ReaxFF molecular dynamics simulations of methane clathrate combustion.

Understanding the ignition and dynamic processes for the combustion of hydrate is crucial for efficient energy utilization. Through reactive force field molecular dynamics simulations, we studied the high-temperature decomposition and combustion processes of methane hydrates in a pure oxygen environment. We found that at an ignition temperature of 2800 K, hydrates decomposed from the interface to the interior, but the layer-by-layer manner was no longer strictly satisfied. At the beginning of combustion, water molecules reacted first to generate OH•, followed by methane oxidation. The combustion pathway of methane is CH4→CH3•→CH3O•→CH2O→HC•O→HCOO•→CO(CO2). During the combustion process, a liquid water layer was formed between melted methane and oxygen, which hindered the reaction's progress. When there is no heat resistance, oxygen will transform into radicals such as OH• and O•, which have faster diffusion rates, allowing oxygen to conveniently cross the mass transfer barrier of the liquid water layer and participate in the combustion process. Increasing the amount of OH• may cause a surge in the reaction. On the other hand, when significant heat resistance exists, OH• is difficult to react with low-temperature hydrate components, but it can transform into O• to trigger the oxidation of methane. The H• generated has a sufficient lifetime to contact high-temperature oxygen molecules, converting oxygen into radicals that easily cross the water layer to achieve mass transfer. Therefore, finding ways to convert oxygen into various radicals is the key to solving the incomplete combustion of hydrates. Finally, the reaction pathways and microscopic reaction mechanisms of each species are proposed.

In situ restoration of soil ecological function in a coal gangue reclamation area after 10 years of elm/poplar phytoremediation.

The soil ecological health risks and toxic effects of coal gangue accumulation were examined after 10 years of elm/poplar phytoremediation. The changes in soil enzyme activities, ionome metabolism, and microbial community structure were analyzed at shallow (5-15 cm), intermediate (25-35 cm), and deep (45-55 cm) soil depths. Soil acid phosphatase activity in the restoration area increased significantly by 4.36-7.18 fold (p < 0.05). Soil concentrations of the metal ions Cu, Pb, Ni, Co, Bi, U, and Th were significantly reduced, as were concentrations of the non-metallic element S. The repair effect was shallow > middle > deep. The soil community structure, determined by 16S diversity results, was changed significantly in the restoration area, and the abundance of microorganisms increased at shallow soil depths. Altererythrobacter and Sphingomonas species were at the center of the microbial weight network in the restoration area. Redundancy analysis (RDA) showed that S and Na are important driving forces for the microbial community distributions at shallow soil depths. The KEGG function prediction indicated enhancement of the microbial function of the middle depth soil layers in the restoration area. Overall, phytoremediation enhanced the biotransformation of soil phosphorus in the coal gangue restoration area, reduced the soil content of several harmful metal elements, significantly changed the structure and function of the microbial community, and improved the overall soil ecological environment.

Ggct (γ-glutamyl cyclotransferase) plays an important role in erythrocyte antioxidant defense and red blood cell survival.

The expression of GGCT (γ-glutamyl cyclotransferase) is upregulated in various human cancers. γ-glutamyl cyclotransferase enzyme activity was originally purified from human red blood cells (RBCs), but the physiological function of GGCT in RBCs is still not clear. Here we reported that Ggct deletion in mice leads to splenomegaly and progressive anaemia phenotypes, due to elevated oxidative damage and the shortened life span of Ggct-/- RBCs. Ggct-/- RBCs have increased reactive oxygen species (ROS), and are more sensitive to H2 O2 -induced damage compared to control RBCs. Glutathione (GSH) and GSH synthesis precursor l-cysteine are decreased in Ggct-/- RBCs. Our study suggests a critical function of Ggct in RBC redox balance and life span maintenance through regulating GSH metabolism.

Variant Intestinal-Cell Kinase in Juvenile Myoclonic Epilepsy.

BACKGROUND: In juvenile myoclonic epilepsy, data are limited on the genetic basis of networks promoting convulsions with diffuse polyspikes on electroencephalography (EEG) and the subtle microscopic brain dysplasia called microdysgenesis. METHODS: Using Sanger sequencing, we sequenced the exomes of six members of a large family affected with juvenile myoclonic epilepsy and confirmed cosegregation in all 37 family members. We screened an additional 310 patients with this disorder for variants on DNA melting-curve analysis and targeted real-time DNA sequencing of the gene encoding intestinal-cell kinase ( ICK). We calculated Bayesian logarithm of the odds (LOD) scores for cosegregating variants, odds ratios in case-control associations, and allele frequencies in the Genome Aggregation Database. We performed functional tests of the effects of variants on mitosis, apoptosis, and radial neuroblast migration in vitro and conducted video-EEG studies in mice lacking a copy of Ick. RESULTS: A variant, K305T (c.914A→C), cosegregated with epilepsy or polyspikes on EEG in 12 members of the family affected with juvenile myoclonic epilepsy. We identified 21 pathogenic ICK variants in 22 of 310 additional patients (7%). Four strongly linked variants (K220E, K305T, A615T, and R632X) impaired mitosis, cell-cycle exit, and radial neuroblast migration while promoting apoptosis. Tonic-clonic convulsions and polyspikes on EEG resembling seizures in human juvenile myoclonic epilepsy occurred more often in knockout heterozygous mice than in wild-type mice (P=0.02) during light sleep with isoflurane anesthesia. CONCLUSIONS: Our data provide evidence that heterozygous variants in ICK caused juvenile myoclonic epilepsy in 7% of the patients included in our analysis. Variant ICK affects cell processes that help explain microdysgenesis and polyspike networks observed on EEG in juvenile myoclonic epilepsy. (Funded by the National Institutes of Health and others.).

Induction of cell cycle arrest and apoptosis by CPUC002 through stabilization of p53 and suppression of STAT3 signaling pathway in multiple myeloma.

Multiple myeloma has always been an important health problem in human beings due to its high morbidity, high mortality, and lack of effective therapeutic drugs. This study investigated the anticancer effect and mechanism of the newly synthesized small molecule compound CPUC002 on multiple myeloma. Our results confirmed that CPUC002 inhibited proliferation and induced G0/G1 cell cycle arrest in multiple myeloma cells. Moreover, CPUC002 also induced apoptosis by mitochondrial pathway and exogenous pathway. In mechanism, CPUC002 triggered apoptosis by stabilizing p53 in NCI-H929 cells which expressed wt-p53. Knockdown of p53 partially suppressed CPUC002-induced apoptosis. This suggests that there are other molecular mechanisms underlying CPUC002's antitumor effect. Further studies showed that the CPUC002 also inhibited the STAT3 signaling pathway, while knockdown of STAT3 abolished CPUC002-induced apoptosis and cell cycle arrest. In vivo, CPUC002 has significant antitumor activity through the same mechanism as our in vitro studies, and is highly safe in xenograft models. Together these findings indicate that CPUC002 induces apoptosis and G0/G1 cell cycle arrest in multiple myeloma cells by stabilizing p53 and inhibiting the STAT3 signaling pathway.

LL202 ameliorates colitis against oxidative stress of macrophage by activation of the Nrf2/HO-1 pathway.

LL202, a newly synthesized flavonoid derivative, has been confirmed to inhibit the mitogen-activated protein kinase pathway and activation protein-1 activation in monocytes; however, the anti-inflammatory mechanism has not been clearly studied. Uncontrolled overproduction of reactive oxygen species (ROS) has involved in oxidative damage of inflammatory bowel disease. In this study, we investigated that LL202 reduced lipopolysaccharide (LPS)-induced ROS production and malondialdehyde levels and increased superoxide dismutase, glutathione, and total antioxidant capacity in RAW264.7 cells. Mechanically, LL202 could upregulate heme oxygenase-1 (HO-1) via promoting nuclear translocation of nuclear factor erythroid 2 (NF-E2)-related factor 2 (Nrf2) to regulate LPS-induced oxidative stress in macrophages. In vivo, we validated the role of LL202 in dextran sulfate sodium- and TNBS-induced colitis models, respectively. The results showed that LL202 decreased the proinflammatory cytokine expression and regulated colonic oxidative stress by activating the Nrf2/HO-1 pathway. In conclusion, our study showed that LL202 exerts an anti-inflammatory effect by enhancing the antioxidant capacity of the Nrf2/HO-1 pathway to macrophages.

Wogonoside impedes the progression of acute myeloid leukemia through inhibiting bone marrow angiogenesis.

Decreasing bone marrow (BM) microvessel density and circulating angiogenic cytokine levels are promising strategies for the treatment of relapsed and resistant acute myeloid leukemia (AML). Previous studies have reported that wogonoside could inhibit the progression of AML and suppress angiogenesis in a solid tumor, but the correlation of these two effects was ignored. In this research, we determined whether wogonoside could inhibit angiogenesis in this hematologic malignancy. We found that wogonoside could inhibit tumor growth and progression, and prolong the survival of nude mice inoculated with U937/MDR. Besides, reducing BM angiogenesis might cause therapeutic effect against resistant AML. Therefore, coculture between AML cells and BM stromal cells was established to imitate their crosstalk. Then, the effect of wogonoside on BM angiogenesis was tested in vitro and in vivo. We found that wogonoside could suppress microvessel formation in the chicken chorioallantoic membrane assay model and matrigel plug assay. The mechanism research revealed that wogonoside could block the JAK2-STAT3 pathway in AML cells and stromal cells to break their positive feedback. We detected several cytokines related to AML or angiogenesis and found that secreted interleukin-8 was a significant angiogenic cytokine to induce BM angiogenesis. These findings supported that new diagnostics and promising treatment strategies could be developed in relapsed and resistant AML patients.

Molecular Dynamics Simulation of Methane Hydrate Decomposition in the Presence of Alcohol Additives.

The decomposition process of methane hydrate in pure water and methanol aqueous solution was studied by molecular dynamics simulation. The effects of temperature and pressure on hydrate structure and decomposition rate are discussed. The results show that decreasing pressure and increasing temperature can significantly enhance the decomposition rate of hydrate. After adding a small amount of methanol molecules, bubbles with a diameter of about 2 nm are formed, and the methanol molecules are mainly distributed at the gas-liquid interface, which greatly accelerates the decomposition rate and gas-liquid separation efficiency. The radial distribution function and sequence parameter analysis show that the water molecules of the undecomposed hydrate with ordered ice-like configuration at a temperature of 275 K evolve gradually into a long-range disordered liquid structure in the dynamic relaxation process. It was found that at temperatures above 280 K and pressures between 10 atm and 100 atm, the pressure has no significant effect on hydrate decomposition rate, but when the pressure is reduced to 1 atm, the decomposition rate increases sharply. These findings provided a theoretical insight for the industrial exploitation of hydrates.

LZ205, a newly synthesized flavonoid compound, exerts anti-inflammatory effect by inhibiting M1 macrophage polarization through regulating PI3K/AKT/mTOR signaling pathway.

Macrophage polarization is involved in the process of inflammation. Regulation of macrophage polarization is considered to be an effective method for the treatment of various inflammatory diseases. In our study, we investigated the potential molecular mechanism of the flavonoid compound LZ205, which exhibits anti-inflammatory property. Results showed that LZ205 significantly reduced M1 macrophage-associated proinflammatory cytokines secretion by regulating PI3K/AKT/mTOR signaling pathway without affecting M2 macrophage-associated cytokines mRNA levels. In vivo studies showed that LZ205 significantly inhibited M1 macrophages polarization in DSS-induced colitis and alum-induced murine peritonitis. Consistent with in vitro studies, LZ205 significantly blocked expression of PI3K, p-AKT and p-mTOR in colon tissues and peritoneal macrophages. Taken together, LZ205 exerts anti-inflammatory effect by inhibiting M1 macrophage polarization via regulating PI3K/AKT/mTOR signaling pathway.

Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution.

High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-scale samples remains challenging. Here, we present hmC-CATCH, a bisulfite-free, base-resolution method for the genome-wide detection of 5hmC. hmC-CATCH is based on selective 5hmC oxidation, chemical labeling and subsequent C-to-T transition during PCR. Requiring only nanoscale input genomic DNA samples, hmC-CATCH enabled us to detect genome-wide hydroxymethylome of human embryonic stem cells in a cost-effective manner. Further application of hmC-CATCH to cell-free DNA (cfDNA) of healthy donors and cancer patients revealed base-resolution hydroxymethylome in the human cfDNA for the first time. We anticipate that our chemical biology approach will find broad applications in hydroxymethylome analysis of limited biological and clinical samples.

Methane Hydrate Nucleation within Elastic Confined Spaces: Suitable Spacing and Elasticity Can Accelerate the Nucleation.

Elastic materials are candidates for process intensification of gas storage by forming gas hydrate. In this work, molecular dynamics simulations of hydrate nucleation in elastic silica double layers were performed to study the effect of elastic confined spaces on hydrate formation. It is found that in narrow confined spaces, hexagonal rings dominated the hydrogen bond network of water molecules established rapidly by a multisite nucleation mechanism. With molecules added, a bilayer water structure was formed finally because elastic space can adapt the volume expansion. In medium and wide confined spaces, hydrates were formed from a series of "pseudo cages" which are considered as precursors of complete hydrate cages. Moreover, the induction time for nucleation was a minimum when the elasticity of the silica layer changes: nucleation is fastest in the weak-elastic system. When the elasticity increases, it becomes hard to adapt the volume expansion during nucleation and also difficult to nucleate in very weak-elastic systems because of the fluctuation of the layers.

Size Effect of Silica Shell on Gas Uptake Kinetics in Dry Water.

Two kinds of dry water (DW) particles are prepared by mixing water and hydrophobic silica particles with nanometer or micrometer dimensions, and the two DW particles are found to have similar size distributions regardless of the size of the silica shell. The CO2 uptake kinetics of DW with nanometer (nanoshell) and micrometer shells (microshell) are measured, and both uptake rate and capacity show the obvious size effect of the silica shell. The DW with a microshell possesses a larger uptake capacity, whereas the DW with a nanoshell has a faster uptake rate. By comparing the uptake kinetics of soluble NH3 and CO2 further, we found that the microshell enhances the stability and the dispersion degree of DW and the nanoshell offers a shorter path for the transit of guest gas into the water core. Furthermore, molecular dynamics simulation is introduced to illustrate the nanosize effect of the silica shell on the initial step of the gas uptake. It is found that the concentration of gas molecules close to the silica shell is higher than that in the bulk water core. With the increase in the size of the silica shell, the amount of CO2 in the silica shell decreases, and it is easier for the gas uptake to reach steady state.

[Transumbilical single-site single-port versus single-site double-port laparoscopic varicocelectomy for varicocele in adolescents].

OBJECTIVE: To compare the effect of transumbilical single-site single-port with that of transumbilical single-site double-port laparoscopic varicocelectomy in the treatment of varicocele in adolescents. METHODS: We randomly assigned 80 varicocele patients aged 10 - 16 years to two groups of equal number to receive transumbilical single-site single-port and single-site double-port laparoscopic varicocelectomy, respectively. We compared the operation time, postoperative hospital stay, incisional pain, complications and satisfaction with the abdominal cosmetic outcomes between the two groups. RESULTS: All the operations were successfully performed. The double-port group showed a significantly higher score on the Visual Analogue Scale than the single-port group (4.8 +/- 1.4 vs 3.6 +/- 1.1, t = -4.986, P < 0.01), but there were no significant differences between the two groups in the operation time ([29.8 +/- 4.2] vs [31.2 +/- 4.6] min, t = 1.383, P = 0.171), postoperative hospital stay ([1.95 +/- 0.7] vs [1.82 +/- 0.8] d, t = -0.784, P = 0.436), complications (0 vs 0) and scores on the satisfaction with abdominal cosmetic outcomes (4.6 +/- 0.6 vs 4.8 +/- 0.5, t = 1.253, P = 0.214). No recurrence, umbilical hernia, hydrocele and orchiatrophy were found in the two groups of patients at 6 months after operation, and no visible scar was observed on the abdominal surface. CONCLUSION: With strict surgical indications, single-site single-port and single-site double-port laparoscopic varicocelectomies have similar clinical effects in the treatment of varicocele, which leave no scar on the abdominal surface. Single-site double-port laparoscopy needs no special instruments and therefore is worthier of wide clinical application.

Effects of Setaria viridis on heavy metal enrichment tolerance and bacterial community establishment in high-sulfur coal gangue.

Plant enrichment and tolerance to heavy metals are crucial for the phytoremediation of coal gangue mountain. However, understanding of how plants mobilize and tolerate heavy metals in coal gangue is limited. This study conducted potted experiments using Setaria viridis as a pioneer remediation plant to evaluate its tolerance to coal gangue, its mobilization and enrichment of metals, and its impact on the soil environment. Results showed that the addition of 40% gangue enhanced plant metal and oxidative stress resistance, thereby promoting plant growth. However, over 80% of the gangue inhibited the chlorophyll content, photoelectron conduction rate, and biomass of S. viridis, leading to cellular peroxidative stress. An analysis of metal resistance showed that endogenous S in coal gangue promoted the accumulation of glutathione, plant metal chelators, and non-protein thiols, thereby enhancing its resistance to metal stress. Setaria viridis cultivation affected soil properties by decreasing nitrogen, phosphorus, conductivity, and urease and increasing sucrase and acid phosphatase in the rhizosphere soil. In addition, S. viridis planting increased V, Cr, Ni, As, and Zn in the exchangeable and carbonate-bound states within the gangue, effectively enriching Cd, Cr, Fe, S, U, Cu, and V. The increased mobility of Cd and Pb was correlated with a higher abundance of Proteobacteria and Acidobacteria. Heavy metals, such as As, Fe, V, Mn, Ni, and Cu, along with environmental factors, including total nitrogen, total phosphorus, urease, and acid phosphatase, were the primary regulatory factors for Sphingomonas, Gemmatimonas, and Bryobacter. In summary, S. viridis adapted to gangue stress by modulating antioxidant and elemental enrichment systems and regulating the release and uptake of heavy metals through enhanced bacterial abundance and the recruitment of gangue-tolerant bacteria. These findings highlight the potential of S. viridis for plant enrichment in coal gangue areas and will aid the restoration and remediation of these environments.

The role of afforestation with diverse woody species in enhancing and restructuring the soil microenvironment in polymetallic coal gangue dumps.

To elucidate the effects of long-term (20 years) afforestation with different woody plant species on the soil microenvironment in coal gangue polymetallic contaminated areas. This study analyzed the soil physicochemical properties, soil enzyme activities, soil ionophore, bacterial community structure, soil metabolite, and their interaction relationships at different vertical depths. Urease, sucrase, and acid phosphatase activities in the shallow soil layers increased by 4.70-7.45, 3.83-7.64, and 3.27-4.85 times, respectively, after the restoration by the four arboreal plant species compared to the plant-free control soil. Additionally, it reduced the content of available elements in the soil and alleviated the toxicity stress for Cd, Ni, Co, Cr, As, Fe, Cu, U, and Pb. After the long-term restoration of arboreal plants, the richness and Shannon indices of soil bacteria significantly increased by 4.77-23.81% and 2.93-7.93%, respectively, broadening the bacterial ecological niche. The bacterial community structure shaped by different arboreal plants exhibited high similarity, but the community similarity decreased with increasing vertical depth. Soils Zn, U, Sr, S, P, Mg, K, Fe, Cu, Ca, Ba, and pH were identified as important influencing factors for the community structure of Sphingomonas, Pseudarthrobacter, Nocardioides, and Thiobacillus. The metabolites such as sucrose, raffinose, L-valine, D-fructose 2, 6-bisphosphate, and oxoglutaric acid were found to have the greatest effect on the bacterial community in the rhizosphere soils for arboreal plants. The results of the study demonstrated that long-term planting for woody plants in gangue dumps could regulate microbial abundance and symbiotic patterns through the accumulation of rhizosphere metabolites in the soil, increase soil enzyme activity, reduce heavy metal levels, and improve the soil environment in coal gangue dumps.

Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq.

Dynamic 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications to DNA regulate gene expression in a cell-type-specific manner and are associated with various biological processes, but the two modalities have not yet been measured simultaneously from the same genome at the single-cell level. Here we present SIMPLE-seq, a scalable, base resolution method for joint analysis of 5mC and 5hmC from thousands of single cells. Based on orthogonal labeling and recording of 'C-to-T' mutational signals from 5mC and 5hmC sites, SIMPLE-seq detects these two modifications from the same molecules in single cells and enables unbiased DNA methylation dynamics analysis of heterogeneous biological samples. We applied this method to mouse embryonic stem cells, human peripheral blood mononuclear cells and mouse brain to give joint epigenome maps at single-cell and single-molecule resolution. Integrated analysis of these two cytosine modifications reveals distinct epigenetic patterns associated with divergent regulatory programs in different cell types as well as cell states.

TrxR1 is involved in the activation of Caspase-11 by regulating the oxidative-reductive status of Trx-1.

Sepsis is a common complication of infections that significantly impacts the survival of critically patients. Currently, effective pharmacological treatment strategies are lacking. Auranofin, known as an inhibitor of Thioredoxin reductase (TrxR), exhibits anti-inflammatory activity, but its role in sepsis is not well understood. Here, we demonstrate the significant inhibitory effect of Auranofin on sepsis in a cecal ligation and puncture (CLP) mouse model. In vitro, Auranofin inhibits pyroptosis triggered by Caspase-11 activation. Further investigations reveal that inhibiting TrxR1 suppresses macrophage pyroptosis induced by E. coli, while TrxR2 does not exhibit this effect. TrxR1, functioning as a reductase, regulates the oxidative-reductive status of Thioredoxin-1 (Trx-1). Mechanistically, the modulation of Trx-1's reductive activity by TrxR1 may be involved in Caspase-11 activation-induced pyroptosis. Additionally, inhibiting TrxR1 maintains Trx-1 in its oxidized state. The oxidized form of Trx-1 interacts with Caveolin-1 (CAV1), regulating outer membrane vesicle (OMV) internalization. In summary, our study suggests that inhibiting TrxR1 suppresses OMV internalization by maintaining the oxidized form of Trx-1, thereby restricting Caspase-11 activation and alleviating sepsis.

Eubacterium coprostanoligenes alleviates chemotherapy-induced intestinal mucositis by enhancing intestinal mucus barrier.

Chemotherapy-induced mucositis represents a severe adverse outcome of cancer treatment, significantly curtailing the efficacy of these treatments and, in some cases, resulting in fatal consequences. Despite identifying intestinal epithelial cell damage as a key factor in chemotherapy-induced mucositis, the paucity of effective treatments for such damage is evident. In our study, we discovered that Eubacterium coprostanoligenes promotes mucin secretion by goblet cells, thereby fortifying the integrity of the intestinal mucus barrier. This enhanced barrier function serves to resist microbial invasion and subsequently reduces the inflammatory response. Importantly, this effect remains unobtrusive to the anti-tumor efficacy of chemotherapy drugs. Mechanistically, E. copr up-regulates the expression of AUF1, leading to the stabilization of Muc2 mRNA and an increase in mucin synthesis in goblet cells. An especially significant finding is that E. copr activates the AhR pathway, thereby promoting the expression of AUF1. In summary, our results strongly indicate that E. copr enhances the intestinal mucus barrier, effectively alleviating chemotherapy-induced intestinal mucositis by activating the AhR/AUF1 pathway, consequently enhancing Muc2 mRNA stability.

Mutations in EFHC1 cause juvenile myoclonic epilepsy.

Juvenile myoclonic epilepsy (JME) is the most frequent cause of hereditary grand mal seizures. We previously mapped and narrowed a region associated with JME on chromosome 6p12-p11 (EJM1). Here, we describe a new gene in this region, EFHC1, which encodes a protein with an EF-hand motif. Mutation analyses identified five missense mutations in EFHC1 that cosegregated with epilepsy or EEG polyspike wave in affected members of six unrelated families with JME and did not occur in 382 control individuals. Overexpression of EFHC1 in mouse hippocampal primary culture neurons induced apoptosis that was significantly lowered by the mutations. Apoptosis was specifically suppressed by SNX-482, an antagonist of R-type voltage-dependent Ca(2+) channel (Ca(v)2.3). EFHC1 and Ca(v)2.3 immunomaterials overlapped in mouse brain, and EFHC1 coimmunoprecipitated with the Ca(v)2.3 C terminus. In patch-clamp analysis, EFHC1 specifically increased R-type Ca(2+) currents that were reversed by the mutations associated with JME.