The cis-Regulatory Atlas of the Mouse Immune System.

A complete chart of cis-regulatory elements and their dynamic activity is necessary to understand the transcriptional basis of differentiation and function of an organ system. We generated matched epigenome and transcriptome measurements in 86 primary cell types that span the mouse immune system and its differentiation cascades. This breadth of data enable variance components analysis that suggests that genes fall into two distinct classes, controlled by either enhancer- or promoter-driven logic, and multiple regression that connects genes to the enhancers that regulate them. Relating transcription factor (TF) expression to the genome-wide accessibility of their binding motifs classifies them as predominantly openers or closers of local chromatin accessibility, pinpointing specific cis-regulatory elements where binding of given TFs is likely functionally relevant, validated by chromatin immunoprecipitation sequencing (ChIP-seq). Overall, this cis-regulatory atlas provides a trove of information on transcriptional regulation through immune differentiation and a foundational scaffold to define key regulatory events throughout the immunological genome.

Responses of Rice and Related Cadmium Transporter Genes to the Passivating Microbial Agent MBLHAP.

Alkali-producing microorganisms and hydroxyapatite (HAP), a chemical passivation agent, have a certain remediation effect on cadmium (Cd) -contaminated soil. They can decrease the available Cd content in the soil to a certain extent and reduce the overall Cd content of rice planted in the soil. The Cd-contaminated soil was treated with the passivating bacterial agent that had been developed. Changes in the Cd concentration of rice leaves and soil were observed. Real-time PCR was used to analyse the expression levels of Cd transport protein genes in rice. Then, we determined the activities of super-oxide dismutase (SOD), catalase (CAT) and peroxidase (POD) at different stages of rice growth. The results showed that after HAP, alkali-producing microorganisms and passivating microbial agents were applied to the Cd treated soil. The total Cd content in rice leaves was reduced by 66.80%, 80.32% and 81.35%. The expression differences of genes related to Cd transporter proteins were measured, and the results showed that the changes in gene regulation were consistent with the changes in Cd content of rice leaves. The changes in SOD activity, CAT activity and POD activity further indicated that the three enzymes could alleviate the adverse effects of Cd stress by regulating the related enzyme activities in rice. In conclusion, alkali-producing microorganisms, HAP and passivating bacterial agents can effectively reduce the toxicity of Cd to rice, and reduce the absorption and accumulation of Cd in rice leaves.

Carbon Monoxide Suppresses Neointima Formation in Transplant Arteriosclerosis by Inhibiting Vascular Progenitor Cell Differentiation.

[Figure: see text].

Competitive SWIFT cluster templates enhance detection of aging changes.

Clustering-based algorithms for automated analysis of flow cytometry datasets have achieved more efficient and objective analysis than manual processing. Clustering organizes flow cytometry data into subpopulations with substantially homogenous characteristics but does not directly address the important problem of identifying the salient differences in subpopulations between subjects and groups. Here, we address this problem by augmenting SWIFT--a mixture model based clustering algorithm reported previously. First, we show that SWIFT clustering using a "template" mixture model, in which all subpopulations are represented, identifies small differences in cell numbers per subpopulation between samples. Second, we demonstrate that resolution of inter-sample differences is increased by "competition" wherein a joint model is formed by combining the mixture model templates obtained from different groups. In the joint model, clusters from individual groups compete for the assignment of cells, sharpening differences between samples, particularly differences representing subpopulation shifts that are masked under clustering with a single template model. The benefit of competition was demonstrated first with a semisynthetic dataset obtained by deliberately shifting a known subpopulation within an actual flow cytometry sample. Single templates correctly identified changes in the number of cells in the subpopulation, but only the competition method detected small changes in median fluorescence. In further validation studies, competition identified a larger number of significantly altered subpopulations between young and elderly subjects. This enrichment was specific, because competition between templates from consensus male and female samples did not improve the detection of age-related differences. Several changes between the young and elderly identified by SWIFT template competition were consistent with known alterations in the elderly, and additional altered subpopulations were also identified. Alternative algorithms detected far fewer significantly altered clusters. Thus SWIFT template competition is a powerful approach to sharpen comparisons between selected groups in flow cytometry datasets.

Dual-Fuel Propelled Nanomotors with Two-Stage Permeation for Deep Bacterial Infection in the Treatment of Pulpitis.

Bacterial infection-induced inflammatory response could cause irreversible death of pulp tissue in the absence of timely and effective therapy. Given that, the narrow structure of root canal limits the therapeutic effects of passive diffusion-drugs, considerable attention has been drawn to the development of nanomotors, which have high tissue penetration abilities but generally face the problem of insufficient fuel concentration. To address this drawback, dual-fuel propelled nanomotors (DPNMs) by encapsulating L-arginine (L-Arg), calcium peroxide (CaO2 ) in metal-organic framework is developed. Under pathological environment, L-Arg could release nitric oxide (NO) by reacting with reactive oxygen species (ROS) to provide the driving force for movement. Remarkably, the depleted ROS could be supplemented through the reaction between CaO2 with acids abundant in the inflammatory microenvironment. Owing to high diffusivity, NO achieves further tissue penetration based on the first-stage propulsion of nanomotors, thereby removing deep-seated bacterial infection. Results indicate that the nanomotors effectively eliminate bacterial infection based on antibacterial activity of NO, thereby blocking inflammatory response and oxidative damage, forming reparative dentine layer to avoid further exposure and infection. Thus, this work provides a propagable strategy to overcome fuel shortage and facilitates the therapy of deep lesions.

Environmental decentralization and carbon emissions: evidence from China.

A robust environmental management system holds great significance for the Chinese government in effectively managing the country's carbon emissions. This study delves into the spatial impact of environmental decentralization on the carbon emissions of 30 Chinese provinces spanning from 2000 to 2019. First, we found that the increase in environmental decentralization promotes carbon emissions, and this effect is primarily driven by the delegation of environmental monitoring authority and environmental supervision authority. Second, we analyzed the heterogeneity of the carbon emission effects of environmental decentralization across different regions and observed that the impact of environmental decentralization is more significant in the western region compared to the central and eastern regions. Furthermore, this study investigates how the industrial structure, government competition, and environmental regulation exert an influence on the carbon emission effects of environmental decentralization. This article presents empirical evidence from the perspective of environmental management systems that underscores the rapid escalation of carbon emissions. Additionally, it contributes to an enhanced comprehension of the economic ramifications linked to the process of environmental decentralization. At the same time, the conclusions of this article have significant practical implications for the rational design of levels of environmental decentralization, thereby accelerating the achievement of carbon neutrality.

Therapeutic nanosweepers promote ß-amyloid removal from the brain for Alzheimer's disease treatment.

Formation of neurotoxic ß-amyloid (Aß) deposits is generally believed to be a crucial pathogenic event in Alzheimer's disease (AD). However, current Aß-targeting medicines show limited therapeutic efficacy due to ineffective Aß removal and limited blood-brain barrier (BBB) penetration capability. Herein, a therapeutic nanosweeper (NS) with Aß removal capability is developed. NS can be efficiently loaded into neutrophils (NE) to form NS/NE to improve its BBB crossing efficiency and preserve its Aß removal capability after being released from neutrophils. With this capability, NS can be efficiently delivered into the brain in the form of NS/NE owing to its chemotaxis to inflammatory factors released from AD brain. Moreover, NS released from NS/NE preserved its Aß removal capability, thereby significantly alleviating the pathological symptoms of Aß deposition and neuronal apoptosis in AD mice. This work demonstrated the potential of NS in the development of novel and effective AD therapies.

Self-Propelled Nanomotors with an Alloyed Engine for Emergency Rescue of Traumatic Brain Injury.

In severe traumatic brain injury (sTBI), acute oxidative stress and inflammatory cascades rapidly spread to cause irreversible brain damage and low survival rate within minutes. Therefore, developing a feasible solution for the quick-treatment of life-threatening emergency is urgently demanded to earn time for hospital treatment. Herein, Janus catalysis-driven nanomotors (JCNs) are carefully constructed via plasma-induced alloying technology and sputtering-caused half-coating strategy. The theoretical calculation and experiment results indicate that the heteroatom-doping alloyed engine endows JCNs with much higher catalytic activity for removing reactive oxygen species and reactive nitrogen species than common Pt-based engines. When JCNs are dropped to the surface of the ruptured skull, they can effectively catalyze endogenous hydrogen peroxide, which induces movement as fuels to promote JCNs to deep brain lesions for further nanocatalyst-mediated cascade-blocking therapy. The results demonstrate that the JCNs successfully block the inflammatory cascades, thereby reversing multiple behavioral defects and dramatically declining the mortality of sTBI mice. This work provides a revolutionary nanomotor-based strategy to sense brain injury and scavenge oxidative stress. Meanwhile, the JCNs provide a feasible strategy to adapt various first-aid scenarios due to their self-propelled movement combined with highly multienzyme-like catalytic activity, exhibiting tremendous therapeutic potential to help people for emergency pretreatment.

Human basophils express amphiregulin in response to T cell-derived IL-3.

BACKGROUND: Amphiregulin, a member of the epidermal growth factor family, is expressed by activated mouse T(H)2 cells. Amphiregulin produced by mouse hematopoietic cells contributes to the elimination of a nematode infection by a type 2 effector response. OBJECTIVE: To identify the human peripheral blood cell population expressing amphiregulin. METHODS: Amphiregulin-expressing cells were identified by flow cytometry of cell surface markers and histologic staining. Histamine and amphiregulin in supernatants were measured by enzyme immunoassay. Quantitative real-time PCR was used to measure mRNA expression. RESULTS: Stimulation of human PBMCs by anti-CD3 + anti-CD28 antibodies induced expression of amphiregulin mRNA and protein by a non-T-cell population. The amphiregulin-producing cells were basophils, as judged by morphology and expression of CD203c and CD123 (IL-3 receptor α chain). Activated mouse basophils also produced amphiregulin. Amphiregulin expression by basophils in response to anti-TCR stimulation required IL-3 produced by T cells, and IL-3 alone induced high levels of amphiregulin expression by purified basophils. Amphiregulin was expressed at much higher levels when human basophils were stimulated by IL-3 than by IgE cross-linking, whereas the opposite was true for IL-4 expression and histamine release. Heparin-binding epidermal growth factor-like growth factor was also expressed by IL-3-stimulated human basophils. PBMCs from human subjects with asthma contained significantly higher numbers of basophils able to produce amphiregulin compared with controls with or without allergy. CONCLUSION: IL-3 can induce basophils to express high levels of amphiregulin, which may contribute to tissue remodeling during type 2 immune responses such as asthma.

Aggregation-induced emission (AIE)-guided dynamic assembly for disease imaging and therapy.

The phenomenon of aggregation-induced emission (AIE) is inseparable from molecular aggregation and self-assembly. Therefore, the combination of AIE and supramolecular self-assembly is well-matched. AIE-guided dynamic assembly (AGDA) could effectively respond to the endogenous stimuli (such as pH, enzymes, redox molecules) and exogenous stimuli (temperature, light, ultrasound) in the disease microenvironment, so as to achieve specific imaging and diagnosis of the disease lesions. Moreover, AGDA also dynamically adjust the intramolecular motions of AIE molecules, thereby adjusting the energy dissipation pathways and realizing the switch between photodynamic therapy and photothermal therapy for superior therapeutic effects. In this review, we aim to give an overview of the constructing strategies, stimuli-responsive imaging, regulation of intramolecular motion of AGDA in recent years, which is expected to grasp the research status and striving directions of AGDA for imaging and therapy.

Calcium supplementation relieves high-fat diet-induced liver steatosis by reducing energy metabolism and promoting lipolysis.

Nonalcoholic fatty liver disease (NAFLD) is a chronic disease affecting the health of many people worldwide. Previous studies have shown that dietary calcium supplementation may alleviate NAFLD, but the underlying mechanism is not clear. In this study investigating the effect of calcium on hepatic lipid metabolism, 8-week-old male C57BL/6J mice were divided into four groups (n = 6): (1) mice given a normal chow containing 0.5% calcium (CN0.5), (2) mice given a normal chow containing 1.2% calcium (CN1.2), (3) mice given a high-fat diet (HFD) containing 0.5% calcium (HFD0.5), and (4) mice fed a HFD containing 1.2% calcium (HFD1.2). To understand the underlying mechanism, cells were treated with oleic acid and palmitic acid to mimic the HFD conditions in vitro. The results showed that calcium alleviated the increase in triglyceride accumulation induced by oleic acid and/or palmitic acid in HepG2, AML12, and primary hepatocyte cells. Our data demonstrated that calcium supplementation alleviated HFD-induced hepatic steatosis through increased liver lipase activity, proving calcium is involved in the regulation of hepatic lipid metabolism. Moreover, calcium also increased the level of glycogen in the liver, and at the same time had the effect of reducing glycolysis and promoting glucose absorption. Calcium addition increased calcium levels in the mitochondria and cytoplasm. Taken together, we concluded that calcium supplementation could relieve HFD-induced hepatic steatosis by changing energy metabolism and lipase activity.

CRISPR/Cas9-Mediated Specific Integration of Fat-1 and IGF-1 at the pRosa26 Locus.

Many researchers have focused on knock-in pigs for site-specific integration, but little attention has been given to genetically modified pigs with the targeted integration of multiple recombinant genes. To establish a multigene targeted knock-in editing system, we used the internal ribosome entry site (IRES) and self-cleaving 2A peptide technology to construct a plasmid coexpressing the fatty acid desaturase (Fat-1) and porcine insulin-like growth factor-1 (IGF-1) genes at equal levels. In this study, pigs were genetically modified with multiple genes that were precisely inserted into the pRosa26 locus by using the clustered regularly spaced short palindrome repeat sequence (CRISPR)/CRISPR-related 9 (Cas9) system and somatic cell nuclear transfer technology (SCNT) in combination. Single copies of the Fat-1 and IGF-1 genes were expressed satisfactorily in various tissues of F0-generation pigs. Importantly, gas chromatography analysis revealed a significantly increased n-3 polyunsaturated fatty acid (PUFA) level in these genetically modified pigs, which led to a significant decrease of the n-6 PUFA/n-3 PUFA ratio from 6.982 to 3.122 (*** p < 0.001). In conclusion, the establishment of an editing system for targeted double-gene knock-in in this study provides a reference for the precise integration of multiple foreign genes and lays a foundation for the development of new transgenic pig breeds with multiple excellent phenotypes.

Effects of lycopene on skeletal muscle-fiber type and high-fat diet-induced oxidative stress.

Increasing studies report that many natural products can participate in formation of muscle fibers. This study aimed to investigate the effect of lycopene on skeletal muscle-fiber type in vivo and in vitro. C2C12 myoblasts were used in vitro study, and the concentration of lycopene was 10 µM. In vivo, 8-week-old male C57/BL6 mice were used and divided into four groups (n=8): (1) ND: normal-fat diet; (2) ND+Lyc: normal-fat diet mixed with 0.33% w/w lycopene; (3) HFD: high-fat diet; and (4) HFD+Lyc: high-fat diet mixed with 0.33% w/w lycopene. The mice tissue samples were collected after 8 weeks feeding. We found that lycopene supplementation enhanced the protein expression of slow-twitch fiber, succinate dehydrogenase, and malic dehydrogenase enzyme activities, whereas lycopene reduced the protein expression of fast-twitch fibers, lactate dehydrogenase, pyruvate kinase enzyme activities. Moreover, lycopene can promote skeletal muscle triglyceride deposition, enhanced the mRNA expression of genes related to lipid synthesis, reduced the mRNA expression of genes related to lipolysis. And high-fat diet-induced dyslipidemia and oxidative stress were attenuated after lycopene supplementation. Additionally, lycopene supplementation reduced the glycolytic reserve but enhanced mitochondrial ATP production in C2C12 cells. These results demonstrated that lycopene affects the activities of metabolic enzymes in muscle fibers, promotes the expression of slow-twitch fibers, and enhanced mitochondrial respiratory capacity. We speculated that lycopene affects the muscle-fiber type through aerobic oxidation, suggesting that lycopene exerts potential beneficial effects on skeletal muscle metabolism.

Zinc Supplementation Alleviates Lipid and Glucose Metabolic Disorders Induced by a High-Fat Diet.

Zinc deficiency is a risk factor for the development of obesity and diabetes. Studies have shown lower serum zinc levels in obese individuals and those with diabetes. We speculate that zinc supplementation can alleviate obesity and diabetes and, to some extent, their complications. To test our hypothesis, we investigated the effects of zinc supplementation on mice with high-fat diet (HFD)-induced hepatic steatosis in vivo and in vitro by adding zinc to the diet of mice and the medium of HepG2 cells. Both results showed that high levels of zinc could alleviate the glucose and lipid metabolic disorders induced by a HFD. High zinc can reduce glucose production, promote glucose absorption, reduce lipid deposition, improve HFD-induced liver injury, and regulate energy metabolism. This study provides novel insight into the treatment of non-alcoholic fatty liver disease and glucose metabolic disorder.

Betaine increases mitochondrial content and improves hepatic lipid metabolism.

The liver plays a critical role in lipid metabolism. Hepatic dysfunction is not only the direct cause of fatty liver disease, but the main risk factor for obesity, diabetes, and other metabolic diseases. So far, therapeutic strategies against fatty liver disease are very limited. Betaine is a methyl donor. Current studies reported that the intake of betaine decreases body fat and is beneficial for treatment of fatty liver disease and metabolic syndrome. However, the underlying mechanisms remain largely unknown. In this study, to investigate the role of betaine on hepatic lipid metabolism and explore the underlying mechanism, HepG2 cells were cultured with fatty acids and betaine. The data indicated that betaine inhibited hepatic fat accumulation and promoted mitochondrial content and activity, suggesting that betaine is involved in the regulation of lipid and energy metabolism. Gene expression analysis implied that betaine inhibits fatty acid synthesis, but stimulates fatty acid oxidation and lipid secretion. Further, to study the mechanism of betaine, FTO (RNA demethylase) and its mutant (loss of demethylase activity) were used. The results showed that FTO blocked the ability of betaine to regulate lipid metabolism and mitochondrial content, but the FTO mutant had no effect, suggesting that betaine influences RNA methylation. This work links betaine administration with mitochondrial activity and RNA methylation, and provides a potential target for the development of new therapeutic strategies for the treatment of fatty liver disease.

SOX4 controls invariant NKT cell differentiation by tuning TCR signaling.

Natural killer T (NKT) cells expressing the invariant T cell receptor (iTCR) serve an essential function in clearance of certain pathogens and have been implicated in autoimmune and allergic diseases. Complex effector programs of these iNKT cells are wired in the thymus, and upon thymic egress, they can respond within hours of antigenic challenges, classifying iNKT cells as innate-like. It has been assumed that the successful rearrangement of the invariant iTCRα chain is the central event in the divergence of immature thymocytes to the NKT cell lineage, but molecular properties that render the iTCR signaling distinct to permit the T cell lineage diversification remain obscure. Here we show that the High Mobility Group (HMG) transcription factor (TF) SOX4 controls the production of iNKT cells by inducing MicroRNA-181 (Mir181) to enhance TCR signaling and Ca2+ fluxes in precursors. These results suggest the existence of tailored, permissive gene circuits in iNKT precursors for innate-like T cell development.

Production of xylitol by expressing xylitol dehydrogenase and alcohol dehydrogenase from Gluconobacter thailandicus and co-biotransformation of whole cells.

In the present study, recombinant strains were constructed for xylitol production by cloning and expressing the novel xylitol dehydrogenase (xdh) and alcohol dehydrogenase (adh) genes in E. coli BL21 (DE3) from Gluconobacter thailandicus CGMCC1.3748. The optimum pH, temperature, specific activity and kinetic parameters were further investigated for purified XDH. The co-culture of G. thailandicus (30 g/L), BL21-xdh (20 g/L) and BL21-adh (20 g/L) produced 34.34 g/L of xylitol after 48 h in the presence of 40 g/L d-arabitol and 2% ethanol. The concentration of xylitol produced in this co-biotransformation was found to be 2.7-folds higher than the xylitol yield of G. thailandicus alone, while the yield was increased by 4.8% when compared to that of G. thailandicus mixed with BL21-xdh under the similar experimental conditions.

Enhanced d-tagatose production by spore surface-displayed l-arabinose isomerase from isolated Lactobacillus brevis PC16 and biotransformation.

In the present study, a new strain of Lactobacillus brevis producing d-tagatose was isolated and identified. Then, the l-arabinose isomerase (L-AI) of this strain was displayed on the spore surface of Bacillus subtilis DB403 by using an anchoring protein CotG and a peptide linker (Gly-Gly-Gly-Gly-Ser). This displayed L-AI with high specific activity and stability was used as a novel immobilized biocatalyst for producing d-tagatose through batch and semi-continuous biotransformation. The conversion rate of d-tagatose from 125 g/L d-galactose was achieved 79.7% at 28 h, and the volumetric productivity reached 4.3 g/L/h at 20 h. Furthermore, the displayed L-AI showed a good performance on the reusability and remained 87% of the specific activity and 40.7% of the conversion rate after five recycles. A high efficient immobilized method for producing food-grade d-tagatose was established using spore surface-displayed L-AI.

Expression and Characterization of a Novel 1,3-Propanediol Dehydrogenase from Lactobacillus brevis.

1,3-Propanediol dehydrogenase (PDOR) is important in the biosynthesis of 1,3-propanediol. In the present study, the dhaT gene encoding PDOR was cloned from Lactobacillus brevis 6239 and expressed in Escherichia coli for the first time. Sequence analysis revealed that PDOR containing two Fe(2+)-binding motifs and a cofactor motif belongs to the type III alcohol dehydrogenase. The purified recombinant PDOR exhibited a single band of 42 kDa according to SDS-PAGE. Optimal temperatures and pH values of this dehydrogenase are 37 °C, 7.5 for reduction and 25 °C, 9.5 for oxidation, respectively. We found that PDOR was more stable in acid buffer than in alkaline condition, and 60 % of its relative activity still remained after a 2-h incubation at 37 °C. The activity of PDOR can be enhanced in the presence of Mn(2+) or Fe(2+) iron and inhibited by EDTA or PMSF by different degrees. The K m and V max of this dehydrogenase are 1.25 mM, 64.02 µM min(-1) mg(-1) for propionaldehyde and 2.26 mM, 35.05 µM min(-1) mg(-1) for 1,3-PD, respectively. Substrate specificity analysis showed that PDOR has a broad range of substrate specificities. The modeling superposition indicated that the structural differences may account for the diversity of PDORs' properties. Thus, our PDOR is a potential candidate for facilitating the 1,3-PD biosynthesis.

Enhanced xylitol production: Expression of xylitol dehydrogenase from Gluconobacter oxydans and mixed culture of resting cell.

Xylitol has numerous applications in food and pharmaceutical industry, and it can be biosynthesized by microorganisms. In the present study, xdh gene, encoding xylitol dehydrogenase (XDH), was cloned from the genome of Gluconobacter oxydans CGMCC 1.49 and overexpressed in Escherichia coli BL21. Sequence analysis revealed that XDH has a TGXXGXXG NAD(H)-binding motif and a YXXXK active site motif, and belongs to the short-chain dehydrogenase/reductase family. And then, the enzymatic properties and kinetic parameter of purified recombinant XDH were investigated. Subsequently, transformations of xylitol from d-xylulose and d-arabitol, respectively, were studied through mixed culture of resting cells of G. oxydans wild-type strain and recombinant strain BL21-xdh. We obtained 28.80 g/L xylitol by mixed culture from 30 g/L d-xylulose in 28 h. The production was increased by more than three times as compared with that of wild-type strain. Furthermore, 25.10 g/L xylitol was produced by the mixed culture from 30 g/L d-arabitol in 30 h with a yield of 0.837 g/g, and the max volumetric productivity of 0.990 g/L h was obtained at 22 h. These contrast to the fact that wild-type strain G. oxydans only produced 8.10 g/L xylitol in 30 h with a yield of 0.270 g/g. To our knowledge, these values are the highest among the reported yields and productivity efficiencies of xylitol from d-arabitol with engineering strains.