High-temperature electrothermal remediation of multi-pollutants in soil.

Soil contamination is an environmental issue due to increasing anthropogenic activities. Existing processes for soil remediation suffer from long treatment time and lack generality because of different sources, occurrences, and properties of pollutants. Here, we report a high-temperature electrothermal process for rapid, water-free remediation of multiple pollutants in soil. The temperature of contaminated soil with carbon additives ramps up to 1000 to 3000 °C as needed within seconds via pulsed direct current input, enabling the vaporization of heavy metals like Cd, Hg, Pb, Co, Ni, and Cu, and graphitization of persistent organic pollutants like polycyclic aromatic hydrocarbons. The rapid treatment retains soil mineral constituents while increases infiltration rate and exchangeable nutrient supply, leading to soil fertilization and improved germination rates. We propose strategies for upscaling and field applications. Techno-economic analysis indicates the process holds the potential for being more energy-efficient and cost-effective compared to soil washing or thermal desorption.

High-surface-area corundum nanoparticles by resistive hotspot-induced phase transformation.

High-surface-area α-Al2O3 nanoparticles are used in high-strength ceramics and stable catalyst supports. The production of α-Al2O3 by phase transformation from γ-Al2O3 is hampered by a high activation energy barrier, which usually requires extended high-temperature annealing (~1500 K, > 10 h) and suffers from aggregation. Here, we report the synthesis of dehydrated α-Al2O3 nanoparticles (phase purity ~100%, particle size ~23 nm, surface area ~65 m2 g-1) by a pulsed direct current Joule heating of γ-Al2O3. The phase transformation is completed at a reduced bulk temperature and duration (~573 K, < 1 s) via an intermediate δ'-Al2O3 phase. Numerical simulations reveal the resistive hotspot-induced local heating in the pulsed current process enables the rapid transformation. Theoretical calculations show the topotactic transition (from γ- to δ'- to α-Al2O3) is driven by their surface energy differences. The α-Al2O3 nanoparticles are sintered to nanograined ceramics with hardness superior to commercial alumina and approaching that of sapphire.

Heteroatom-Doped Flash Graphene.

Heteroatom doping can effectively tailor the local structures and electronic states of intrinsic two-dimensional materials, and endow them with modified optical, electrical, and mechanical properties. Recent studies have shown the feasibility of preparing doped graphene from graphene oxide and its derivatives via some post-treatments, including solid-state and solvothermal methods, but they require reactive and harsh reagents. However, direct synthesis of various heteroatom-doped graphene in larger quantities and high purity through bottom-up methods remains challenging. Here, we report catalyst-free and solvent-free direct synthesis of graphene doped with various heteroatoms in bulk via flash Joule heating (FJH). Seven types of heteroatom-doped flash graphene (FG) are synthesized through millisecond flashing, including single-element-doped FG (boron, nitrogen, oxygen, phosphorus, sulfur), two-element-co-doped FG (boron and nitrogen), as well as three-element-co-doped FG (boron, nitrogen, and sulfur). A variety of low-cost dopants, such as elements, oxides, and organic compounds are used. The graphene quality of heteroatom-doped FG is high, and similar to intrinsic FG, the material exhibits turbostraticity, increased interlayer spacing, and superior dispersibility. Electrochemical oxygen reduction reaction of different heteroatom-doped FG is tested, and sulfur-doped FG shows the best performance. Lithium metal battery tests demonstrate that nitrogen-doped FG exhibits a smaller nucleation overpotential compared to Cu or undoped FG. The electrical energy cost for the synthesis of heteroatom-doped FG synthesis is only 1.2 to 10.7 kJ g-1, which could render the FJH method suitable for low-cost mass production of heteroatom-doped graphene.

Rare earth elements from waste.

Rare earth elements (REEs) are critical materials in electronics and clean technologies. With the diminishing of easily accessible minerals for mining, the REE recovery from waste is an alternative toward a circular economy. Present methods for REE recovery suffer from lengthy purifications, low extractability, and high wastewater streams. Here, we report an ultrafast electrothermal process (~3000°C, ~1 s) based on flash Joule heating (FJH) for activating wastes to improve REE extractability. FJH thermally degrades or reduces the hard-to-dissolve REE species to components with high thermodynamic solubility, leading to ~2× increase in leachability and high recovery yields using diluted acid (e.g., 0.1 M HCl). The activation strategy is feasible for various wastes including coal fly ash, bauxite residue, and electronic waste. The rapid FJH process is energy-efficient with a low electrical energy consumption of 600 kWh ton-1. The potential for this route to be rapidly scaled is outlined.

Phase controlled synthesis of transition metal carbide nanocrystals by ultrafast flash Joule heating.

Nanoscale carbides enhance ultra-strong ceramics and show activity as high-performance catalysts. Traditional lengthy carburization methods for carbide syntheses usually result in coked surface, large particle size, and uncontrolled phase. Here, a flash Joule heating process is developed for ultrafast synthesis of carbide nanocrystals within 1 s. Various interstitial transition metal carbides (TiC, ZrC, HfC, VC, NbC, TaC, Cr2C3, MoC, and W2C) and covalent carbides (B4C and SiC) are produced using low-cost precursors. By controlling pulse voltages, phase-pure molybdenum carbides including ß-Mo2C and metastable α-MoC1-x and η-MoC1-x are selectively synthesized, demonstrating the excellent phase engineering ability of the flash Joule heating by broadly tunable energy input that can exceed 3000 K coupled with kinetically controlled ultrafast cooling (>104 K s-1). Theoretical calculation reveals carbon vacancies as the driving factor for topotactic transition of carbide phases. The phase-dependent hydrogen evolution capability of molybdenum carbides is investigated with ß-Mo2C showing the best performance.

Resolving medulloblastoma cellular architecture by single-cell genomics.

Medulloblastoma is a malignant childhood cerebellar tumour type that comprises distinct molecular subgroups. Whereas genomic characteristics of these subgroups are well defined, the extent to which cellular diversity underlies their divergent biology and clinical behaviour remains largely unexplored. Here we used single-cell transcriptomics to investigate intra- and intertumoral heterogeneity in 25 medulloblastomas spanning all molecular subgroups. WNT, SHH and Group 3 tumours comprised subgroup-specific undifferentiated and differentiated neuronal-like malignant populations, whereas Group 4 tumours consisted exclusively of differentiated neuronal-like neoplastic cells. SHH tumours closely resembled granule neurons of varying differentiation states that correlated with patient age. Group 3 and Group 4 tumours exhibited a developmental trajectory from primitive progenitor-like to more mature neuronal-like cells, the relative proportions of which distinguished these subgroups. Cross-species transcriptomics defined distinct glutamatergic populations as putative cells-of-origin for SHH and Group 4 subtypes. Collectively, these data provide insights into the cellular and developmental states underlying subtype-specific medulloblastoma biology.

Pediatric patients with acute lymphoblastic leukemia generate abundant and functional neoantigen-specific CD8+ T cell responses.

Cancer arises from the accumulation of genetic alterations, which can lead to the production of mutant proteins not expressed by normal cells. These mutant proteins can be processed and presented on the cell surface by major histocompatibility complex molecules as neoepitopes, allowing CD8+ T cells to mount responses against them. For solid tumors, only an average 2% of neoepitopes predicted by algorithms have detectable endogenous antitumor T cell responses. This suggests that low mutation burden tumors, which include many pediatric tumors, are poorly immunogenic. Here, we report that pediatric patients with acute lymphoblastic leukemia (ALL) have tumor-associated neoepitope-specific CD8+ T cells, responding to 86% of tested neoantigens and recognizing 68% of the tested neoepitopes. These responses include a public neoantigen from the ETV6-RUNX1 fusion that is targeted in seven of nine tested patients. We characterized phenotypic and transcriptional profiles of CD8+ tumor-infiltrating lymphocytes (TILs) at the single-cell level and found a heterogeneous population that included highly functional effectors. Moreover, we observed immunodominance hierarchies among the CD8+ TILs restricted to one or two putative neoepitopes. Our results indicate that robust antitumor immune responses are induced in pediatric ALL despite their low mutation burdens and emphasize the importance of immunodominance in shaping cellular immune responses. Furthermore, these data suggest that pediatric cancers may be amenable to immunotherapies aimed at enhancing immune recognition of tumor-specific neoantigens.

A Single-Cell Transcriptional Atlas of the Developing Murine Cerebellum.

The cerebellum develops from a restricted number of cell types that precisely organize to form the circuitry that controls sensory-motor coordination and some higher-order cognitive processes. To acquire an enhanced understanding of the molecular processes that mediate cerebellar development, we performed single-cell RNA-sequencing of 39,245 murine cerebellar cells at twelve critical developmental time points. Using recognized lineage markers, we confirmed that the single-cell data accurately recapitulate cerebellar development. We then followed distinct populations from emergence through migration and differentiation, and determined the associated transcriptional cascades. After identifying key lineage commitment decisions, focused analyses uncovered waves of transcription factor expression at those branching points. Finally, we created Cell Seek, a flexible online interface that facilitates exploration of the dataset. Our study provides a transcriptional summarization of cerebellar development at single-cell resolution that will serve as a valuable resource for future investigations of cerebellar development, neurobiology, and disease.

Genetic evolution of influenza H9N2 viruses isolated from various hosts in China from 1994 to 2013.

Influenza H9N2 subtype viruses and their reassortants (such as H7N9) are posing increasing threats to birds and humans in China. During 2009-2013, multiple novel subtype viruses with H9N2 original genes emerged in China. Yet, the genetic evolution of H9N2 viruses in various host organisms in China has not been systematically investigated since 2009. In the present study, we performed large-scale sequence analysis of H9N2 viral genomes from public databases, representing the spectrum of viruses isolated from birds, mammals and humans in China from 1994 to 2013, and updated the clade classification for each segment. We identified 117 distinct genotypes in 730 H9N2 viruses. We analyzed the sequences of all eight segments in each virus and found three important time points: the years 2000, 2006 and 2010. In the periods divided by these years, genotypic diversity, geographic distribution and host range changed considerably. Genotypic diversity fluctuated greatly in 2000 and 2006. Since 2010, a single genotype became predominant in poultry throughout China, and the eastern coastal region became the newly identified epidemic center. Throughout their 20-year prevalence in China, H9N2 influenza viruses have emerged and adapted from aquatic birds to chickens. The minor avian species and wild birds exacerbated H9N2 genotypes by providing diversified genes, and chickens were the most prevalent vector in which the viruses evolved and expanded their prevalence. It is the necessity for surveillance and disease control on live-bird markets, poultry farms and wild-bird habitats in China.

The neoepitope landscape in pediatric cancers.

BACKGROUND: Neoepitopes derived from tumor-specific somatic mutations are promising targets for immunotherapy in childhood cancers. However, the potential for such therapies in targeting these epitopes remains uncertain due to a lack of knowledge of the neoepitope landscape in childhood cancer. Studies to date have focused primarily on missense mutations without exploring gene fusions, which are a major class of oncogenic drivers in pediatric cancer. METHODS: We developed an analytical workflow for identification of putative neoepitopes based on somatic missense mutations and gene fusions using whole-genome sequencing data. Transcriptome sequencing data were incorporated to interrogate the expression status of the neoepitopes. RESULTS: We present the neoepitope landscape of somatic alterations including missense mutations and oncogenic gene fusions identified in 540 childhood cancer genomes and transcriptomes representing 23 cancer subtypes. We found that 88% of leukemias, 78% of central nervous system tumors, and 90% of solid tumors had at least one predicted neoepitope. Mutation hotspots in KRAS and histone H3 genes encode potential epitopes in multiple patients. Additionally, the ETV6-RUNX1 fusion was found to encode putative neoepitopes in a high proportion (69.6%) of the pediatric leukemia harboring this fusion. CONCLUSIONS: Our study presents a comprehensive repertoire of potential neoepitopes in childhood cancers, and will facilitate the development of immunotherapeutic approaches designed to exploit them. The source code of the workflow is available at GitHub ( https://github.com/zhanglabstjude/neoepitope ).

A Pathogen-Selective Antibiotic Minimizes Disturbance to the Microbiome.

Broad-spectrum antibiotic therapy decimates the gut microbiome, resulting in a variety of negative health consequences. Debio 1452 is a staphylococcus-selective enoyl-acyl carrier protein reductase (FabI) inhibitor under clinical development and was used to determine whether treatment with pathogen-selective antibiotics would minimize disturbance to the microbiome. The effect of oral Debio 1452 on the microbiota of mice was compared to the effects of four commonly used broad-spectrum oral antibiotics. During the 10 days of oral Debio 1452 treatment, there was minimal disturbance to the gut bacterial abundance and composition, with only the unclassified S24-7 taxon reduced at days 6 and 10. In comparison, broad-spectrum oral antibiotics caused ∼100- to 4,000-fold decreases in gut bacterial abundance and severely altered the microbial composition. The gut bacterial abundance and composition of Debio 1452-treated mice were indistinguishable from those of untreated mice 2 days after the antibiotic treatment was stopped. In contrast, the bacterial abundance in broad-spectrum-antibiotic-treated mice took up to 7 days to recover, and the gut composition of the broad-spectrum-antibiotic-treated mice remained different from that of the control group 20 days after the cessation of antibiotic treatment. These results illustrate that a pathogen-selective approach to antibiotic development will minimize disturbance to the gut microbiome.

Critical Role for the DNA Sensor AIM2 in Stem Cell Proliferation and Cancer.

Colorectal cancer is a leading cause of cancer-related deaths. Mutations in the innate immune sensor AIM2 are frequently identified in patients with colorectal cancer, but how AIM2 modulates colonic tumorigenesis is unknown. Here, we found that Aim2-deficient mice were hypersusceptible to colonic tumor development. Production of inflammasome-associated cytokines and other inflammatory mediators was largely intact in Aim2-deficient mice; however, intestinal stem cells were prone to uncontrolled proliferation. Aberrant Wnt signaling expanded a population of tumor-initiating stem cells in the absence of AIM2. Susceptibility of Aim2-deficient mice to colorectal tumorigenesis was enhanced by a dysbiotic gut microbiota, which was reduced by reciprocal exchange of gut microbiota with healthy wild-type mice. These findings uncover a synergy between a specific host genetic factor and gut microbiota in determining the susceptibility to colorectal cancer. Therapeutic modulation of AIM2 expression and microbiota has the potential to prevent colorectal cancer.

Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus.

The emergence of human infection with a novel H7N9 influenza virus in China raises a pandemic concern. Chicken H9N2 viruses provided all six of the novel reassortant's internal genes. However, it is not fully understood how the prevalence and evolution of these H9N2 chicken viruses facilitated the genesis of the novel H7N9 viruses. Here we show that over more than 10 y of cocirculation of multiple H9N2 genotypes, a genotype (G57) emerged that had changed antigenicity and improved adaptability in chickens. It became predominant in vaccinated farm chickens in China, caused widespread outbreaks in 2010-2013 before the H7N9 viruses emerged in humans, and finally provided all of their internal genes to the novel H7N9 viruses. The prevalence and variation of H9N2 influenza virus in farmed poultry could provide an important early warning of the emergence of novel reassortants with pandemic potential.

Unencapsulated Streptococcus pneumoniae from conjunctivitis encode variant traits and belong to a distinct phylogenetic cluster.

Streptococcus pneumoniae, an inhabitant of the upper respiratory mucosa, causes respiratory and invasive infections as well as conjunctivitis. Strains that lack the capsule, a main virulence factor and the target of current vaccines, are often isolated from conjunctivitis cases. Here we perform a comparative genomic analysis of 271 strains of conjunctivitis-causing S. pneumoniae from 72 postal codes in the United States. We find that the vast majority of conjunctivitis strains are members of a distinct cluster of closely related unencapsulated strains. These strains possess divergent forms of pneumococcal virulence factors (such as CbpA and neuraminidases) that are not shared with other unencapsulated nasopharyngeal S. pneumoniae. They also possess putative adhesins that have not been described in encapsulated pneumococci. These findings suggest that the unencapsulated strains capable of causing conjunctivitis utilize a pathogenesis strategy substantially different from that described for S. pneumoniae at other infection sites.

Dietary modulation of the microbiome affects autoinflammatory disease.

The incidences of chronic inflammatory disorders have increased considerably over the past three decades. Recent shifts in dietary consumption may have contributed importantly to this surge, but how dietary consumption modulates inflammatory disease is poorly defined. Pstpip2(cmo) mice, which express a homozygous Leu98Pro missense mutation in the Pombe Cdc15 homology family protein PSTPIP2 (proline-serine-threonine phosphatase interacting protein 2), spontaneously develop osteomyelitis that resembles chronic recurrent multifocal osteomyelitis in humans. Recent reports demonstrated a crucial role for interleukin-1ß (IL-1ß) in osteomyelitis, but deletion of the inflammasome components caspase-1 and NLRP3 failed to rescue Pstpip2(cmo) mice from inflammatory bone disease. Thus, the upstream mechanisms controlling IL-1ß production in Pstpip2(cmo) mice remain to be identified. In addition, the environmental factors driving IL-1ß-dependent inflammatory bone erosion are unknown. Here we show that the intestinal microbiota of diseased Pstpip2(cmo) mice was characterized by an outgrowth of Prevotella. Notably, Pstpip2(cmo) mice that were fed a diet rich in fat and cholesterol maintained a normal body weight, but were markedly protected against inflammatory bone disease and bone erosion. Diet-induced protection against osteomyelitis was accompanied by marked reductions in intestinal Prevotella levels and significantly reduced pro-IL-1ß expression in distant neutrophils. Furthermore, pro-IL-1ß expression was also decreased in Pstpip2(cmo) mice treated with antibiotics, and in wild-type mice that were kept under germ-free conditions. We further demonstrate that combined deletion of caspases 1 and 8 was required for protection against IL-1ß-dependent inflammatory bone disease, whereas the deletion of either caspase alone or of elastase or neutrophil proteinase 3 failed to prevent inflammatory disease. Collectively, this work reveals diet-associated changes in the intestinal microbiome as a crucial factor regulating inflammasome- and caspase-8-mediated maturation of IL-1ß and osteomyelitis in Pstpip2(cmo) mice.

The fhu genes of Rhizobium leguminosarum, specifying siderophore uptake proteins: fhuDCB are adjacent to a pseudogene version of fhuA.

A mutant of Rhizobium leguminosarum was isolated which fails to take up the siderophore vicibactin. The mutation is in a homologue of fhuB, which in Escherichia coli specifies an inner-membrane protein of the ferric hydroxamate uptake system. In Rhizobium, fhuB is in an operon fhuDCB, which specifies the cytoplasmic membrane and periplasmic proteins involved in siderophore uptake. fhuDCB mutants make vicibactin when grown in Fe concentrations that inhibit its production in the wild-type. Nodules on peas induced by fhuDCB mutants were apparently normal in N2 fixation. Transcription of an fhuDCB-lacZ fusion was Fe-regulated, being approximately 10-fold higher in Fe-depleted cells. Downstream of fhuB, in the opposite orientation, is a version of fhuA whose homologues in other bacteria specify hydroxamate outer-membrane receptors. This fhuA gene appears to be a pseudogene with stop codons and undetectable expression.