The global landscapes of lysine crotonylation in pseudorabies virus infection.

Lysine crotonylation is a common occurrence in eukaryotic cells, regulating various physiological functions, including chromatin remodeling, cellular growth, and development. However, its involvement in viral infections has rarely been documented. In this study, we reveal that pseudorabies virus (PRV) infection significantly alters the global lysine crotonylation levels in porcine kidney PK-15 cells. Specifically, we identified a few viral proteins, including UL54, gM, gD, UL19, UL37, and UL46, which undergo crotonylation modification. Our observations indicate that at 20 h post-infection (hpi), 551 crotonylation sites were reduced across 345 proteins, while 47 new sites emerged in 37 proteins compared to the control group. By 40 hpi, 263 sites had decreased in 190 proteins, while 389 new sites appeared in 240 proteins. Deeper analysis revealed that the proteins with altered crotonylation levels were primarily involved in binding, catalytic activity, biosynthetic processes, ribosome activity, and metabolic processes. Additionally, our findings underscored the significance of ribosomes and the endoplasmic reticulum (ER), which were enriched with proteins exhibiting altered crotonylation. Overall, our study for the first time offers new insights into the relationship between crotonylation and herpes virus infection, paving the way for future investigations into the role of crotonylation in viral infections.

Characterization the microbial diversity and functional genes in the multi-component contaminated groundwater in a petrochemical site.

Microorganisms in groundwater at petroleum hydrocarbon (PHC)-contaminated sites are crucial for PHC natural attenuation. Studies mainly focused on the microbial communities and functions in groundwater contaminated by PHC only. However, due to diverse raw and auxiliary materials and the complex production processes, in some petrochemical sites, groundwater suffered multi-component contamination, but the microbial structure remains unclear. To solve the problem, in the study, a petrochemical enterprise site, where the groundwater suffered multi-component pollution by PHC and sulfates, was selected. Using hydrochemistry, 16S rRNA gene, and metagenomic sequencing analyses, the relationships among electron acceptors, microbial diversity, functional genes, and their interactions were investigated. Results showed that different production processes led to different microbial structures. Overall, pollution reduced species richness but increased the abundance of specific species. The multi-component contamination multiplied a considerable number of hydrocarbon-degrading and sulfate-reducing microorganisms, and the introduced sulfates might have promoted the biodegradation of PHC. PRACTITIONER POINTS: The compound pollution of the site changed the microbial community structure. Sulfate can promote the degradation of petroleum hydrocarbons by hydrocarbon-degrading microorganisms. The combined contamination of petroleum hydrocarbons and sulfates will decrease the species richness but increase the abundance of endemic species.

Comparative analysis of changes in diarrhea and gut microbiota in Beigang pigs.

Increasing evidence indicated that the gut microbiota is a large and complex organic combination, which is closely related to the host health. Diarrhea is a disease with devastating effects on livestock that has been demonstrated to be associated with gut microbiota. Currently, studies on gut microbiota and diarrhea have involved multiple species, but changes in gut microbiota of Beigang pigs during diarrhea have not been characterized. Here, we described gut microbial changes of Beigang pigs during diarrhea. Results indicated that a total of 4423 OTUs were recognized in diarrheic and healthy Beigang pigs, and Firmicutes and Bacteroidota were the most dominant phyla regardless of health status. However, the major components of the gut microbiota changed between diarrheic and healthy Beigang pigs. Bacterial taxonomic analysis revealed that the relative abundances of 3 phyla (Synergistota, Actinobacteriota and Spirochaetota) and 30 genera increased significantly during diarrhea, whereas the relative abundances of 3 phyla (Patescibacteria, Bacteroidota and Fibrobacterota) and 41 genera decreased significantly. In conclusion, this study found significant changes in the gut microbiota of Beigang pigs during diarrhea. Meanwhile, this also lays the foundation for the prevention and treatment of diarrhea in Beigang pigs and the further discovery of more anti-diarrhea probiotics.

The therapeutic potential of natural killer cells in neuropathic pain.

Novel disease-modifying treatments for neuropathic pain are urgently required. The cellular immune response to nerve injury represents a promising target for therapeutic development. Recently, the role of natural killer (NK) cells in both CNS and PNS disease has been the subject of growing interest. In this opinion article, we set out the case for NK cell-based intervention as a promising avenue for development in the management of neuropathic pain. We explore the potential cellular and molecular targets of NK cells in the PNS by contrasting with their reported functional roles in CNS diseases, and we suggest strategies for using the beneficial functions of NK cells and immune-based therapeutics in the context of neuropathic pain.

Fracture strength and failure mechanism of graphene-containing grain boundaries and pores.

Grain boundaries and pores commonly manifest in graphene sheets during experimental preparation. Additionally, pores have been intentionally incorporated into graphene to fulfill specific functions for various applications. However, how does the simultaneous presence of pores and grain boundaries impact the mechanical properties of graphene? This paper establishes uniaxial tension models of single-layer graphene-containing pores and three types of experimentally observed. The effect of interaction between pores and grain boundaries on the fracture strength of graphene was studied respectively for three types of grain boundaries by employing molecular dynamics simulations and considering factors such as pore size, the distance between pores and grain boundaries, and loading angle. A competitive mechanism between the intrinsic strength of pristine graphene with grain boundaries (referred to as pristine GGBs), which varies with the loading angle and the fracture strength of graphene sheets with pores that changes with the size of the pores, governs the fracture strength and failure modes of GGBs with pores. When the former exceeds the latter, the fracture strength of GGBs with pores primarily depends on the size of the pores, and fractures occur at the edges of the pores. Conversely, when the former is lower, the fracture strength of GGBs with pores relies on the loading angle and the distance between pores and grain boundaries, leading to grain boundary rupture. If the two strengths are comparable, the failure modes are influenced by the distance between pores and grain boundaries as well as the loading angle. The findings further elucidate the impact of coexisting grain boundaries and pores on the fracture behavior of graphene, providing valuable guidance for the precise design of graphene-based devices in the future.

The impact of environmental factors on the transport and survival of pathogens in agricultural soils from karst areas of Yunnan province, China: Laboratory column simulated leaching experiments.

Introduction: Groundwater is considered the best candidate for drinking water supply in the karst area. The groundwater water resources, however, are vulnerable to pathogenic microorganism contamination because of the typically thin soil layers overlying aquifers and the high permeability of the aquifer host rock, resulting in short residence times and low natural attenuation capacities. Until now, little attention has been paid to the critical environmental factors affecting the pathogenic microorganism contamination in soil-groundwater systems in the karst area. Methods: In the study, orthogonality column experiments with controlling ambient temperatures, pH values of inlet water, and soil porosities were carried out to investigate the transport and lifespan of pathogenic microorganisms in the leachate of agricultural soils in the karst area of Yunnan province, China. The pathogenic indicators, i.e., total bacteria count (TBC) and total coliforms count (TCC), and hydrochemical parameters, i.e., pH and permanganate index (CODMn) in the leaching water, were systematically monitored. Results and Discussion: The results showed that bacteria including coliforms can survive for prolonged periods of time in karst soils. The soils overlying the karst rocks were unable to impede the bacteria from seeping into the groundwater. The soils, in turn, likely served as both reservoirs and incubators for pathogenic bacteria. The ambient temperature was the most predominant influential factor affecting both TBC and TCC. The bacteria concentrations were proportional to the temperature in the leachate. Therefore, more attention should be paid to temperature variations in protecting the water supply, particularly in the high-temperature period, such as during the summer months.

Brain endothelial CXCL12 attracts protective natural killer cells during ischemic stroke.

BACKGROUND: The innate lymphoid cell (ILC) family consists of NK cells, ILC type 1, 2, 3 and lymphoid tissue inducer cells. They have been shown to play important roles in homeostasis and immune responses and are generally considered tissue resident. Not much is known about the presence of ILC members within the central nervous system and whether they are tissue resident in this organ too. Therefore, we studied the presence of all ILC members within the central nervous system and after ischemic brain insult. METHODS: We used the photothrombotic ischemic lesion method to induce ischemic lesions within the mouse brain. Using whole-mount immunofluorescence imaging, we established that the ILCs were present at the rim of the lesion. We quantified the increase of all ILC members at different time-points after the ischemic lesion induction by flow cytometry. Their migration route via chemokine CXCL12 was studied by using different genetic mouse models, in which we induced deletion of Cxcl12 within the blood-brain barrier endothelium, or its receptor, Cxcr4, in the ILCs. The functional role of the ILCs was subsequently established using the beam-walk sensorimotor test. RESULTS: Here, we report that ILCs are not resident within the mouse brain parenchyma during steady-state conditions, but are attracted towards the ischemic stroke. Specifically, we identify NK cells, ILC1s, ILC2s and ILC3s within the lesion, the highest influx being observed for NK cells and ILC1s. We further show that CXCL12 expressed at the blood-brain barrier is essential for NK cells and NKp46+ ILC3s to migrate toward the lesion. Complementary, Cxcr4-deficiency in NK cells prevents NK cells from entering the infarct area. Lack of NK cell migration results in a higher neurological deficit in the beam-walk sensorimotor test. CONCLUSIONS: This study establishes the lack of ILCs in the mouse central nervous system at steady-state and their migration towards an ischemic brain lesion. Our data show a role for blood-brain barrier-derived CXCL12 in attracting protective NK cells to ischemic brain lesions and identifies a new CXCL12/CXCR4-mediated component of the innate immune response to stroke.

Comprehensive analysis of lipid metabolism in influenza virus infection.

Influenza A virus (IAV) exploits host metabolic pathways to support its replication. To improve the understanding of lipid metabolic changes that could occur upon IAV infection, a comprehensive analysis of lipid metabolites in A549 cells infected with the avian H9N2 virus at the different time points was performed. It was found that H9N2 infection could largely promote the level of lipid metabolites. Further, these metabolites were mainly included in glycerophospholipids (GPs), sphingolipids (SPs), glycerolipids (GLs), fatty acids (FAs), sterollipids (STs), triglycerides (TGs), and prenol lipids (PRs). Specifically, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that these metabolites were mainly associated with the glycerphospholipid metabolism, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, and autophagy. Furthermore, it is interesting to note that these metabolites, including FFA(19:1), PE(P-17:0_20:3), PE(P-18:1_20:2), LPC(14:0/0:0), PE(O-18:0_20:3), and MGDG(16:0_18:1), are upregulated and shared in the top 10 at 12 h, 24 h, 36 h, and 48 h after H9N2 infection, indicative of the possibility of acting as biomarkers for the diagnosis in the lung infected with influenza virus. These pathways and altered metabolites could provide new understandings about biological characteristics and pathogenicity of influenza virus and have the potential to serve as biomarkers for influenza.

Auxetic ographene: a new 2D Dirac nodal-ring semimetal carbon-based material with a high negative Poisson's ratio.

Auxetic and semimetallic materials possess many advanced applications due to the negative Poisson's ratio (NPR) effect and unique electronic properties. However, candidates with the above properties are rather scarce, especially in the 2D carbon materials. Here, a new 2D NPR material with a Dirac nodal ring, named ographene, is identified using first-principles calculations. Ographene possesses anisotropic Young's modulus and unusual in-plane NPR (-0.11), which mainly originated from its puckered tetrahedron structure. In addition, the electronic band structure calculations show that ographene is a topological node-ring semimetal with high Fermi velocity. Moreover, the electronic band structure is robust against external strain. The intrinsic NPR coupled with robust electronic properties renders auxetic ographene promising for applications in electronics and mechanics areas.

Proteomic analysis reveals zinc-finger CCHC-type containing protein 3 as a factor inhibiting virus infection by promoting innate signaling.

Influenza a virus exploits host machinery to benefit its replication in host cells. Knowledge of host factors reveals the complicated interaction and provides potential targets for antiviral treatment. Here, instead of the traditional proteomic analysis, we employed a 4D label free proteomic method to identify cellular factors in A549 cells treated with avian H9N2 virus. We observed that 425 proteins were upregulated and 502 proteins were downregulated. Western blotting and quantitative real-time PCR results showed that the zinc-finger CCHC-type containing protein 3 (ZCCHC3) levels were markedly induced by H9N2 infection. Transient expression assay showed that ZCCHC3 expression decreased NP protein levels and viral titers, whereas knockdown of ZCCHC3 enhanced viral growth. Specifically, ZCCHC3 promoted the expression of IFN-ß, leading to the increased transcription of IFN downstream antiviral factors. Surprisingly, viral NS1 protein was able to antagonize the antiviral effect of ZCCHC3 by downregulating IFN-ß. Eventually, we observed that chicken finger CCCH-type containing protein 3, named ZC3H3, could also suppress the replication of H9N2 virus and the coronavirus-infectious bronchitis virus (IBV) in DF-1 cells. Together, our results showed the cellular proteomic response to H9N2 infection and identified ZCCHC3 as a novel antiviral factor against H9N2 infection, contributing to the understanding of host-virus interaction.

Gallic acid induces T-helper-1-like Treg cells and strengthens immune checkpoint blockade efficacy.

BACKGROUND: Foxp3+ regulatory T (Treg) cells facilitate tumor immune evasion by forming a suppressive tumor microenvironment. Therefore, immune therapies promoting Treg fragility may greatly enhance immune checkpoint blockade (ICB) efficacy in cancers. METHODS: We have screened 2640 compounds and identified the gut microbial metabolite gallic acid, which promotes Foxp3 degradation and Treg instability by repressing Usp21 gene transcription. In vivo and in vitro experiments have been performed to explore the roles of Usp21 in Treg cells. Importantly, we treated tumor-bearing mice with gallic acid and anti-PD-1 antibody to explore the potential therapeutic value of gallic acid in clinical cancer immunotherapy. RESULTS: Mechanistically, gallic acid prevents STAT3 phosphorylation and the binding of phosphorylated STAT3 to Usp21 gene promoter. The deubiquitinated Usp21 and stabilized PD-L1 proteins boost the function of Treg cells. Combination of gallic acid and anti-PD-1 antibody, in colorectal cancer (CRC) treatment, not only significantly dampen Treg cell function by impairing PD-L1/PD-1 signaling and downregulating Foxp3 stability, but also promote CD8+ T cells' production of IFN-γ and limited tumor growth. CONCLUSION: Our findings have implications for improving the efficacy of ICB therapy in CRC by inducing T-helper-1-like Foxp3lo Treg cells.

Innate Lymphoid Cells in the Central Nervous System.

Immune cells are present within the central nervous system and play important roles in neurological inflammation and disease. As relatively new described immune cell population, Innate Lymphoid Cells are now increasingly recognized within the central nervous system and associated diseases. Innate Lymphoid Cells are generally regarded as tissue resident and early responders, while conversely within the central nervous system at steady-state their presence is limited. This review describes the current understandings on Innate Lymphoid Cells in the central nervous system at steady-state and its borders plus their involvement in major neurological diseases like ischemic stroke, Alzheimer's disease and Multiple Sclerosis.

The Role of Connexin Hemichannels in Inflammatory Diseases.

The connexin protein family consists of approximately 20 members, and is well recognized as the structural unit of the gap junction channels that perforate the plasma membranes of coupled cells and, thereby, mediate intercellular communication. Gap junctions are assembled by two preexisting hemichannels on the membranes of apposing cells. Non-junctional connexin hemichannels (CxHC) provide a conduit between the cell interior and the extracellular milieu, and are believed to be in a protectively closed state under physiological conditions. The development and characterization of the peptide mimetics of the amino acid sequences of connexins have resulted in the development of a panel of blockers with a higher selectivity for CxHC, which have become important tools for defining the role of CxHC in various biological processes. It is increasingly clear that CxHC can be induced to open by pathogen-associated molecular patterns. The opening of CxHC facilitates the release of damage-associated molecular patterns, a class of endogenous molecules that are critical for the pathogenesis of inflammatory diseases. The blockade of CxHC leads to attenuated inflammation, reduced tissue injury and improved organ function in human and animal models of about thirty inflammatory diseases and disorders. These findings demonstrate that CxHC may contribute to the intensification of inflammation, and serve as a common target in the treatments of various inflammatory diseases. In this review, we provide an update on the progress in the understanding of CxHC, with a focus on the role of these channels in inflammatory diseases.

Incorporating the Soil Gas Gradient Method and Functional Genes to Assess the Natural Source Zone Depletion at a Petroleum-Hydrocarbon-Contaminated Site of a Purification Plant in Northwest China.

An increasing number of studies have demonstrated that natural source zone depletion (NSZD) in the vadose zone accounts for the majority (90%~99%) of the natural attenuation of light non-aqueous phase liquid (LNAPL). Until now, 0.05 to 12 kg/a.m2 NSZD rates at tens of petroleum LNAPL source zones have been determined in the middle or late evolution stage of LNAPL release, in which limited volatile organic compounds (VOCs) and methane (CH4) were detected. NSZD rates are normally estimated by the gradient method, yet the associated functional microbial activity remains poorly investigated. Herein, the NSZD at an LNAPL-releasing site was studied using both soil gas gradient methods quantifying the O2, CO2, CH4, and VOCs concentrations and molecular biology methods quantifying the abundance of the pmoA and mcrA genes. The results showed that the methanogenesis rates were around 4 to 40 kg/a.m2. The values were greater than the rates calculated by the sum of CH4 escaping (0.3~1.2 kg/a.m2) and O2 consuming (3~13 kg/a.m2) or CO2 generating rates (2~4 kg/a.m2), suggesting that the generated CH4 was oxidized but not thoroughly to CO2. The functional gene quantification also supported the indication of this process. Therefore, the NSZD rates at the site roughly equaled the methanogenesis rates (4~40 kg/a.m2), which were greater than most of the previously studied sites with a 90th percentile value of 4 kg/a.m2. The study extended the current knowledge of the NSZD and has significant implications for LNAPL remediation management.

A Dirac nodal surface semi-metallic carbon-based structure as a universal anode material for metal-ion batteries with high performance.

The rapid development of electronic devices requires high power storage batteries. However, reported 3D carbon-based materials are semiconductors or metals and are used in Li- or Na-ion batteries with low capacities. Thus, it is of interest to discover whether there is a universal semi-metallic material for use in high performance Li-, Na-, and K-ion batteries. Inspired by the recent synthesis of 3D carbon-based materials, in the research reported here, a 3D regular porous structure (bct-C56) is designed using graphene sheets. The porous carbon-based material has mechanical, dynamic, thermal, and mechanical stabilities. Interestingly, bct-C56 exhibits semi-metallic features with two Dirac nodal surfaces with mirror symmetry, as well as high Fermi velocities, indicating high electron-transport abilities. More excitingly, its theoretical capacities are 743.8, 478.2, and 425.0 mA h g-1, with diffusion barriers of 0.05-0.12, 0.07-0.12, and 0.03-0.05 eV, average OCVs of 0.31, 0.45, and 0.59 V, and volume expansion levels of 1.2%, 0.02%, and 3.1%, in Li-, Na-, and K-ion batteries, respectively. All these excellent characteristics suggest that semi-metallic bct-C56 is a universal anode material for use in metal-ion batteries with a fast charge-discharge rate. In this research, not only was a new material with a Dirac nodal surface feature designed, but it also offers an approach for the creation of high performance and universal metal-ion battery anodes with 3D porous carbon materials.

Reconfiguring graphene to achieve intrinsic negative Poisson's ratio and strain-tunable bandgap.

A new two-dimensional carbon-based material consisting of pentagonal and hexagonal elements is identified by numerical experiments, which is called phgraphene and possesses not only a tunable semimetallic feature but also a direction-dependent even sign-changed Poisson's ratio. The structural stability of such a new material is first checked systematically. It is found that phgraphene has a similar energy as theγ-graphyne, a thermally stable structure from the room temperature to 1500 K, and elastic constants satisfying the Born-Huang criterion. Both the band structure and density of states are further verified with different techniques, which demonstrate a Dirac semimetallic characteristic of phgraphene. A more interesting finding is that the band structure can be easily tuned by an external loading, resulting in the transition from semimetal to semiconductor or from type I to type III. As a new material that may be applied in the future, the mechanical property of phgraphene is further evaluated. It shows that phgraphene is a typically anisotropic material, which has not only direction-dependent Young's moduli but also direction-dependent even sign-changed Poisson's ratios. The microscopic mechanisms of both the electrical and mechanical properties are revealed. Such a versatile material with tunable band structure and auxetic effect should have promising applications in the advanced nano-electronic field in the future.

Auxetic Carbon Honeycomb: Strain-Tunable Phase Transitions and Novel Negative Poisson's Ratio.

Auxetic structure and tunable phase transitions are fascinating properties for future application. Herein, we propose two three-dimensional (3D) carbon honeycombs (CHC), known as Cmcm -CHC and Cmmm-CHC. Based on first-principles calculations, these novel 3D materials exhibit auxeticity with a fascinating negative Poisson's ratio, which stems from (i) the puckered structure of Cmcm -CHC along the tube axis and (ii) significant change of angle-dominant deformation for Cmmm-CHC in the armchair direction. In addition, the moderate strain drives semimetal to semiconductor phase transition in CHCs, which thoroughly establishes its C-C bond formation. In the meantime, two new phases, namely P63/mmc-CHC and P6/mmm-CHC, form and exhibit semiconductor characteristics. Our results also show that Cmcm -CHC and P63/mmc-CHC are superhard materials. The outstanding negative Poisson's ratio and phase transition properties make CHCs highly versatile for innovative applications in microelectromechanical and nanoelectronic devices.

A modified slow sand filtration system of epikarst spring water in karst mountainous areas, China.

Epikarst springs are commonly used for drinking water in karst mountainous areas, but they tend to bring health risks to residents because of their vulnerability. In this work, a modified slow sand filtration system (M-SSF) was established as a case study to purify and conserve the epikarst spring water. The outcomes indicate that the purification of M-SSF relies mainly on the adsorption and ion exchange of the filter medium (mixtures of heat-treated red clay and crushed limestone, MHRCCL) during the schmutzdecke juvenility, and on the schmutzdecke-formed food chain of pollutants → bacteria → protozoa after the schmutzdecke maturity. The closed water cellar lined with ceramic tiles could reduce the deterioration of epikarst spring water during storage. Via 16S rRNA sequencing, it was found that the high abundance of TM6_Dependentiae in purified epikarst spring water (PESW) suggested that the M-SSF system relies on the formation of a closed food chain to achieve effective water purification. The decrease of Pseudarcicella abundance in PESW indicated that M-SSF could effectively prevent the water quality from external influences represented by leeches. Besides, the 16S function prediction was used to qualitatively characterize microbial nitrogen metabolism, as well as organic matter degradation in water purification.

Increase in plasma Niemann-Pick disease type C2 protein is associated with poor prognosis of sepsis.

The functional significance of extracellular Niemann-Pick disease type C2 protein (NPC2) is poorly defined. It is not known whether there is an association between plasma NPC2 and sepsis. Our exploratory, quantitative proteomic analysis showed a significant increase in the level of plasma NPC2 in moribund sepsis patients. Thus, we subsequently determined NPC2 concentration in plasma from healthy subjects, pneumonia patients and sepsis patients with comorbid pneumonia; and analyzed the association of plasma NPC2 with organ dysfunction and prognosis of sepsis patients. Our data shows that plasma NPC2 concentration was significantly higher in pneumonia and sepsis patients than healthy subjects, and was further increased in sepsis patients when the SOFA score reached 14. In addition, NPC2 concentration was significantly higher in patients that subsequently developed septic shock or died within 30 days. Moreover, NPC2 level showed the strongest association with the degree of renal dysfunction in sepsis patients. In moribund sepsis patients, however, NPC2 had highest correlation coefficient with indicators of coagulation anomaly. Based on these results, we conclude that the increase in plasma NPC2 in sepsis patients is associated with multiple organ failure, possibly results from a deficiency in renal clearance, and may serve as a prognostic marker for sepsis.