Listeria hijacks host mitophagy through a novel mitophagy receptor to evade killing.

Cells use mitophagy to remove damaged or unwanted mitochondria to maintain homeostasis. Here we report that the intracellular bacterial pathogen Listeria monocytogenes exploits host mitophagy to evade killing. We found that L. monocytogenes induced mitophagy in macrophages through the virulence factor listeriolysin O (LLO). We discovered that NLRX1, the only Nod-like receptor (NLR) family member with a mitochondrial targeting sequence, contains an LC3-interacting region (LIR) and directly associated with LC3 through the LIR. NLRX1 and its LIR motif were essential for L. monocytogenes-induced mitophagy. NLRX1 deficiency and use of a mitophagy inhibitor both increased mitochondrial production of reactive oxygen species and thereby suppressed the survival of L. monocytogenes. Mechanistically, L. monocytogenes and LLO induced oligomerization of NLRX1 to promote binding of its LIR motif to LC3 for induction of mitophagy. Our study identifies NLRX1 as a novel mitophagy receptor and discovers a previously unappreciated strategy used by pathogens to hijack a host cell homeostasis system for their survival.

Transcription factor Hoxb5 reprograms B cells into functional T lymphocytes.

Deletion of master regulators of the B cell lineage reprograms B cells into T cells. Here we found that the transcription factor Hoxb5, which is expressed in uncommitted hematopoietic progenitor cells but is not present in cells committed to the B cell or T cell lineage, was able to reprogram pro-pre-B cells into functional early T cell lineage progenitors. This reprogramming started in the bone marrow and was completed in the thymus and gave rise to T lymphocytes with transcriptomes, hierarchical differentiation, tissue distribution and immunological functions that closely resembled those of their natural counterparts. Hoxb5 repressed B cell 'master genes', activated regulators of T cells and regulated crucial chromatin modifiers in pro-pre-B cells and ultimately drove the B cell fate-to-T cell fate conversion. Our results provide a de novo paradigm for the generation of functional T cells through reprogramming in vivo.

Publisher Correction: Transcription factor Hoxb5 reprograms B cells into functional T lymphocytes.

In the version of this article initially published, some identification of the supplementary information was incorrect. The items originally called Supplementary Tables 1, 2, 3, 4 and 5 should be Source Data Figures 1, 2, 4, 5 and 7, respectively; those originally called Supplementary Tables 6, 7 and 8 should be Supplementary Tables 1, 2 and 3, respectively; and those originally called Source Data Figures 1, 2, 4, 5 and 7 should be Supplementary Tables 4, 5, 6, 7 and 8, respectively. The errors have been corrected in the HTML version of the article.

Mutations in atypical hemolytic uremic syndrome provide evidence for the role of calcium in complement factor I.

Atypical hemolytic uremic syndrome (aHUS) is a rare thrombotic microangiopathy. Genetic variants in complement proteins are found in ≈60% of patients. Of these patients, ≈15% carry mutations in complement factor I (CFI). Factor I (FI) is a multidomain serine protease that cleaves and thereby inactivates C3b and C4b in the presence of cofactor proteins. Crystal structures have shown that FI possesses 2 calcium-binding domains, low-density lipoprotein receptor class A (LDLRA) 1 and LDLRA2. Yet, the role of calcium in FI is unknown. We determined that 9 genetic variants identified in aHUS (N151S, G162D, G188A, V230E, A240G, G243R, C247G, A258T, and Q260D) cluster around the calcium-binding site of LDLRA1. Using site-directed mutagenesis, we established that the synthesis of all, except A258T, was impaired, implying defective protein folding, perhaps due to loss of calcium binding. To further explore this possibility, we generated 12 alanine mutants that coordinate with the calcium in LDLRA1 and LDLRA2 (K239A, D242A, I244A, D246A, D252A, E253A, Y276A, N279A, E281A, D283A, D289A, and D290A) and are expected to perturb calcium binding. Except for K239A and Y276A, none of the mutants was secreted. These observations suggest that calcium ions play key structural and functional roles in FI.

Global transmission of broad-host-range plasmids derived from the human gut microbiome.

Broad-host-range (BHR) plasmids in human gut bacteria are of considerable interest for their ability to mediate horizontal gene transfer (HGT) across large phylogenetic distance. However, the human gut plasmids, especially the BHR plasmids, remain largely unknown. Here, we identified the plasmids in the draft genomes of gut bacterial isolates from Chinese and American donors, resulting in 5372 plasmid-like clusters (PLCs), of which, 820 PLCs (comPLCs) were estimated with > 60% completeness genomes and only 155 (18.9%) were classified to known replicon types (n = 37). We observed that 175 comPLCs had a broad host range across distinct bacterial genera, of which, 71 were detected in at least two human populations of Chinese, American, Spanish, and Danish, and 13 were highly prevalent (>10%) in at least one human population. Haplotype analyses of two widespread PLCs demonstrated their spreading and evolutionary trajectory, suggesting frequent and recent exchanges of the BHR plasmids in environments. In conclusion, we obtained a large collection of plasmid sequences in human gut bacteria and demonstrated that a subset of the BHR plasmids can be transmitted globally, thus facilitating extensive HGT (e.g. antibiotic resistance genes) events. This study highlights the potential implications of the plasmids for global human health.

HPV integration generates a cellular super-enhancer which functions as ecDNA to regulate genome-wide transcription.

Human papillomavirus (HPV) integration is a critical step in cervical cancer development; however, the oncogenic mechanism at the genome-wide transcriptional level is still poorly understood. In this study, we employed integrative analysis on multi-omics data of six HPV-positive and three HPV-negative cell lines. Through HPV integration detection, super-enhancer (SE) identification, SE-associated gene expression and extrachromosomal DNA (ecDNA) investigation, we aimed to explore the genome-wide transcriptional influence of HPV integration. We identified seven high-ranking cellular SEs generated by HPV integration in total (the HPV breakpoint-induced cellular SEs, BP-cSEs), leading to intra-chromosomal and inter-chromosomal regulation of chromosomal genes. The pathway analysis revealed that the dysregulated chromosomal genes were correlated to cancer-related pathways. Importantly, we demonstrated that BP-cSEs existed in the HPV-human hybrid ecDNAs, explaining the above transcriptional alterations. Our results suggest that HPV integration generates cellular SEs that function as ecDNA to regulate unconstrained transcription, expanding the tumorigenic mechanism of HPV integration and providing insights for developing new diagnostic and therapeutic strategies.

Oxygen-Bridged Cu Binuclear Sites for Efficient Electrocatalytic CO2 Reduction to Ethanol at Ultralow Overpotential.

Electrocatalytic CO2 reduction (CO2RR) to alcohols offers a promising strategy for converting waste CO2 into valuable fuels/chemicals but usually requires large overpotentials. Herein, we report a catalyst comprising unique oxygen-bridged Cu binuclear sites (CuOCu-N4) with a Cu···Cu distance of 3.0-3.1 Å and concomitant conventional Cu-N4 mononuclear sites on hierarchical nitrogen-doped carbon nanocages (hNCNCs). The catalyst exhibits a state-of-the-art low overpotential of 0.19 V (versus reversible hydrogen electrode) for ethanol and an outstanding ethanol Faradaic efficiency of 56.3% at an ultralow potential of -0.30 V, with high-stable Cu active-site structures during the CO2RR as confirmed by operando X-ray adsorption fine structure characterization. Theoretical simulations reveal that CuOCu-N4 binuclear sites greatly enhance the C-C coupling at low potentials, while Cu-N4 mononuclear sites and the hNCNC support increase the local CO concentration and ethanol production on CuOCu-N4. This study provides a convenient approach to advanced Cu binuclear site catalysts for CO2RR to ethanol with a deep understanding of the mechanism.

Selective Cleavage of α-Olefins to Produce Acetylene and Hydrogen.

Acetylene production from mixed α-olefins emerges as a potentially green and energy-efficient approach with significant scientific value in the selective cleavage of C-C bonds. On the Pd(100) surface, it is experimentally revealed that C2 to C4 α-olefins undergo selective thermal cleavage to form surface acetylene and hydrogen. The high selectivity toward acetylene is attributed to the 4-fold hollow sites which are adept at severing the terminal double bonds in α-olefins to produce acetylene. A challenge arises, however, because acetylene tends to stay at the Pd(100) surface. By using the surface alloying methodology with alien Au, the surface Pd d-band center has been successfully shifted away from the Fermi level to release surface-generated acetylene from α-olefins as a gaseous product. Our study actually provides a technological strategy to economically produce acetylene and hydrogen from α-olefins.

Functional analysis of rare genetic variants in complement factor I in advanced age-related macular degeneration.

Factor I (FI) is a serine protease inhibitor of the complement system. Heterozygous rare genetic variants in complement factor I (CFI) are associated with advanced age-related macular degeneration (AMD). The clinical impact of these variants is unknown since a majority have not been functionally characterized and are classified as 'variants of uncertain significance' (VUS). This study assessed the functional significance of VUS in CFI. Our previous cross-sectional study using a serum-based assay demonstrated that CFI variants in advanced AMD can be categorized into three types. Type 1 variants cause a quantitative deficiency of FI. Type 2 variants demonstrate a qualitative deficiency. However, Type 3 variants consist of VUS that are less dysfunctional than Types 1 and 2 but are not as biologically active as wild type (WT). In this study, we employed site-directed mutagenesis followed by expression of the recombinant variant and a comprehensive set of functional assays to characterize nine Type 3 variants that were identified in 37 individuals. Our studies establish that the expression of the recombinant protein compared with WT is reduced for R202I, Q217H, S221Y and G263V. Further, G362A and N536K, albeit expressed normally, have significantly less cofactor activity. These results led to re-categorization of CFI variants R202I, Q217H, S221Y and G263V as Type 1 variants and to reclassification of N536K and G362A as Type 2. The variants K441R, Q462H and I492L showed no functional defect and remained as Type 3. This study highlights the utility of an in-depth biochemical analysis in defining the pathologic and clinical implications of complement variants underlying AMD.

A MOF-Gel Based Separator for Suppressing Redox Mediator Shuttling in Li-O2 Batteries.

Redox mediators (RMs) are widely utilized in the electrolytes of Li-O2 batteries to catalyze the formation/decomposition of Li2O2, which significantly enhances the cycling performance and reduces the charge overpotential. However, RMs have a shuttle effect by migrating to the Li anode side and inducing Li metal degradation through a parasitic reaction. Herein, a metal-organic framework gel (MOF-gel) separator is proposed to restrain the shuttling of RMs. Compared to traditional MOF nanoparticles, MOF gels form uniform and dense films on the separators. When using Ru(acac)3 (ruthenium acetylacetonate) as an RM, the MOF-gel separator suppresses the shuttling of Ru(acac)3 toward the Li anode side and significantly enhances the performance of Li-O2 batteries. Specifically, Li-O2 batteries exhibit an ultralong cycling life (410 cycles) at a current density of 0.5 A g-1. Moreover, the batteries using the MOF-gel/celgard separator exhibit significantly improved cycling performance (increase by ≈1.6 times) at a high current density of 1.0 A g-1 and a decreased charge/discharge overpotential. This result is expected to guide future development of battery separators and the exploration of redox mediators.

Solution-Processed 1D Wurtzite ZnS Nanostructures with Controlled Crystallographic Orientation and Tunable Band-Edge Emission.

1D compound semiconductor nanomaterials possess unique physicochemical properties that strongly depend on their size, composition, and structures. ZnS has been widely investigated as one of the most important semiconductors, and the control of crystallographic orientation of 1D ZnS nanostructures is still challenging and crucial to exploring their anisotropic properties. Herein, a solution-processed strategy is developed to synthesize 1D wurtzite (w-)ZnS nanostructures with the specific <002> and <210> orientations by co-decomposing the copper dibutyldithiocarbamate {[(C4 H9 )2 NCS2 ]2 Cu, i.e., R2 Cu} and zinc dibutyldithiocarbamate (R2 Zn) precursors in the mixed solvents of oleylamine and 1-dodecanethoil. A solution-solid-solid (SSS)-Oriented growth mechanism is proposed, which includes oriented nucleation dominated and SSS growth dominated stages. The crystallographic orientation mainly depends on the interfacial energy and ligand effect. The 1D w-ZnS nanostructures with controlled crystallographic orientation display unique morphologies, i.e., <002>-oriented w-ZnS nanorod enclosed with {110} facets while <210>-oriented w-ZnS nanobelt enclosed with wide (002) and narrow (110) facets. The bandgap of 1D w-ZnS nanostructures can be tuned from 3.94 to 3.82 eV with the crystallographic growth direction varied from <002> to <210>, thus leading to the tunable band-edge emission from ≈338 to ≈345 nm.

Constructing Gold Single-Atom Catalysts on Hierarchical Nitrogen-Doped Carbon Nanocages for Carbon Dioxide Electroreduction to Syngas.

Precious-metal single-atom catalysts (SACs), featured by high metal utilization and unique coordination structure for catalysis, demonstrate distinctive performances in the fields of heterogeneous and electrochemical catalysis. Herein, gold SACs are constructed on hierarchical nitrogen-doped carbon nanocages (hNCNC) via a simple impregnation-drying process and first exploited for electrocatalytic carbon dioxide reduction reaction (CO2RR) to produce syngas. The as-constructed Au SAC exhibits the high mass activity of 3319 A g-1 Au at -1.0 V (vs reversible hydrogen electrode, RHE), much superior to the Au nanoparticles supported on hNCNC. The ratio of H2/CO can be conveniently regulated in the range of 0.4-2.2 by changing the applied potential. Theoretical study indicates such a potential-dependent H2/CO ratio is attributed to the different responses of HER and CO2RR on Au single-atom sites coordinating with one N atom at the edges of micropores across the nanocage shells. The catalytic mechanism of the Au active sites is associated with the smooth switch between twofold and fourfold coordination during CO2RR, which much decreases the free energy changes of the rate-determining steps and promotes the reaction activity.

Underwater entanglement propagation of auto-focusing Airy beams.

In underwater wireless optical communication, orbital angular momentum (OAM) states suffer from turbulence distortions. This study aims to investigate the effectiveness of auto-focusing and OAM entanglement of the beams in reducing the turbulence effects. We implement the single-phase approximation and the extended Huygens-Fresnel principle to derive the detection probability of the entangled Airy beams under unstable oceanic turbulence. The results show that auto-focusing can protect the signal OAM mode and suppress modal crosstalks, while entangled OAM states can further enhance the resistance against oceanic turbulence around the focus position. The numerical analysis demonstrates that after the auto-focusing position, the beams evolve in completely opposite directions, indicating that the focal length should be modulated according to the length of a practical link to enhance received signals. These findings suggest that entangled auto-focusing vortex beams may be a desirable light source in underwater communication systems.

Exploration of Human Lung-Resident Immunity and Response to Respiratory Viral Immunization in a Humanized Mouse Model.

There are urgent needs for humanized mouse models of viral respiratory diseases to study immunopathogenesis and therapeutic interventions. Although human immune system (HIS) mice permit analysis in real time of human immune responses in vivo, evolutionary divergences preclude their usefulness for the respiratory viruses that do not infect mouse lungs. In this study, we sought to use HIS mice with human lung (HL) tissue xenografts (HISL mice) to address this issue. The grafted HL tissue maintained histologically normal structure, and populated with human tissue-resident immune cells, including CD11c+ dendritic cells and CD4+ and CD8+ tissue-resident memory T cells. HISL mice showed a marked expansion of tissue-resident memory T cells and generation of viral Ag-specific T cells in the HL xenografts, and production of antiviral IgM and IgG Abs upon immunization of the HL xenograft by H1N1 influenza viruses. RNA-seq analysis on H1N1-infected and control HL xenografts identified a total of 5089 differentially expressed genes with enrichments for genes involved in respiratory diseases, viral infections, and associated immune responses. Furthermore, prophylactic viral exposures resulted in protection against subsequent lethal challenge by intranasal viral inoculation. This study supports the usefulness of this preclinical model in exploring the immunopathology and therapies of respiratory viral diseases.

GGC repeat expansion in NOTCH2NLC induces dysfunction in ribosome biogenesis and translation.

GGC repeat expansion in the 5' untranslated region (UTR) of NOTCH2NLC is associated with a broad spectrum of neurological disorders, especially neuronal intranuclear inclusion disease (NIID). Studies have found that GGC repeat expansion in NOTCH2NLC induces the formation of polyglycine (polyG)-containing protein, which is involved in the formation of neuronal intranuclear inclusions. However, the mechanism of neurotoxicity induced by NOTCH2NLC GGC repeats is unclear. Here, we used NIID patient-specific induced pluripotent stem cell (iPSC)-derived 3D cerebral organoids (3DCOs) and cellular models to investigate the pathophysiological mechanisms of NOTCH2NLC GGC repeat expansion. IPSC-derived 3DCOs and cellular models showed the deposition of polyG-containing intranuclear inclusions. The NOTCH2NLC GGC repeats could induce the upregulation of autophagic flux, enhance integrated stress response and activate EIF2α phosphorylation. Bulk RNA sequencing for iPSC-derived neurons and single-cell RNA sequencing (scRNA-seq) for iPSC-derived 3DCOs revealed that NOTCH2NLC GGC repeats may be associated with dysfunctions in ribosome biogenesis and translation. Moreover, NOTCH2NLC GGC repeats could induce the NPM1 nucleoplasm translocation, increase nucleolar stress, impair ribosome biogenesis and induce ribosomal RNA sequestration, suggesting dysfunction of membraneless organelles in the NIID cellular model. Dysfunctions in ribosome biogenesis and phosphorylated EIF2α and the resulting increase in the formation of G3BP1-positive stress granules may together lead to whole-cell translational inhibition, which may eventually cause cell death. Interestingly, scRNA-seq revealed that NOTCH2NLC GGC repeats may be associated with a significantly decreased proportion of immature neurons while 3DCOs were developing. Together, our results underscore the value of patient-specific iPSC-derived 3DCOs in investigating the mechanisms of polyG diseases, especially those caused by repeats in human-specific genes.

A potential slow-release fertilizer based on biogas residue biochar: Nutrient release patterns and synergistic mechanism for improving soil fertility.

The large yield of anaerobic digestates and the suboptimal efficacy of nutrient slow-release severely limit its practical application. To address these issues, a new biochar based fertilizer (MAP@BRC) was developed using biogas residue biochar (BRC) to recover nitrogen and phosphorus from biogas slurry. The nutrient release patterns of MAP@BRC and mechanisms for enhancing soil fertility were studied, and it demonstrated excellent performance, with 59% total nitrogen and 50% total phosphorus nutrient release rates within 28 days. This was attributed to the coupling of the mechanism involving the dissolution of struvite skeletons and the release of biochar pores. Pot experiments showed that crop yield and water productivity were doubled in the MAP@BRC group compared with unfertilized planting. The application of MAP@BRC also improved soil nutrient levels, reduced soil acidification, increased microbial populations, and decreased soil heavy metal pollution risk. The key factors that contributed to the improvement in soil fertility by MAP@BRC were an increase in available nitrogen and the optimization of pH levels in the soil. Overall, MAP@BRC is a safe, slow-release fertilizer that exhibits biochar-fertilizer interactions and synergistic effects. This slow-release fertilizer was prepared by treating a phosphorus-rich biogas slurry with a nitrogen-rich biogas slurry, and it simultaneously addresses problems associated with livestock waste treatment and provides a promising strategy to promote zero-waste agriculture.

Propagation of auto-focusing hypergeometric Gaussian beams along a slant path in oceanic turbulence.

Compared to horizontal transmission, the oceanic dissipation rate and temperature-salinity distribution ratio are no longer constant but vary with depth, imposing greater complexity on oceanic turbulence when beams propagate through a slant path and resulting in more limitations on the performance of underwater wireless optical communication (UWOC) links. This study focuses on investigating the performance, especially the auto-focusing characteristic, of auto-focusing hypergeometric Gaussian (AHGG) beams propagating along slant paths in oceanic turbulence. We theoretically derive the spatial coherence radius and the relative probability of the orbital angular momentum (OAM) mode for AHGG beams passing through such links. Numerical simulations reveal that AHGG beams exhibit superior propagation performance compared to hypergeometric Gaussian beams. Lower beam orders and OAM numbers contribute to improved performance, while careful selection of auto-focusing length can tangibly enhance detection performance as well. Additionally, tidal velocities and wind speeds have nonnegligible effects on OAM signal probability. Our results further demonstrate that surface buoyancy flux, temperature gradients, and waterside friction velocity significantly affect beam transmission under varying wind conditions. These findings, particularly controlling the auto-focusing length of AHGG beams to match the transmission distance, provide valuable insights for enhancing the quality of UWOC links.

Targeted disruption of the BCR-ABL fusion gene by Cas9/dual-sgRNA inhibits proliferation and induces apoptosis in chronic myeloid leukemia cells.

The BCR-ABL fusion gene, formed by the fusion of the breakpoint cluster region protein ( BCR) and the Abl Oncogene 1, Receptor Tyrosine Kinase ( ABL) genes, encodes the BCR-ABL oncoprotein, which plays a crucial role in leukemogenesis. Current therapies have limited efficacy in patients with chronic myeloid leukemia (CML) because of drug resistance or disease relapse. Identification of novel strategies to treat CML is essential. This study aims to explore the efficiency of novel CRISPR-associated protein 9 (Cas9)/dual-single guide RNA (sgRNA)-mediated disruption of the BCR-ABL fusion gene by targeting BCR and cABL introns. A co-expression vector for Cas9 green fluorescent protein (GFP)/dual-BA-sgRNA targeting BCR and cABL introns is constructed to produce lentivirus to affect BCR-ABL expression in CML cells. The effects of dual-sgRNA virus-mediated disruption of BCR-ABL are analyzed via the use of a genomic sequence and at the protein expression level. Cell proliferation, cell clonogenic ability, and cell apoptosis are assessed after dual sgRNA virus infection, and phosphorylated BCR-ABL and its downstream signaling molecules are detected. These effects are further confirmed in a CML mouse model via tail vein injection of Cas9-GFP/dual-BA-sgRNA virus-infected cells and in primary cells isolated from patients with CML. Cas9-GFP/dual-BA-sgRNA efficiently disrupts BCR-ABL at the genomic sequence and gene expression levels in leukemia cells, leading to blockade of the BCR-ABL tyrosine kinase signaling pathway and disruption of its downstream molecules, followed by cell proliferation inhibition and cell apoptosis induction. This method prolongs the lifespan of CML model mice. Furthermore, the effect is confirmed in primary cells derived from patients with CML.

Correlation between Heteroatom Coordination and Hydrogen Evolution for Single-site Pt on Carbon-based Nanocages.

The electrocatalytic performance of single-site catalysts (SSCs) is closely correlated with the electronic structure of metal atoms. Herein we construct a series of Pt SSCs on heteroatom-doped hierarchical carbon nanocages, which exhibit increasing hydrogen evolution reaction (HER) activities along S-doped, P-doped, undoped and N-doped supports. Theoretical simulation indicates a multi-H-atom adsorption process on Pt SSCs due to the low coordination, and a reasonable descriptor is figured out to evaluate the HER activities. Relative to C-coordinated Pt, N-coordinated Pt has higher reactivity due to the electron transfer of N-to-Pt, which enriches the density of states of Pt 5d orbital near the Fermi level and facilitates the capturing of protons, just the opposite to the situations for P- and S-coordinated ones. The stable N-coordinated Pt originates from the kinetic stability throughout the multi-H-atom adsorption process. This finding provides a significant guidance for rational design of advanced Pt SSCs on carbon-based supports.

A Genetic Bottleneck of Mitochondrial DNA During Human Lymphocyte Development.

Mitochondria are essential organelles in eukaryotic cells that provide critical support for energetic and metabolic homeostasis. Although the elimination of pathogenic mitochondrial DNA (mtDNA) mutations in somatic cells has been observed, the mechanisms to maintain proper functions despite their mtDNA mutation load are poorly understood. In this study, we analyzed somatic mtDNA mutations in more than 30,000 single human peripheral and bone marrow mononuclear cells. We observed a significant overrepresentation of homoplasmic mtDNA mutations in B, T, and natural killer (NK) lymphocytes. Intriguingly, their overall mutational burden was lower than that in hematopoietic progenitors and myeloid cells. This characteristic mtDNA mutational landscape indicates a genetic bottleneck during lymphoid development, as confirmed with single-cell datasets from multiple platforms and individuals. We further demonstrated that mtDNA replication lags behind cell proliferation in both pro-B and pre-B progenitor cells, thus likely causing the genetic bottleneck by diluting mtDNA copies per cell. Through computational simulations and approximate Bayesian computation (ABC), we recapitulated this lymphocyte-specific mutational landscape and estimated the minimal mtDNA copies as <30 in T, B, and NK lineages. Our integrative analysis revealed a novel process of a lymphoid-specific mtDNA genetic bottleneck, thus illuminating a potential mechanism used by highly metabolically active immune cells to limit their mtDNA mutation load.