NF-κB subunits direct kinetically distinct transcriptional cascades in antigen receptor-activated B cells.

The nuclear factor kappa B (NF-κB) family of transcription factors orchestrates signal-induced gene expression in diverse cell types. Cellular responses to NF-κB activation are regulated at the level of cell and signal specificity, as well as differential use of family members (subunit specificity). Here we used time-dependent multi-omics to investigate the selective functions of Rel and RelA, two closely related NF-κB proteins, in primary B lymphocytes activated via the B cell receptor. Despite large numbers of shared binding sites genome wide, Rel and RelA directed kinetically distinct cascades of gene expression in activated B cells. Single-cell RNA sequencing revealed marked heterogeneity of Rel- and RelA-specific responses, and sequential binding of these factors was not a major mechanism of protracted transcription. Moreover, nuclear co-expression of Rel and RelA led to functional antagonism between the factors. By rigorously identifying the target genes of each NF-κB subunit, these studies provide insights into exclusive functions of Rel and RelA in immunity and cancer.

Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus.

Immunoglobulin heavy-chain (IgH) genes are assembled by DNA rearrangements that juxtapose a variable (VH), a diversity (DH), and a joining (JH) gene segment. Here, we report that in the absence of intergenic control region 1 (IGCR1), the intronic enhancer (Eµ) associates with the next available CTCF binding site located close to VH81X via putative heterotypic interactions involving YY1 and CTCF. The alternate Eµ/VH81X loop leads to formation of a distorted recombination center and altered DH rearrangements and disrupts chromosome conformation that favors distal VH recombination. Cumulatively, these features drive highly skewed, Eµ-dependent recombination of VH81X. Sequential deletion of CTCF binding regions on IGCR1-deleted alleles suggests that they influence recombination of single proximal VH gene segments. Our observations demonstrate that Eµ interacts differently with IGCR1- or VH-associated CTCF binding sites and thereby identify distinct roles for insulator-like elements in directing enhancer activity.

Differential roles of positive and negative supercoiling in organizing the E. coli genome.

This study aims to explore whether and how positive and negative supercoiling contribute to the three-dimensional (3D) organization of the bacterial genome. We used recently published Escherichia coli GapR ChIP-seq and TopoI ChIP-seq (also called EcTopoI-seq) data, which marks positive and negative supercoiling sites, respectively, to study how supercoiling correlates with the spatial contact maps obtained from chromosome conformation capture sequencing (Hi-C and 5C). We find that supercoiled chromosomal loci have overall higher Hi-C contact frequencies than sites that are not supercoiled. Surprisingly, positive supercoiling corresponds to higher spatial contact than negative supercoiling. Additionally, positive, but not negative, supercoiling could be identified from Hi-C data with high accuracy. We further find that the majority of positive and negative supercoils coincide with highly active transcription units, with a minor group likely associated with replication and other genomic processes. Our results show that both positive and negative supercoiling enhance spatial contact, with positive supercoiling playing a larger role in bringing genomic loci closer in space. Based on our results, we propose new physical models of how the E. coli chromosome is organized by positive and negative supercoils.

DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence.

Epigenetic information defines tissue identity and is largely inherited in development through DNA methylation. While studied mostly for mean differences, methylation also encodes stochastic change, defined as entropy in information theory. Analyzing allele-specific methylation in 49 human tissue sample datasets, we find that methylation entropy is associated with specific DNA binding motifs, regulatory DNA, and CpG density. Then applying information theory to 42 mouse embryo methylation datasets, we find that the contribution of methylation entropy to time- and tissue-specific patterns of development is comparable to the contribution of methylation mean, and methylation entropy is associated with sequence and chromatin features conserved with human. Moreover, methylation entropy is directly related to gene expression variability in development, suggesting a role for epigenetic entropy in developmental plasticity.

Emergency Myelopoiesis Distinguishes Multisystem Inflammatory Syndrome in Children From Pediatric Severe Coronavirus Disease 2019.

BACKGROUND: Multisystem inflammatory syndrome in children (MIS-C) is a hyperinflammatory condition caused by recent infection with severe acute respiratory syndrome coronavirus 2, but the underlying immunological mechanisms driving this distinct syndrome are unknown. METHODS: We utilized high-dimensional flow cytometry, cell-free (cf) DNA, and cytokine and chemokine profiling to identify mechanisms of critical illness distinguishing MIS-C from severe acute coronavirus disease 2019 (SAC). RESULTS: Compared to SAC, MIS-C patients demonstrated profound innate immune cell death and features of emergency myelopoiesis (EM), an understudied phenomenon observed in severe inflammation. EM signatures were characterized by fewer mature myeloid cells in the periphery and decreased expression of HLA-DR and CD86 on antigen-presenting cells. Interleukin 27 (IL-27), a cytokine known to drive hematopoietic stem cells toward EM, was increased in MIS-C, and correlated with immature cell signatures in MIS-C. Upon recovery, EM signatures decreased and IL-27 plasma levels returned to normal levels. Despite profound lymphopenia, we report a lack of cfDNA released by adaptive immune cells and increased CCR7 expression on T cells indicative of egress out of peripheral blood. CONCLUSIONS: Immune cell signatures of EM combined with elevated innate immune cell-derived cfDNA levels distinguish MIS-C from SAC in children and provide mechanistic insight into dysregulated immunity contributing toward MIS-C, offering potential diagnostic and therapeutic targets.

The BAF chromatin complex component SMARCC1 does not mediate GLI transcriptional repression of Hedgehog target genes in limb buds.

Transcriptional responses to the Hedgehog (HH) signaling pathway are primarily modulated by GLI repression in the mouse limb. Previous studies suggested a role for the BAF chromatin remodeling complex in mediating GLI repression. Consistent with this possibility, the core BAF complex protein SMARCC1 is present at most active limb enhancers including the majority of GLI enhancers. However, in contrast to GLI repression which reduces chromatin accessibility, SMARCC1 maintains chromatin accessibility at most enhancers, including those bound by GLI. Moreover, SMARCC1 binding at GLI-regulated enhancers occurs independently of GLI3. Consistent with previous studies, some individual GLI target genes are mis-regulated in Smarcc1 conditional knockouts, though most GLI target genes are unaffected. Moreover, SMARCC1 is not necessary for mediating constitutive GLI repression in HH mutant limb buds. We conclude that SMARCC1 does not mediate GLI3 repression, which we propose utilizes alternative chromatin remodeling complexes.

Effect of Aggregation Structure on Capacitive Energy Storage in Conducting Polymer Films.

Conducting polymers (CPs), a significant class of electrochemical capacitor electrode materials, exhibit exceptional capacitive energy storage performance in aqueous electrolytes. Current research primarily concentrates on enhancing the electrical conductivity and capacitive performance of CPs via molecular design and structural control. However, the absence of a comprehensive understanding of the impact of molecular chain spatial order on ion/electron transport and capacitive performance impedes the development and optimization of advanced electrode materials. Here, a solvent treatment strategy is employed to modulate the molecular chain spatial order of PEDOT : PSS films. The results of electrochemical performance tests and Grazing Incidence Wide Angle X-ray Scattering (GIWAXS) show that Poly(3,4-ethylenedioxythiophene) : poly(styrenesulfonic acid) (PEDOT : PSS) films with both face-on and edge-on orientations exhibit exceptional electronic conductivity and ion diffusion efficiency, with capacitive performance 1.33 times higher than that of PEDOT : PSS films with only edge-on orientation. Consequently, molecular chain orientations conducive to charge transport not only enhance inter-chain coupling, but also effectively reduce ion transport resistance, enabling efficient capacitive energy storage. This research provides novel insights for the design and development of higher performance CPs-based electrode materials.

Advances in Functionalized Biocomposites of Living Cells Combined with Metal-Organic Frameworks.

Motivated by the remarkable innate characteristics of cells in living organisms, we have found that hybrid materials that combine bioorganisms with nanomaterials have significantly propelled advancements in industrial applications. However, the practical deployment of unmodified living entities is inherently limited due to their sensitivity to environmental fluctuations. To surmount these challenges, an efficacious strategy for the biomimetic mineralization of living organisms with nanomaterials has emerged, demonstrating extraordinary potential in biotechnology. Among them, innovative composites have been engineered by enveloping bioorganisms with a metal-organic framework (MOF) coating. This review systematically summarizes the latest developments in living cells/MOF-based composites, detailing the methodologies employed in structure fabrication and their diverse applications, such as bioentity preservation, sensing, catalysis, photoluminescence, and drug delivery. Moreover, the synergistic benefits arising from the individual compounds are elucidated. This review aspires to illuminate new prospects for fabricating living cells/MOF composites and concludes with a perspective on the prevailing challenges and impending opportunities for future research in this field.

Rational Design of FeCo-S/Ni2P/NF Heterojunction as a Robust Electrocatalyst for Water Splitting.

The rational design of nonnoble-metal-based catalysts with high electroactivity and long-term stability, featuring controllable active sites, remains a significant challenge for achieving effective water electrolysis. Herein, a heterogeneous catalyst with a FeCo-S and Ni2P heterostructure (denoted FeCo-S/Ni2P/NF) grown on nickel foam (NF) was synthesized by a solvothermal method and low-temperature phosphorization. The FeCo-S/Ni2P/NF catalyst shows excellent electrocatalytic performance and stability in alkaline solution. The FeCo-S/Ni2P/NF catalyst demonstrates low overpotentials (η) for both the hydrogen evolution reaction (HER) (49 mV@10 mA cm-2) and the oxygen evolution reaction (OER) (279 mV@100 mA cm-2). Assembling the FeCo-S/Ni2P/NF catalyst as both cathode and anode in an electrolytic cell for overall water splitting (OWS) needs an ultralow cell voltage of 1.57 V to attain a current density (CD) of 300 mA cm-2. Furthermore, it demonstrates excellent durability, significantly outperforming the commercial Pt/C∥IrO2 system. The results of experiments indicate that the heterostructure and synergistic effect of FeCo-S and Ni2P can significantly enhance conductivity, facilitate mass/ion transport and gas evolution, and expose more active sites, thereby improving the catalytic activity of the electrocatalyst for the OWS. This study provides a rational approach for the development of commercially promising dual-functional electrocatalysts.

Rational Design of NiCo-borate/GO Heterojunction as a High-Performance Supercapacitor Electrode.

The bottleneck in the preparation of supercapacitors is how to develop high-energy and high-power-density devices by using appropriate materials. Herein, a novel NixCo3-x-B/GO heterostructure material was synthesized through a simple ultrasonic and precipitation method. The prepared NixCo3-x-B/GO heterostructure exhibits significant improvements in supercapacitor performance than NixCo3-x-B. The presence of GO effectively suppresses the excessive growth and accumulation of NixCo3-x-B; therefore, Ni2.7Co0.3-B/GO exhibits the best performance as an electrode material for supercapacitors: a high specific capacitance (Cm, 1789.72 F g-1@1 A g-1) and excellent rate performance. The asymmetric supercapacitor (ASC) device of Ni2.7Co0.3-B/GO//AC exhibits a Cm of 76.6 F g-1@1 A g-1, a large voltage window of 1.6 V, and a high energy density (ED) of 98.0 Wh kg-1. Furthermore, a flexible, all-solid-state supercapacitor assembled with Ni2.7Co0.3-B/GO as both the positive and negative electrodes demonstrates a Cm of 46.9 F g-1@1 A g-1. Even after multiple folding and bending at various angles, the device maintains excellent performance, showcasing remarkable stability. With a power density (PD) of 479.7 W kg-1, the device achieves a high ED of 60.0 Wh kg-1. This work provides valuable insights into the synergistic effects in electrochemical processes based on heterostructure materials.

Unlocking growth potential in Halomonas bluephagenesis for enhanced PHA production with sulfate ions.

The mutant strain Halomonas bluephagenesis (TDH4A1B5P) was found to produce PHA under low-salt, non-sterile conditions, but the yield was low. To improve the yield, different nitrogen sources were tested. It was discovered that urea was the most effective nitrogen source for promoting growth during the stable stage, while ammonium sulfate was used during the logarithmic stage. The growth time of H. bluephagenesis (TDH4A1B5P) and its PHA content were significantly prolonged by the presence of sulfate ions. After 64 hr in a 5-L bioreactor supplemented with sulfate ions, the dry cell weight (DCW) of H. bluephagenesis weighed 132 g/L and had a PHA content of 82%. To promote the growth and PHA accumulation of H. bluephagenesis (TDH4A1B5P), a feeding regimen supplemented with nitrogen sources and sulfate ions with ammonium sodium sulfate was established in this study. The DCW was 124 g/L, and the PHA content accounted for 82.3% (w/w) of the DCW, resulting in a PHA yield of 101 g/L in a 30-L bioreactor using the optimized culture strategy. In conclusion, stimulating H. bluephagenesis (TDH4A1B5P) to produce PHA is a feasible and suitable strategy for all H. bluephagenesis.

Research and application progress of microbial ß-mannanases: a mini-review.

Mannan is a predominant constituent of cork hemicellulose and is widely distributed in various plant tissues. ß-Mannanase is the principal mannan-degrading enzyme, which breaks down the ß-1,4-linked mannosidic bonds in mannans in an endo-acting manner. Microorganisms are a valuable source of ß-mannanase, which exhibits catalytic activity in a wide range of pH and temperature, making it highly versatile and applicable in pharmaceuticals, feed, paper pulping, biorefinery, and other industries. Here, the origin, classification, enzymatic properties, molecular modification, immobilization, and practical applications of microbial ß-mannanases are reviewed, the future research directions for microbial ß-mannanases are also outlined.

Impact of Seasonal Coronavirus Antibodies on Severe Acute Respiratory Syndrome Coronavirus 2 Vaccine Responses in Solid Organ Transplant Recipients.

Antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination are reduced in solid organ transplant recipients (SOTRs). We report that increased levels of preexisting antibodies to seasonal coronaviruses are associated with decreased antibody response to SARS-CoV-2 vaccination in SOTRs, supporting that antigenic imprinting modulates vaccine responses in SOTRs.

Rare Earth Doping Engineering Tailoring Advanced Oxygen-Vacancy Co3 O4 with Tunable Structures for High-Efficiency Energy Storage.

Co3 O4  with high theoretical capacitance is a promising electrode material for high-end energy applications, yet the unexcited bulk electrochemical activity, low conductivity, and poor kinetics of Co3 O4  lead to unsatisfactory charge storage capacity. For boosting its energy storage capability, rare earth (RE)-doped Co3 O4  nanostructures with abundant oxygen vacancies are constructed by simple, economical, and universal chemical precipitation. By changing different types of RE (RE = La, Yb, Y, Ce, Er, Ho, Nd, Eu) as dopants, the RE-doped Co3 O4  nanostructures can be well transformed from large nanosheets to coiled tiny nanosheets and finally to ultrafine nanoparticles, meanwhile, their specific surface area, pore distribution, the ratio of Co2+ /Co3+ , oxygen vacancy content, crystalline phase, microstrain parameter, and the capacitance performance are regularly affected. Notably, Eu-doped Co3 O4  nanoparticles with good cycle stability show a maximum specific capacitance of 1021.3 F g-1 (90.78 mAh g-1 ) at 2 A g-1 , higher than 388 F g-1 (34.49 mAh g-1 ) of pristine Co3 O4  nanosheets. The assembling asymmetric supercapacitor delivers a high energy density of 48.23 Wh kg-1  at high power density of 1.2 kW kg-1 . These findings denote the significance and great potential of RE-doped Co3 O4  in the development of high-efficiency energy storage.

Recent Progress of Crystalline Porous Frameworks for Intermediate-Temperature Proton Conduction.

Proton exchange membranes (PEMs), especially for work under intermediate temperatures (100-200 °C), have attracted great interest because of the high CO toleration and facial water management of the corresponding proton exchange membrane fuel cells (PEMFCs). Traditional polymer PEMs faced challenges of low stability and proton carrier leaking. Crystalline porous materials, such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), are promising to overcome these issues contributed by nanometer-sized channels. Herein we summarized the recent development of MOF/COF-based intermediate-temperature proton conductors. The strategies of framework engineering and pore impregnation were introduced in detail for raising proton conductivity. The proton-conducting mechanism was described as well. This spotlight will provide new insight into the fabrication of MOF/COF proton conductors under intermediate-temperature and anhydrous conditions.

Differential Cytokine Signatures of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Influenza Infection Highlight Key Differences in Pathobiology.

BACKGROUND: Several inflammatory cytokines are upregulated in severe coronavirus disease 2019 (COVID-19). We compared cytokines in COVID-19 versus influenza to define differentiating features of the inflammatory response to these pathogens and their association with severe disease. Because elevated body mass index (BMI) is a known risk factor for severe COVID-19, we examined the relationship of BMI to cytokines associated with severe disease. METHODS: Thirty-seven cytokines and chemokines were measured in plasma from 135 patients with COVID-19, 57 patients with influenza, and 30 healthy controls. Controlling for BMI, age, and sex, differences in cytokines between groups were determined by linear regression and random forest prediction was used to determine the cytokines most important in distinguishing severe COVID-19 and influenza. Mediation analysis was used to identify cytokines that mediate the effect of BMI and age on disease severity. RESULTS: Interleukin-18 (IL-18), IL-1ß, IL-6, and tumor necrosis factor-α (TNF-α) were significantly increased in COVID-19 versus influenza patients, whereas granulocyte macrophage colony-stimulating factor, interferon-γ (IFN-γ), IFN-λ1, IL-10, IL-15, and monocyte chemoattractant protein 2 were significantly elevated in the influenza group. In subgroup analysis based on disease severity, IL-18, IL-6, and TNF-α were elevated in severe COVID-19, but not in severe influenza. Random forest analysis identified high IL-6 and low IFN-λ1 levels as the most distinct between severe COVID-19 and severe influenza. Finally, IL-1RA was identified as a potential mediator of the effects of BMI on COVID-19 severity. CONCLUSIONS: These findings point to activation of fundamentally different innate immune pathways in severe acute respiratory syndrome coronavirus 2 and influenza infection, and emphasize drivers of severe COVID-19 to focus both mechanistic and therapeutic investigations.

Directing the Architecture of Surface-Clean Cu2O for CO Electroreduction.

Tailoring the morphology of nanocrystals is a promising way to enhance their catalytic performance. In most previous shape-controlled synthesis strategies, surfactants are inevitable due to their capability to stabilize different facets. However, the adsorbed surfactants block the intrinsic active sites of the nanocrystals, reducing their catalytic performance. For now, strategies to control the morphology without surfactants are still limited but necessary. Herein, a facile surfactant-free synthesis method is developed to regulate the morphology of Cu2O nanocrystals (e.g., solid nanocube, concave nanocube, cubic framework, branching nanocube, branching concave nanocube, and branching cubic framework) to enhance the electrocatalytic performance for the conversion of CO to n-propanol. Specifically, the Cu2O branching cubic framework (BCF-Cu2O), which is difficult to fabricate using previous surfactant-free methods, is fabricated by combining the concentration depletion effect and the oxidation etching process. More significantly, the BCF-Cu2O-derived catalyst (BCF) presents the highest n-propanol current density (-0.85 mA cm-2) at -0.45 V versus the reversible hydrogen electrode (VRHE), which is fivefold higher than that of the surfactant-coated Cu2O nanocube-derived catalyst (SFC, -0.17 mA cm-2). In terms of the n-propanol Faradaic efficiency in CO electroreduction, that of the BCF exhibits a 41% increase at -0.45 VRHE as compared with SFC. The high catalytic activity of the BCF that results from the clean surface and the coexistence of Cu(100) and Cu(110) in the lattice is well-supported by density functional theory calculations. Thus, this work presents an important paradigm for the facile fabrication of surface-clean nanocrystals with an enhanced application performance.

Tailored Linker Defects in UiO-67 with High Ligand-to-Metal Charge Transfer toward Efficient Photoreduction of CO2.

Defect engineering can be used as a potential tool to activate metal-organic frameworks by regulating the pore structure, electronic properties, and catalytic activity. Herein, linker defects were effectively controlled by adjusting the amount of formic acid, and UiO-67 with different CO2 reduction capabilities was obtained. Among them, UiO-67-200 had the highest ability to selectively reduce CO2 to CO (12.29 µmol g-1 h-1). On the one hand, the results based on time-resolved photoluminescence decay curves and photochemical experiments revealed that UiO-67-200 had the highest charge separation efficiency. On the other hand, the linker defects affected the band structure of UiO-67 by changing the lowest unoccupied molecular orbital (LUMO) based on the density functional theory and UV-vis spectra. Hence, the proper linker defects enhanced the ligand-to-metal charge transfer process by promoting the transfer of electrons between the highest occupied molecular orbital and LUMO. Additionally, in situ Fourier transform infrared spectra and 13CO2 labeling experiments also indicated that COOH* was an important intermediate for CO formation and that CO originated from the photoreduction of CO2.

Pd Nanosheet-Decorated 2D/2D g-C3N4/WO3·H2O S-Scheme Photocatalyst for High Selective Photoreduction of CO2 to CO.

The development of the global economy in recent years, environmental problems, greenhouse effect, and so forth have been of concern for countries all over the world. The key for solving the greenhouse effect is the reduction of CO2. With the development of photocatalytic reduction of CO2, hybrid photocatalytic nanostructures composed of noble metals and plasmonic semiconductors are being widely studied. In this work, S-scheme photocatalysts with a g-C3N4/WO3·H2O/Pd heterostructure was constructed by introducing ultrathin Pd nanosheets into the optimized 2D/2D g-C3N4/WO3·H2O binary system. The S-scheme charge transfer generated by the matched band gap of g-C3N4 and WO3·H2O can effectually improve the electron transfer rate and the redox ability of photogenerated carriers. The introduction of Pd nanosheets can inject a large number of hot electrons into the semiconductor on the basis of the S-scheme heterojunction to participate in the reaction. The S-scheme electron transfer method is used to improve the utilization rate of thermionic electrons and achieve the effect of widening the near-infrared-light absorption area of the composite material. Moreover, the reaction was carried out in water without the addition of any sacrificial agent, which can better reflect the green environmental protection of the experiment. This investigation will promote the broad-spectrum application of new and environment-friendly thermoelectron-assisted S-scheme photocatalysts, and on this basis, the possible reaction mechanism is discussed.

Distinct Cytokine and Chemokine Dysregulation in Hospitalized Children With Acute Coronavirus Disease 2019 and Multisystem Inflammatory Syndrome With Similar Levels of Nasopharyngeal Severe Acute Respiratory Syndrome Coronavirus 2 Shedding.

BACKGROUND: Multisystem inflammatory syndrome in children (MIS-C) is a severe clinical phenotype of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that remains poorly understood. METHODS: Hospitalized children <18 years of age with suspected coronavirus disease 2019 (COVID-19) (N = 53) were recruited into a prospective cohort study; 32 had confirmed COVID-19, with 16 meeting the US Centers for Disease Control criteria for MIS-C. Differences in nasopharyngeal viral ribonucleic acid (RNA) levels, SARS-CoV-2 seropositivity, and cytokine/chemokine profiles were examined, including after adjustments for age and sex. RESULTS: The median ages for those with and without MIS-C were 8.7 years (interquartile range [IQR], 5.5-13.9) and 2.2 years (IQR, 1.1-10.5), respectively (P = .18), and nasopharyngeal levels of SARS-CoV-2 RNA did not differ significantly between the 2 groups (median 63 848.25 copies/mL versus 307.1 copies/mL, P = .66); 75% of those with MIS-C were antibody positive compared with 44% without (P = .026). Levels of 14 of 37 cytokines/chemokines (interleukin [IL]-1RA, IL-2RA, IL-6, IL-8, tumor necrosis factor-α, IL-10, IL-15, IL-18, monocyte chemoattractant protein [MCP]-1, IP-10, macrophage-inflammatory protein [MIP]-1α, MCP-2, MIP-1ß, eotaxin) were significantly higher in children with MIS-C compared to those without, irrespective of age or sex (false discovery rate <0.05; P < .05). CONCLUSIONS: The distinct pattern of heightened cytokine/chemokine dysregulation observed with MIS-C, compared with acute COVID-19, occurs across the pediatric age spectrum and with similar levels of nasopharyngeal SARS-CoV-2 RNA.