes exhibit either semiconducting or metallic behavior depending on the crystal structures. Meanwhile, field-effect transistors based on the semiconducting In2Se3 flakes showed an efficient photoresponse. The controlled growth of atomically thin In2Se3 flakes with diverse conductivity and efficient photoresponsivity could lead to new applications in photodetectors and phase change memory devices.

Controlled synthesis of topological insulator nanoplate arrays on mica.

The orientation- and position-controlled synthesis of single-crystal topological insulator (Bi(2)Se(3) and Bi(2)Te(3)) nanoplate arrays on mica substrates was achieved using van der Waals epitaxy. Individual ultrathin nanoplates with the lateral dimension up to ~0.1 mm or uniform thickness down to 1-2 nm were produced. Single-Dirac-cone surface states of nanoplate aggregates were confirmed by angle-resolved photoemission spectroscopy measurements. The large-grain-size, single-crystal nanoplate arrays grown on mica can act as facile platforms for a combination of spectroscopy and in situ transport measurements, which may open up new avenues for studying exotic physical phenomena, surface chemical reactions, and modification in topological insulators.

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome.

Characterizing complex microbial communities with single-cell resolution has been a long-standing goal of microbiology. We present Microbe-seq, a high-throughput method that yields the genomes of individual microbes from complex microbial communities. We encapsulate individual microbes in droplets with microfluidics and liberate their DNA, which we then amplify, tag with droplet-specific barcodes, and sequence. We explore the human gut microbiome, sequencing more than 20,000 microbial single-amplified genomes (SAGs) from a single human donor and coassembling genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe microbial interactions, reconstructing the horizontal gene transfer (HGT) network and observing HGT between 92 species pairs; we also identify a significant in vivo host-phage association between crAssphage and one strain of Bacteroides vulgatus. Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution.

Dendronized fluorosurfactant for highly stable water-in-fluorinated oil emulsions with minimal inter-droplet transfer of small molecules.

Fluorosurfactant-stabilized microfluidic droplets are widely used as pico- to nanoliter volume reactors in chemistry and biology. However, current surfactants cannot completely prevent inter-droplet transfer of small organic molecules encapsulated or produced inside the droplets. In addition, the microdroplets typically coalesce at temperatures higher than 80 °C. Therefore, the use of droplet-based platforms for ultrahigh-throughput combination drug screening and polymerase chain reaction (PCR)-based rare mutation detection has been limited. Here, we provide insights into designing surfactants that form robust microdroplets with improved stability and resistance to inter-droplet transfer. We used a panel of dendritic oligo-glycerol-based surfactants to demonstrate that a high degree of inter- and intramolecular hydrogen bonding, as well as the dendritic architecture, contribute to high droplet stability in PCR thermal cycling and minimize inter-droplet transfer of the water-soluble fluorescent dye sodium fluorescein salt and the drug doxycycline.

Patterning two-dimensional chalcogenide crystals of Bi2Se3 and In2Se3 and efficient photodetectors.

Patterning of high-quality two-dimensional chalcogenide crystals with unique planar structures and various fascinating electronic properties offers great potential for batch fabrication and integration of electronic and optoelectronic devices. However, it remains a challenge that requires accurate control of the crystallization, thickness, position, orientation and layout. Here we develop a method that combines microintaglio printing with van der Waals epitaxy to efficiently pattern various single-crystal two-dimensional chalcogenides onto transparent insulating mica substrates. Using this approach, we have patterned large-area arrays of two-dimensional single-crystal Bi2Se3 topological insulator with a record high Hall mobility of ∼1,750 cm(2) V(-1) s(-1) at room temperature. Furthermore, our patterned two-dimensional In2Se3 crystal arrays have been integrated and packaged to flexible photodetectors, yielding an ultrahigh external photoresponsivity of ∼1,650 A W(-1) at 633 nm. The facile patterning, integration and packaging of high-quality two-dimensional chalcogenide crystals hold promise for innovations of next-generation photodetector arrays, wearable electronics and integrated optoelectronic circuits.

Selective-area van der Waals epitaxy of topological insulator grid nanostructures for broadband transparent flexible electrodes.

Broadband transparent electrodes based on a two-dimensional grid of topological insulator Bi2Se3 are synthesized by a facile selective-area van der Waals epitaxy method. These two-dimensional grid electrodes exhibit high uniformity over large area, outstanding mechanical durability, and excellent chemical resistance to environmental perturbations. Remarkably, the topological grid electrode has high transmittance of more than 85% from the visible to the near-infrared region.

Topological insulator nanostructures for near-infrared transparent flexible electrodes.

Topological insulators are an intriguing class of materials with an insulating bulk state and gapless Dirac-type edge/surface states. Recent theoretical work predicts that few-layer topological insulators are promising candidates for broadband and high-performance optoelectronic devices due to their spin-momentum-locked massless Dirac edge/surface states, which are topologically protected against all time-reversal-invariant perturbations. Here, we present the first experimental demonstration of near-infrared transparent flexible electrodes based on few-layer topological-insulator Bi(2)Se(3) nanostructures epitaxially grown on mica substrates by means of van der Waals epitaxy. The large, continuous, Bi(2)Se(3)-nanosheet transparent electrodes have single Dirac cone surface states, and exhibit sheet resistances as low as ~330 Ω per square, with a transparency of more than 70% over a wide range of wavelengths. Furthermore, Bi(2)Se(3)-nanosheet transparent electrodes show high chemical and thermal stabilities as well as excellent mechanical durability, which may lead to novel optoelectronic devices with unique properties.