Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm.

Tumor heterogeneity presents a challenge for inferring clonal evolution and driver gene identification. Here, we describe a method for analyzing the cancer genome at a single-cell nucleotide level. To perform our analyses, we first devised and validated a high-throughput whole-genome single-cell sequencing method using two lymphoblastoid cell line single cells. We then carried out whole-exome single-cell sequencing of 90 cells from a JAK2-negative myeloproliferative neoplasm patient. The sequencing data from 58 cells passed our quality control criteria, and these data indicated that this neoplasm represented a monoclonal evolution. We further identified essential thrombocythemia (ET)-related candidate mutations such as SESN2 and NTRK1, which may be involved in neoplasm progression. This pilot study allowed the initial characterization of the disease-related genetic architecture at the single-cell nucleotide level. Further, we established a single-cell sequencing method that opens the way for detailed analyses of a variety of tumor types, including those with high genetic complex between patients.

Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor.

Clear cell renal cell carcinoma (ccRCC) is the most common kidney cancer and has very few mutations that are shared between different patients. To better understand the intratumoral genetics underlying mutations of ccRCC, we carried out single-cell exome sequencing on a ccRCC tumor and its adjacent kidney tissue. Our data indicate that this tumor was unlikely to have resulted from mutations in VHL and PBRM1. Quantitative population genetic analysis indicates that the tumor did not contain any significant clonal subpopulations and also showed that mutations that had different allele frequencies within the population also had different mutation spectrums. Analyses of these data allowed us to delineate a detailed intratumoral genetic landscape at a single-cell level. Our pilot study demonstrates that ccRCC may be more genetically complex than previously thought and provides information that can lead to new ways to investigate individual tumors, with the aim of developing more effective cellular targeted therapies.

Multistress Interplay: Time and Duration of Ocean Acidification Modulate the Toxicity of Mercury and Other Metals.

The current understanding of multistress interplay assumes stresses occur in perfect synchrony, but this assumption is rarely met in the natural marine ecosystem. To understand the interplay between nonperfectly overlapped stresses in the ocean, we manipulated a multigenerational experiment (F0-F3) to explore how different temporal scenarios of ocean acidification will affect mercury toxicity in a marine copepod Pseudodiaptomus annandalei. We found that the scenario of past acidification aggravated mercury toxicity but current and persistent acidification mitigated its toxicity. We specifically performed a proteomics analysis for the copepods of F3. The results indicated that current and persistent acidification initiated the energy compensation for development and mercury efflux, whereas past acidification lacked the barrier of H+ and had dysfunction in the detoxification and efflux system, providing a mechanistic understanding of mercury toxicity under different acidification scenarios. Furthermore, we conducted a meta-analysis on marine animals, demonstrating that different acidification scenarios could alter the toxicity of several other metals, despite evidence from nonsynchronous scenarios remaining limited. Our study thus demonstrates that time and duration of ocean acidification modulate mercury toxicity in marine copepods and suggests that future studies should move beyond the oversimplified scenario of perfect synchrony in understanding multistress interaction.

Long-Term Highly Stable High-Voltage LiCoO2 Synthesized via a Solid Sulfur-Assisted One-Pot Approach.

Commercialized lithium cobalt oxide (LCO) only shows a relatively low capacity of ≈175 mAh g-1 despite a high theoretical capacity of ≈274 mAh g-1 . As an effective and direct strategy, increasing its charge cutoff voltage can, in principle, escalate the capacity, which is however precluded by the irreversible phase transition, oxygen loss, and severe side reactions with electrolytes normally. Herein, an in situ sulfur-assisted solid-state approach is proposed for one-pot synthesis of long-term highly stable high-voltage LCO with a novel compound structure. The coating of coherent spinel Lix Co2 O4 shells on and the gradient doping of SO4 2- polyanions into LCO are in situ realized simultaneously in terms of gas-solid interface reactions between metal oxides and generated SO2 gas from sulfur during synthesis. At 4.6 V, this LCO shows the discharge capacities of 232.4 mAh g-1 at 0.1 C (1 C = 280 mA g-1 ), 215 mAh g-1 at 1 C and 139 mAh g-1 even at 20 C and the capacity retentions of 97.4% (89.7%) after 100 (300) cycles at 1 C. This approach is facile, low-cost and up-scalable and may provide a route to improve the performance of LCO and other electrode materials greatly.

Enhanced Oxygen Reduction Catalysis of Carbon Nanohybrids from Nitrogen-Rich Edges.

The edge doping effect would help improve the carbon-based electrocatalysis. Herein, we present an all-mechanical technique for the fabrication of cut, exfoliated N-doped carbon nanotubes (C, E-N-CNTs). Such nanohybrids with an edge-N-rich structure are obtained through sequential doping and mechanical treatments of the pristine bulk-CNTs. The C, E-N-CNT/carbon black (C, E-N-CNT/C) demonstrates exciting oxygen reduction reaction (ORR) electrocatalysis with exceptionally low-onset potential (E0, 913 mV versus RHE) and satisfactory half-wave potential (E1/2, merely -7.3 mV shift compared with that of commercial 20% platinum/C (Pt/C)). Besides, the C, E-N-CNT/C presents significantly enhanced durability and tolerance in chronoamperometry test with methanol injection compared with the Pt/C. Our work would facilitate the mass production and full exploration of nonmetallic electrocatalysts.

Sustainable Hydrothermal Carbonization Synthesis of Iron/Nitrogen-Doped Carbon Nanofiber Aerogels as Electrocatalysts for Oxygen Reduction.

It is urgent to develop new kinds of low-cost and high-performance nonprecious metal (NPM) catalysts as alternatives to Pt-based catalysts for oxygen reduction reaction (ORR) in fuel cells and metal-air batteries, which have been proved to be efficient to meet the challenge of increase of global energy demand and CO2 emissions. Here, an economical and sustainable method is developed for the synthesis of Fe, N codoped carbon nanofibers (Fe-N/CNFs) aerogels as efficient NPM catalysts for ORR via a mild template-directed hydrothermal carbonization (HTC) process, where cost-effective biomass-derived d(+)-glucosamine hydrochloride and ferrous gluconate are used as precursors and recyclable ultrathin tellurium nanowires are used as templates. The prepared Fe/N-CNFs catalysts display outstanding ORR activity, i.e., onset potential of 0.88 V and half-wave potential of 0.78 V versus reversible hydrogen electrode in an alkaline medium, which is highly comparable to that of commercial Pt/C (20 wt% Pt) catalyst. Furthermore, the Fe/N-CNFs catalysts exhibit superior long-term stability and better tolerance to the methanol crossover effect than the Pt/C catalyst in both alkaline and acidic electrolytes. This work suggests the great promise of developing new families of NPM ORR catalysts by the economical and sustainable HTC process.

Carbon nanofibers decorated with molybdenum disulfide nanosheets: synergistic lithium storage and enhanced electrochemical performance.

Traditional lithium-ion batteries that are based on layered Li intercalation electrode materials are limited by the intrinsically low theoretical capacities of both electrodes and cannot meet the increasing demand for energy. A facile route for the synthesis of a new type of composite nanofibers, namely carbon nanofibers decorated with molybdenum disulfide sheets (CNFs@MoS2), is now reported. A synergistic effect was observed for the two-component anode, triggering new electrochemical processes for lithium storage, with a persistent oxidation from Mo (or MoS2) to MoS3 in the repeated charge processes, leading to an ascending capacity upon cycling. The composite exhibits unprecedented electrochemical behavior with high specific capacity, good cycling stability, and superior high-rate capability, suggesting its potential application in high-energy lithium-ion batteries.

Unveiling the Roles of Trace Fe and F Co-doped into High-Ni Li-Rich Layered Oxides in Performance Improvement.

High-Ni Li-rich layered oxides (HNLOs) derived from Li-rich Mn-based layered oxides (LRMLOs) can effectively mitigate the voltage decay of LRMLOs but normally suffered from decreased capacity and cycling stability. Herein, an effective, simple, and up-scalable co-doping strategy of trace Fe and F ions via a facile expanded graphite template-sacrificed approach was proposed for improving the performance of HNLOs. The trace Fe and F co-doping can far more effectively improve both its rate capability and cycling stability in a synergistic manner compared to the introduction of individual Fe cations and F anions. The co-doping of Fe and F increased the Li-O bonds by a magnitude far larger than the summation of the increments by their individual doping, quite favorable for the performance. The trace Fe doping can escalate the capacity and enhance the rate capability significantly by increasing the components of lower valence transition metals to activate their redox reactions more effectively and improving both the electronic and ionic conduction. In contrast, trace F can improve the cycling stability remarkably by lowering the O 2p band top to suppress the lattice oxygen escape effectively which were revealed by density functional theory calculations. The co-doped cathode exhibited excellent cycling stability with a superior capacity retention of 90% after 200 cycles at 1 C, much higher than 64% for the pristine sample. This study offers an idea for synergistically improving the performance of Li-rich layered oxides by co-doping trace Fe cations and F anions simultaneously, which play a complementary role in performance improvement.

Lithium Antievaporation-Loss Engineering via Sodium/Potassium Doping Enables Superior Electrochemical Performance of High-Nickel Li-Rich Layered Oxide Cathodes.

Low-cost Mn- and Li-rich layered oxides suffer from rapid voltage decay, which can be improved by increasing the nickel content to derive high nickel Li-rich layered oxides (HNLO) but is normally accompanied by reduced capacity and inferior cycling stability. Herein, Na or K ions are successfully doped into the lattice of high nickel Li-rich Li1.2-xMxNi0.32Mn0.48O2 (M = Na, K) layered oxides via a facile expanded graphite template-sacrificed approach. Both Na- and K-doped samples exhibit excellent rate capability and cycling stability compared with the un-doped one. The Na-doped sample shows a capacity retention of 93% after 200 cycles at 1C, which is quite outstanding for HNLO. The greatly improved electrochemical performances are attributed to the increased effective Li content in the lattice via Li antievaporation-loss engineering, the expanded Li slab, the pillaring effect, the increased C2/m component, and the improved electronic conductivity. Different performances by the introduction of sodium and potassium ions may be ascribed to their different ionic radii, which give rise to their different doping behaviors and threshold doping amounts. This work provides a new idea of enhancing electrochemical performance of HNLO by doping proper alien elements to increase the lattice lithium content effectively.

Aerobactin-Mediated Iron Acquisition Enhances Biofilm Formation, Oxidative Stress Resistance, and Virulence of Yersinia pseudotuberculosis.

Aerobactin is a citrate-hydroxamate siderophore that is critical for the virulence of pathogenic enteric bacteria. However, although the aerobactin-producing iucABCD-iutA operon is distributed widely in the genomes of Yersinia species, none of the pathogenic Yersinia spp. was found to produce aerobactin. Here, we showed that the iucABCD-iutA operon in the food-borne enteric pathogen Yersinia pseudotuberculosis YPIII is a functional siderophore system involved in iron acquisition. The expression of the operon was found to be directly repressed by the ferric uptake regulator (Fur) in an iron concentration-dependent manner. In addition, we demonstrated that the aerobactin-mediated iron acquisition contributes to bacterial growth under iron-limited conditions. Moreover, we provided evidence that aerobactin plays important roles in biofilm formation, resistance to oxidative stress, ROS removal, and virulence of Y. pseudotuberculosis. Overall, our study not only uncovered a novel strategy of iron acquisition in Y. pseudotuberculosis but also highlighted the importance of aerobactin in the pathogenesis of Y. pseudotuberculosis.

A general strategy for semiconductor quantum dot production.

Mass production of semiconductor quantum dots (QDs) from bulk materials is highly desired but far from being satisfactory. Herein, we report a general strategy to mechanically tailor semiconductor bulk materials into QDs. Semiconductor bulk materials are routinely available via simple chemical precipitation. From their bulk materials, a variety of semiconductor (e.g., lead sulfide (PbS), cadmium sulfide (CdS), copper sulfide (CuS), ferrous sulfide (FeS), and zinc sulfide (ZnS)) QDs are successfully produced in high yields (>15 wt%). This is achieved by a combination of silica-assisted ball-milling and sonication-assisted solvent treatment. The as-produced QDs show intrinsic characteristics and outstanding water solubility (up to 5 mg mL-1), facilitating their practical applications. The QD dispersions present remarkable photoluminescence (PL) with exciton-dependence and nanosecond (ns)-scale lifetimes. The QDs-poly(methyl methacrylate) (PMMA) hybrid thin films demonstrate exciting solid-state fluorescence and exceptional nonlinear saturation absorption (NSA). Absolute modulation depths of up to 58% and saturation intensities down to 0.40 MW cm-2 were obtained. Our strategy could be applied to any semiconductor bulk materials and therefore paves the way for the construction of the complete library of semiconductor QDs.

Tailoring Multi-Walled Carbon Nanotubes into Graphene Quantum Sheets.

Transformation of carbon nanotubes (CNTs) into sub-10 nm pieces is highly required but remains a great challenge. Herein, we report a robust strategy capable of mechanically tailoring pristine multi-walled carbon nanotubes (MWCNTs) into graphene quantum sheets (M-GQSs) with an extremely high yield of up to 44.6 wt %. The method combines silica-assisted ball-milling and sonication-assisted solvent exfoliation and therefore enables reproducible high-yield production of M-GQSs directly from MWCNTs. Remarkable solvent diversity and extraordinary solvability (up to 7 mg/mL) are demonstrated facilitating the solution processing of the M-GQSs. The M-GQSs are essentially monolayers with intrinsic curvature, which could be determinative to their outstanding performances in both dispersions and thin films. Besides the excitation wavelength-, concentration-, and solvent-dependent photoluminescence in dispersions, the solid-state fluorescence and exceptional nonlinear saturation absorption (NSA) in thin films are demonstrated. Particularly, NSA with relative modulation depth up to 46% and saturation intensity down to 1.53 MW/cm2 are achieved in M-GQS/poly(methyl methacrylate) hybrid thin films with a loading content of merely 0.2 wt %. Our method opens up a new avenue toward conversion and utilization of CNTs.

Cobalt/nitrogen codoped carbon nanosheets derived from catkins as a high performance non-noble metal electrocatalyst for oxygen reduction reaction and hydrogen evolution reaction.

Novel energy devices which are capable of alleviating and/or solving the energy dilemma such as overall water splitting and fuel cells require the development of highly efficient catalysts, especially cheap high performance non-precious metal (NPM) catalysts. Here, we prepare highly efficient NPM catalysts of cobalt and nitrogen codoped carbon nanosheets (Co/N-CNSs) for oxygen reduction reaction (ORR) and hydrogen evolution reaction (HER) using harmful environment-polluting waste of biomass catkins as carbon precursors via a mild mechanical exfoliation and chemical process which is facile, low-cost, environmentally friendly and up-scalable. Compared with a commercial platinum-based catalyst (commercial 20% Pt/C), the Co/N-CNS electrocatalysts show outstanding ORR activity, acceptable HER activity and long term stability with an onset potential of 0.92 V versus the reversible hydrogen electrode (vs. RHE) and a half-wave potential of 0.83 V vs. the RHE in alkaline electrolytes. The excellent performance is closely related to the presence of abundant CoN x active sites. This work offers a novel and effective approach for preparing highly efficient ORR and HER NPM electrocatalysts from waste biomass materials.

Robust Assembly of Colloidal Nanoparticles for Controlled-Reflectance Surface Construction.

Controlled placement of nanoscale particles with nanometer precision on substrates/surfaces is highly desired toward functional nanodevices. Herein, we report the robust assembly of colloidal nanoparticles onto nanostructured aluminum surfaces. The surfaces are configured by porous anodic alumina (PAA) membranes on top of textured aluminum substrates. Capillary force and geometry confinement enable rapid and precise transfer of colloidal nanoparticles from solutions into PAA templates. Such top-down control of bottom-up assembly demonstrates large-area (>1 × 1 cm2) integration of nanoscale particles with exceedingly high yield (>95%) and exceptionally high density (>1010 particles/cm2). The plasmonic coupling between gold nanoparticles and aluminum surfaces, as well as between adjacent nanoparticles, is responsible for the unique reflectance from the assembled surfaces. The reflectance minimum (resonant absorption) can be readily shifted from visible to near-infrared by simple structural variation. The apparent surface colors are thus broadly manipulated. Our work offers a straightforward platform toward construction of surfaces with controlled reflectance.

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing.

BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate-oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed. RESULTS: We systematically compared the advantages and disadvantages of different WGA methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly higher genome recovery sensitivity (~84 %) than DOP-PCR (~6 %) and MALBAC (~52 %) at high sequencing depth. MALBAC and MDA had comparable single-nucleotide variations detection efficiency, false-positive ratio, and allele drop-out ratio. We further demonstrated that SCRS data amplified by either MDA or MALBAC from a gastric cancer cell line could accurately detect gastric cancer CNVs with comparable sensitivity and specificity, including amplifications of 12p11.22 (KRAS) and 9p24.1 (JAK2, CD274, and PDCD1LG2). CONCLUSIONS: Our findings provide a comprehensive comparison of variations detection performance using SCRS amplified by different WGA methods. It will guide researchers to determine which WGA method is best suited to individual experimental needs at single-cell level.

Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer.

BACKGROUND: Cancers arise through an evolutionary process in which cell populations are subjected to selection; however, to date, the process of bladder cancer, which is one of the most common cancers in the world, remains unknown at a single-cell level. RESULTS: We carried out single-cell exome sequencing of 66 individual tumor cells from a muscle-invasive bladder transitional cell carcinoma (TCC). Analyses of the somatic mutant allele frequency spectrum and clonal structure revealed that the tumor cells were derived from a single ancestral cell, but that subsequent evolution occurred, leading to two distinct tumor cell subpopulations. By analyzing recurrently mutant genes in an additional cohort of 99 TCC tumors, we identified genes that might play roles in the maintenance of the ancestral clone and in the muscle-invasive capability of subclones of this bladder cancer, respectively. CONCLUSIONS: This work provides a new approach of investigating the genetic details of bladder tumoral changes at the single-cell level and a new method for assessing bladder cancer evolution at a cell-population level.