Seeing Is Not Necessarily Believing: Is the Surface-Enhanced Raman Spectroscopy Signal Really from the Target?

Reagent purity is crucial to experimental research, considering that the ignorance of ultratrace impurities may induce wrong conclusions in either revealing the reaction nature or qualifying the target. Specifically, in the field of surface science, the strong interaction between the impurity and the surface will bring a non-negligible negative effect. Surface-enhanced Raman spectroscopy (SERS) is a highly surface-sensitive technique, providing fingerprint identification and near-single molecule sensitivity. In the SERS analysis of trace chloromethyl diethyl phosphate (DECMP), we figured out that the SERS performance of DECMP is significantly distorted by the trace impurities from DECMP. With the aid of gas chromatography-based techniques, one strongly interfering impurity (2,2-dichloro-N,N-dimethylacetamide), the byproduct during the synthesis of DECMP, was confirmed. Furthermore, the nonignorable interference of impurities on the SERS measurement of NaBr, NaI, or sulfadiazine was also observed. The generality ignited us to refresh and consolidate the guideline for the reliable SERS qualitative analysis, by which the potential misleading brought by ultratrace impurities, especially those strongly adsorbed on Au or Ag surfaces, could be well excluded.

Ticlopidine induces embryonic development toxicity and hepatotoxicity in zebrafish by upregulating the oxidative stress signaling pathway.

Ticlopidine exerts its anti-platelet effects mainly by antagonizing platelet p2y12 receptors. Previously, a few studies have shown that ticlopidine can induce liver injury, but the exact mechanism of hepatotoxicity remains unclear. Oxidative stress, metabolic disorders, hepatocyte apoptosis, lipid peroxidation, and inflammatory responses can all lead to hepatic liver damage, which can cause hepatotoxicity. In this study, in order to deeply explore the potential molecular mechanisms of ticlopidine -induced hepatotoxicity, we used zebrafish as a model organism to comprehensively evaluate the hepatotoxicity of ticlopidine and its associated mechanism. Three days post-fertilization, zebrafish larvae were exposed to varying concentrations (1.5, 1.75 and 2 µg/mL) of ticlopidine for 72 h, in contrast, adult zebrafish were exposed exposure to 4 µg/mL of ticlopidine for 28 days. Ticlopidine-exposed zebrafish larvae showed changes in liver morphology, shortened body length, and delayed development of the swim bladder development. Liver tissues of ticlopidine-exposed zebrafish larvae and adults stained with Hematoxylin & Eosin revealed vacuolization and increased cellular interstitial spaces in liver tissues. Furthermore, using Oil Red O and periodic acid-Schiff staining methods and evaluating different metabolic enzymes of ticlopidine-exposed zebrafish larvae and adults suggested abnormal liver metabolism and liver injury in both ticlopidine-exposed zebrafish larvae and adults. Ticlopidine also significantly elevated inflammation and oxidative stress and reduced hepatocyte proliferation. During the rescue intervention using N-acetylcysteine, we observed significant improvement in ticlopidine-induced morphological changes in the liver, shortened body length, delayed swim bladder development, and proliferation of liver tissues showed significant improvement. In conclusion, ticlopidine might inhibit normal development and liver proliferation in zebrafish by upregulation of oxidative stress levels, thus leading to embryonic developmental toxicity and hepatotoxicity. In this study, we used zebrafish as a model organism to elucidate the developmental toxicity and hepatotoxicity induced by ticlopidine upregulation of oxidative stress signaling pathway in zebrafish, providing a theoretical basis for clinical application.

Isobaric Stable Isotope N-Phosphorylation Labeling (iSIPL) for Ultrasensitive Proteome Quantification.

Stable isotope chemical labeling methods have been widely used for high-throughput mass spectrometry (MS)-based quantitative proteomics in biological and clinical applications. However, the existing methods are far from meeting the requirements for high sensitivity detection. In the present study, a novel isobaric stable isotope N-phosphorylation labeling (iSIPL) strategy was developed for quantitative proteome analysis. The tryptic peptides were selectively labeled with iSIPL tag to generate the novel reporter ions containing phosphoramidate P-N bond with high intensities under lower collision energies. iSIPL strategy are suitable for peptide sequencing and quantitative analysis with high sensitivity and accuracy even for samples of limited quantity. Furthermore, iSIPL coupled with affinity purification and mass spectrometry was applied to measure the dynamics of cyclin dependent kinase 9 (CDK9) interactomes during transactivation of the HIV-1 provirus. The interaction of CDK9 with PARP13 was found to significantly decrease during Tat-induced activation of HIV-1 gene transcription, suggesting the effectiveness of iSIPL strategy in dynamic analysis of protein-protein interaction in vivo. More than that, the proposed iSIPL strategy would facilitate large-scale accurate quantitative proteomics by increasing multiplexing capability.

A Combined Experimental and Computational Study on the Adsorption Sites of Zinc-Based MOFs for Efficient Ammonia Capture.

Ammonia (NH3) is a common pollutant mostly derived from pig manure composting under humid conditions, and it is absolutely necessary to develop materials for ammonia removal with high stability and efficiency. To this end, metal-organic frameworks (MOFs) have received special attention because of their high selectivity of harmful gases in the air, resulting from their large surface area and high density of active sites, which can be tailored by appropriate modifications. Herein, two synthetic metal-organic frameworks (MOFs), 2-methylimidazole zinc salt (ZIF-8) and zinc-trimesic acid (ZnBTC), were selected for ammonia removal under humid conditions during composting. The two MOFs, with different organic linkers, exhibit fairly distinctive ammonia absorption behaviors under the same conditions. For the ZnBTC framework, the ammonia intake is 11.37 mmol/g at 298 K, nine times higher than that of the ZIF-8 framework (1.26 mmol/g). In combination with theoretical calculations, powder XRD patterns, FTIR, and BET surface area tests were conducted to reveal the absorption mechanisms of ammonia for the two materials. The adsorption of ammonia on the ZnBTC framework can be attributed to both physical and chemical adsorption. A strong coordination interaction exists between the nitrogen atom from the ammonia molecule and the zinc atom in the ZnBTC framework. In contrast, the absorption of ammonia in the ZIF-8 framework is mainly physical. The weak interaction between the ammonia molecule and the ZIF-8 framework mainly results from the inherent severely steric hindrance, which is related to the coordination mode of the imidazole ligands and the zinc atom of this framework. Therefore, this study provides a method for designing promising MOFs with appropriate organic linkers for the selective capture of ammonia during manure composting.

Novisyntrophococcus fermenticellae gen. nov., sp. nov., isolated from an anaerobic fermentation cellar of Chinese strong-flavour baijiu.

A Gram-stain-negative, coccus-shaped, obligately anaerobic, non-motile and non-spore-forming bacterium, designated strain JN500902T, was isolated from the mud in a fermentation cellar used continuously over 30 years for Chinese strong-flavour baijiu production. Colonies were white, circular, convex and smooth-edged. Growth was observed at 20-40 °C (optimum, 37 °C), at pH 5.0-10 (optimum, pH 7.5), with 0-2 % (w/v) NaCl and with 0-4 % (v/v) ethanol. The Biolog assay demonstrated positive reactions of strain JN500902T in the metabolism of l-fucose and pyruvate. The predominant cellular fatty acids (>10 %) consisted of C16 : 0 and C14 : 0. The major end metabolites of strain JN500902T were acetic acid and ethanol when incubated anaerobically in liquid reinforced clostridial medium. Acetate was the major organic acid end product. The complete genome size of strain JN500902T was 3 420 321 bp with 3327 identified genes. The G+C content was 43.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain JN500902T with the family Lachnospiraceae, having low sequence similarity (92.8 %) to the nearest type strain, Syntrophococcus sucromutans DSM 3224T and forming a clearly distinct branch. Core genome phylogenetic analysis of the isolate and 134 strains belonging to the family Lachnospiraceae also revealed that strain JN500902T was well-separated from other genera of this family as a monophyletic clade. The average nucleotide identity and amino acid identity values between strain JN500902T and 134 Lachnospiraceae strains were less than 74 and 65 %, respectively. Considering its polyphasic characteristics, strain JN500902T represents a novel genus and species within the family Lachnospiraceae, for which the name Novisyntrophococcus fermenticellae gen. nov., sp. nov. is proposed. The type strain is JN500902T (=CICC 24502T=JCM 33939T).

Genetic variants in MIR17HG affect the susceptibility and prognosis of glioma in a Chinese Han population.

BACKGROUND: lncRNA MIR17HG was upregulated in glioma, and participated in promoting proliferation, migration and invasion of glioma. However, the role of MIR17HG polymorphisms in the occurrence and prognosis of glioma is still unclear. METHODS: In the study, 592 glioma patients and 502 control subjects were recruited. Agena MassARRAY platform was used to detect the genotype of MIR17HG polymorphisms. Logistic regression analysis was used to evaluate the relationship between MIR17HG single nucleotide polymorphisms (SNPs) and glioma risk by odds ratio (OR) and 95% confidence intervals (CIs). Kaplan-Meier curves, Cox hazards models were performed for assessing the role of these SNPs in glioma prognosis by hazard ratios (HR) and 95% CIs. RESULTS: We found that rs7318578 (OR = 2.25, p = 3.18 × 10- 5) was significantly associated with glioma susceptibility in the overall participants. In the subgroup with age <  40 years, rs17735387 (OR = 1.53, p = 9.05 × 10- 3) and rs7336610 (OR = 1.35, p = 0.016) were related to the higher glioma susceptibility. More importantly, rs17735387 (HR = 0.82, log-rank p = 0.026) were associated with the longer survival of glioma patients. The GA genotype of rs17735387 had a better overall survival (HR = 0.75, log-rank p = 0.013) and progression free survival (HR = 0.73, log-rank p = 0.032) in patients with I-II glioma. We also found that rs72640334 was related to the poor prognosis (HR = 1.49, Log-rank p = 0.035) in female patients. In the subgroup of patients with age ≥ 40 years, rs17735387 was associated with a better prognosis (HR = 0.036, Log-rank p = 0.002). CONCLUSION: Our study firstly reported that MIR17HG rs7318578 was a risk factor for glioma susceptibility and rs17735387 was associated with the longer survival of glioma among Chinese Han population, which might help to enhance the understanding of MIR17HG gene in gliomagenesis. In subsequent studies, we will continue to collect samples and follow up to further validate our findings and further explore the function of these MIR17HG SNPs in glioma in a larger sample size.

TfOH-Catalyzed Phosphinylation of 2,3-Allenols into γ-Ketophosphine Oxides.

The first facile and efficient acid-catalyzed direct coupling of a wide range of unprotected 2,3-allenols with arylphosphine oxides was developed, offering a general, one-step approach for the synthesis of structurally diverse γ-ketophosphine oxides accompanied by concurrent C-P/C═O bond formation with remarkable functional group tolerance and complete atom-economy under metal- and additive-free conditions. Mechanistic studies showed that this transformation involved a rearrangement and a phospha-Michael reaction.

Clostridium fermenticellae sp. nov., isolated from the mud in a fermentation cellar for the production of the Chinese liquor, baijiu.

A novel Gram-stain-positive, rod-shaped, obligately anaerobic, non-motile, spore-forming and binary fission encapsulated bacterium, designated strain JN500901T, was isolated from a mud cellar which has been continuously used for the fermentation of Chinese strong-flavour baijiu for over 100 years. Growth of JN500901Toccurred at pH 4.5-8.0 (optimum, pH 5.0), 20-40 °C (37 °C), 0-2 % (w/v) NaCl and 0-10 % (v/v) ethanol. The Biolog assay revealed that strain JN500901T metabolized d-fructose, l-fucose, isomaltulose and l-rhamnose among the 95 studied carbon sources. p-Cresol was the predominant volatile metabolite in the fermentation broth of strain JN500901T incubated in liquid reinforced clostridial medium under anaerobic conditions. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JN500901T belongs to Clostridiumsensu stricto, and shared the highest sequence similarity to Clostridiumcarboxidivorans DSM 15243T (94.2 %), followed by Clostridiumscatologenes DSM 757T (94.1 %). The dominant cellular fatty acids (>10 %) were C16 : 0 FAME (36.6 %), C19 : 0 cyc 9,10 DMA (19.8 %) and C16 : 1 cis 9 DMA (11.8 %). The complete genome of strain JN500901T contained a circular chromosome of 2.812 Mb with 2611 genes and 31.0 mol% G+C content. Comparative genome analysis of the strain JN500901T, Clostridiumcarboxidivorans DSM 15243T and Clostridiumscatologenes DSM 757T revealed 74.5 and 74.8 % average nucleotide identity, respectively. Based on the phenotypic, biochemical and phylogenetic analyses presented here, strain JN500901T is considered to be a novel species of the genus Clostridiumsensustricto, for which the name Clostridium fermenticellae sp. nov. is proposed. The type strain is JN500901T (=CICC 24501T=JCM 32827T).

Supramolecular multicompartment gels formed by ABC graft copolymers: high toughness and recovery properties.

We conceptually design multicompartment gels with supramolecular characteristics by taking advantage of amphiphilic ABC graft copolymers. The ABC graft copolymers contain a solvophilic A backbone and solvophobic B and C grafts, where the C grafts interact with each other via hydrogen bonds. The mechanical properties of supramolecular multicompartment gels under uniaxial tension are studied by coupling dissipative particle dynamics simulations with the nonequilibrium deformation technique. The results show that the supramolecular multicompartment gels exhibit high toughness and recovery properties, while their stiffness is maintained. Due to the physical origin, the superior mechanical properties of supramolecular gels have a tight relation with the structural relaxation of grafts and the association-disassociation dynamics of hydrogen bonds. In addition, the toughness of the multicompartment gels can be further tuned by adjusting the strength and directivity of the hydrogen bonds. The present work unveils the physical origin of the distinct mechanical properties of supramolecular gels, which may provide useful guidance for designing functional gels with superior toughness.

Molecular dynamics simulation on the mechanical properties of natural-rubber-graft-rigid-polymer/rigid-polymer systems.

A coarse-grained model-based molecular dynamics simulation was employed to investigate the mechanical properties of NR-graft-rigid-polymer/rigid-polymer systems (N30-g-(R3)6/R10). An external factor (the strain rate) as well as internal factors such as the nonbonding interaction strength, the proportion of rigid polymers, and architecture parameters (the length and number of graft chains in a molecule) were examined for their effect on the tensional behavior of N30-g-(R3)6/R10 systems. Simulation results show that a higher strain rate can promote the enhancement of mechanical performance, such as a higher modulus or yield stress. Moreover, the stress and modulus increase with an increase of the nonbonding interaction strength within rigid polymers or of the rigid polymer proportion in the systems. However, the increasing stress was found to reach a limit with a continuously increasing rigid polymer proportion. On increasing the number of graft chains in a molecule, the stress increases at small strains. However, at large strains, the evident increase in stress was found in systems in which a graft molecule has longer graft chains. In addition, our research shows that N30-g-(R3)6/R10 blends exhibit improved mechanical properties and better compatibilities relative to N30/R10, which is consistent with the experimental results. Lastly, comparisons with experimental observations were also made to ensure the rationality of the simulation results. Overall, bond stretching, bond orientation, and nonbonding interactions were found to be crucial in governing the mechanical properties of the N30-g-(R3)6/R10 systems. These findings may provide important information for further experimental and simulation studies of NR hybrid materials.

Zn(OTf)2-Catalyzed Phosphinylation of Propargylic Alcohols: Access to γ-Ketophosphine Oxides.

The first facile and efficient Zn(OTf)2-catalyzed direct coupling of unprotected propargylic alcohols with arylphosphine oxides has been developed, affording a general, one-step approach to access structurally diverse γ-ketophosphine oxides via sequential Meyer-Schuster rearrangement/phospha-Michael reaction along with new C(sp3)-P and C═O bond formations, operational simplicity, and complete atom economy under ligand-free and base-free conditions.

An insight into polymerization-induced self-assembly by dissipative particle dynamics simulation.

Polymerization-induced self-assembly is a one-pot route to produce concentrated dispersions of block copolymer nano-objects. Herein, dissipative particle dynamics simulations with a reaction model were employed to investigate the behaviors of polymerization-induced self-assembly. The polymerization kinetics in the polymerization-induced self-assembly were analyzed by comparing with solution polymerization. It was found that the polymerization rate enhances in the initial stage and decreases in the later stage. In addition, the effects of polymerization rate, length of macromolecular initiators, and concentration on the aggregate morphologies and formation pathway were studied. The polymerization rate and the length of the macromolecular initiators are found to have a marked influence on the pathway of the aggregate formations and the final structures. Morphology diagrams were mapped correspondingly. A comparison between simulation results and experimental findings is also made and an agreement is shown. This work can enrich our knowledge about polymerization-induced self-assembly.

Silver-Catalyzed, Aldehyde-Induced α-C-H Functionalization of Tetrahydroisoquinolines with Concurrent C-P Bond Formation/N-Alkylation.

The first facile and efficient silver-catalyzed, aldehyde-induced three-component reaction of N-unprotected tetrahydroisoquinolines, aldehydes, and dialkyl phosphonates has been developed, providing a general one-step approach to structurally diverse C1-phosphonylated THIQs accompanied by concurrent C-P bond formation/N-alkylation with remarkable functional group tolerance and excellent regioselectivity for endo products.

Nickel-catalyzed one-pot tandem 1,4-1,2-addition of P(O)H compounds to 1,10-phenanthrolines.

A novel and efficient nickel-catalyzed tandem 1,4-1,2-addition of P(O)H compounds to 1,10-phenanthrolines forming various 2,4-diphosphono-1,2,3,4-tetrahydro-1,10-phenanthrolines has been developed. This reaction breaks up the aromatic stabilization and directly introduces two phosphorus moieties in one single step. This finding is the first example of transition-metal-catalyzed double hydrophosphonylation of 1,10-phenanthrolines.

Tracing the nitrogen metabolites of glycine using (15)N-glycine and mass spectrometry.

RATIONALE: Glycine is the smallest amino acid used in protein synthesis, but it is also a very important precursor for the biosynthesis of other nitrogen-containing metabolites, such as purine nucleosides and nucleotides for synthesis of RNA, DNA etc. Abnormalities in glycine metabolism therefore cause diseases such as cancer. A quick and unambiguous method to trace the metabolites arising from glycine is required for targeting defect points within metabolic networks. METHODS: This paper describes a method for using (15)N-glycine to culture A549 cancer cells for use with high-resolution mass spectrometry (HRMS) and tandem mass spectrometry (HRMS(2)) that can detect the (M+1)/M pair peaks appearing in the cell metabolites. The 1 Da difference in the pair peaks can be used to point out and identify the nitrogen metabolites of glycine. RESULTS: Thirteen nitrogen-containing metabolites derived from glycine were confirmed. Among them were metabolites containing purine, such as adenine, adenosine, AMP, ADP, ATP, S-adenosylmethionine and γ-glutathione; these were the most sensitive to the (15)N-glycine-enrichment technique. Therefore, they are promising biomarkers for monitoring the glycine metabolism network. CONCLUSIONS: The method developed here could be applied to investigations of metabolism of other amino acids, and for drug discovery studies targeting the enzymes related to amino acid metabolism.

Palladium-catalyzed Suzuki cross-coupling of arylhydrazines via C-N bond cleavage.

The first example of Pd-catalyzed Suzuki cross-coupling of readily available arylhydrazines with arylboronic acids via C-N bond cleavage was developed under air, affording various biaryl compounds with broad substrate applicability and moderate to good yields. Moreover, the rigorous exclusion of air/moisture is not required in these transformations. Thus, the protocol represents a simple and efficient procedure to access biaryl compounds.

Nickel-catalyzed decarboxylative C-P cross-coupling of alkenyl acids with P(O)H compounds.

The first nickel-catalyzed decarboxylative C-P coupling of a wide range of alkenyl acids with various P(O)H compounds, especially for H-phosphonates, has been developed, affording a versatile and efficient tool for the preparation of valuable (E)-1-alkenylphosphonates, (E)-1-alkenylphosphinate oxides, and (E)-1-alkenylphosphine oxides with high stereoselectivity and broad substrate applicability. DFT calculation revealed that the phosphine ligand exhibits better catalytic performance than the nitrogen ligand in the reductive elimination step owing to the stronger nucleophilicity and larger size.

Potential of novel iron 1,3,5-benzene tricarboxylate loaded on biochar to reduce ammonia and nitrous oxide emissions and its associated biological mechanism during composting.

In this study, a novel iron 1,3,5-benzene tricarboxylate loaded on biochar (BC-FeBTC) was developed and applied to kitchen waste composting. The results demonstrated that the emissions of NH3 and N2O were significantly reduced by 57.2% and 37.8%, respectively, compared with those in control group (CK). Microbiological analysis indicated that BC-FeBTC addition altered the diversity and abundance of community structure as well as key functional genes. The nitrification genes of ammonia-oxidizing bacteria were enhanced, thereby promoting nitrification and reducing the emission of NH3. The typical denitrifying bacterium, Pseudomonas, and critical functional genes (nirS, nirK, and nosZ) were significantly inhibited, contributing to reduced N2O emissions. Network analysis further revealed the important influence of BC-FeBTC in nitrogen transformation driven by functional microbes. These findings offer crucial scientific foundation and guidance for the application of novel materials aimed at mitigating nitrogen loss and environmental pollution during composting.

ß-Thalassemia gene editing therapy: Advancements and difficulties.

ß-Thalassemia is the world's number 1 single-gene genetic disorder and is characterized by suppressed or impaired production of ß-pearl protein chains. This results in intramedullary destruction and premature lysis of red blood cells in peripheral blood. Among them, patients with transfusion-dependent ß-thalassemia face the problem of long-term transfusion and iron chelation therapy, which leads to clinical complications and great economic stress. As gene editing technology improves, we are seeing the dawn of a cure for the disease, with its reduction of ineffective erythropoiesis and effective prolongation of survival in critically ill patients. Here, we provide an overview of ß-thalassemia distribution and pathophysiology. In addition, we focus on gene therapy and gene editing advances. Nucleic acid endonuclease tools currently available for gene editing fall into 3 categories: zinc finger nucleases, transcription activator-like effector nucleases, and regularly interspaced short palindromic repeats (CRISPR-Cas9) nucleases. This paper reviews the exploratory applications and exploration of emerging therapeutic tools based on 3 classes of nucleic acid endonucleases in the treatment of ß-thalassemia diseases.