Boronic acid and fructose-1,6-diphosphate dual-functionalized highly hydrophilic Zr-MOF for HILIC enrichment of N-linked glycopeptides.

The HILIC enrichment is a greatly compatible strategy for the extraction of glycopeptides in proteomics. Herein, a boric acid and fructose-1,6-diphosphate (FDP) dual-functionalized Zr-based metal-organic framework material UIO-PBA&FDP (UIO is the abbreviation for the University of Oslo, and PBA is the abbreviation for carboxy phenylboronic acid) was synthesized, characterized with the desirable excellent hydrophilicity and thus was explored for the enrichment of N-linked glycopeptides utilizing the HILIC interaction between the glycopeptides and the hydrophilic UIO-PBA&FDP at a high level of ACN concentration. A total of 359 N-linked glycopeptides corresponding to 104 glycoproteins were identified from only 1 µL of digested human serum by the enrichment of UIO-PBA&FDP, which showed a superiorly high coverage of the identified glycopeptides. The dual hydrophilic functionalized UIO-PBA&FDP could be an efficient HILIC material for the enrichment of N-linked glycopeptides from complex biological samples.

Simultaneous enrichment optimization of glycopeptides and phosphopeptides with the highly hydrophilic DZMOF-FDP.

Protein glycosylation and phosphorylation play essential roles in biological systems. The crosstalk of both glycosylation and phosphorylation on one protein represents an unveiled biological function. To realize the analyses of both glycopeptides and phosphopeptides, a simultaneous enrichment method of N-glycopeptides, mono-phosphopeptides and multi-phosphopeptides was developed based on a multi-functional dual-metal centered zirconium metal-organic framework that provided multiple interactions for HILIC, IMAC, and MOAC for glycopeptides and phosphopeptides. Based on a careful optimization of sample loading and elution conditions for the simultaneous enrichment of glycopeptides and phosphopeptides with the zirconium metal-organic framework, a total of 1011 N-glycopeptides derived from 410 glycoproteins and 1996 phosphopeptides including 741 multi-phosphopeptides derived from 1189 phosphoproteins could be identified from a HeLa cell digest. The simultaneous enrichment approach for glycopeptides and mono-/multi-phosphopeptides demonstrates the great potential of the combined interactions for HILIC, IMAC, and MOAC in integrated post-translational modification proteomics research.

Solvent-mediated precipitating synthesis and optical properties of polyhydrido Cu13 nanoclusters with four vertex-sharing tetrahedrons.

Structurally defined metal nanoclusters facilitate mechanism studies and promote functional applications. However, precisely constructing copper nanoclusters remains a long-standing challenge in nanoscience. Developing new efficient synthetic strategies for Cu nanoclusters is highly desirable. Here, we propose a solvent-mediated precipitating synthesis (SMPS) to prepare Cu13H10(SR)3(PPh3)7 nanoclusters (H-SR = 2-chloro-4-fluorobenzenethiol). The obtained Cu13 nanoclusters are high purity and high yield (39.5%, based on Cu atom), proving the superiority of the SMPS method. The Cu13 nanoclusters were comprehensively studied via a series of characterizations. Single crystal X-ray crystallography shows that the Cu13 nanoclusters contain a threefold symmetry axis and the Cu13 kernel is protected by a monolayer of ligands, including PPh3 and thiolates. Unprecedentedly, the aesthetic Cu13 kernel is composed of four vertex-sharing tetrahedrons, rather than the common icosahedral or cuboctahedral M13. The intramolecular π⋯π interactions between thiolates and PPh3 on the surface contribute to the stable configuration. Furthermore, electrospray ionization mass spectrometry (ESI-MS) and nuclear magnetic resonance (NMR) revealed the existence of ten hydrides, including four types of hydrides. Density functional theory (DFT) calculations without simplifying the ligands simulated the location of the 10 hydrides in the crystal structure. Additionally, the steady-state ultraviolet-visible absorption and fluorescence spectra of the Cu13 nanoclusters exhibit unique optical absorbance and photoluminescence. The ultrafast relaxation dynamics were also studied via transient absorption spectroscopy, and the three decay components are attributed to the relaxation pathways of internal conversion, structural relaxation and radiative relaxation. This work provides not only a novel SMPS strategy to efficiently synthesize Cu13 nanoclusters, but also a better insight into the structural characteristics and optical properties of the Cu nanoclusters.

Recognizing the Minimum Structural Units Driving the Crystallization of SAPO-34 in a Top-Down Process.

Recognizing the structure and nature of the nuclei for zeolites crystallization on an atomic level is of great importance, which can provide guidance on the control of crystallization kinetics and the rational synthesis of zeolites. However, it remains a long-standing challenge due to the difficulty in characterization of amorphous precursor with limited crystal nuclei. Herein, a top-down synthesis system was designed for SAPO-34 molecular sieve and well investigated. A clear precursor solution with abundant SAPO-34 crystal nuclei was obtained under a depolymerization-dominant condition. The species in the liquid precursor were identified by FT-ICR MS, solid-state MAS NMR and atomic pair distribution function analyses. In combination with various designed experiments, it is revealed that both the formation of small species containing Si-O-Al bonds and reaching a certain concentration, is crucial for driving the crystallization of SAPO-34, rather than structural units with specific spatial conformation. This work provides an important understanding on the (pre)nucleation of SAPO-34 and sheds light on the synthesis control of SAPO molecular sieves.

Impact of casein-to-whey protein ratio on gastric emptying, proteolysis, and peptidome profile of fermented milk during in vitro dynamic gastrointestinal digestion in preschool children.

The effects of casein-to-whey ratios (i.e., 4:1, 2:1, 1:1, 1:1.5) in fermented milk on gastric emptying, proteolysis and intestinal peptidome were investigated using an in vitro dynamic stomach-intestine system mimicking preschool children digestion. The gastric emptying rate varied insignificantly among the milk samples. After 120 min digestion, the protein digestibility was found in the range of 73.3-93.5 %, with the highest extent of proteolysis observed at a casein-to-whey ratio of 2:1 due to the fewest gastric protein aggregates and relatively abundant caseins. Intestinal peptides derived from caseins or whey proteins showed a positive correlation with their parent protein content. The most abundant bioactive whey peptides were found at casein-to-whey ratio of 1:1.5 after intestinal digestion. These findings demonstrated the importance of protein compositions in fermented milk on the gastrointestinal proteolysis and peptide release in vitro. This will be meaningful for future development of milk products that are more suitable for children.

An alkali-resistant zirconium-biligand organic framework with dual-metal centers for highly selective capture of phosphopeptides.

The stability of MOFs plays one of the most important roles in material applications, while the delicate structure of MOFs suffers from the limitation of poor alkali tolerance. A new biligand Zr-MOF (biUIO-66-NH2NO2) with alkali-resistance performance and active functional groups has been synthesized in this study. The biUIO-66-NH2NO2 demonstrated a much better stability in 1% NH3·H2O solution than its parent material, UIO-66-NH2. Following further immobilization of Zr4+ ions, the biDZMOF consisting of dual-zirconium centers was prepared and was further applied in global enrichment of phosphopeptides by avoiding the instability of enrichment materials in the essential alkali elution procedure for the phosphopeptide enrichment workflow. The alkali-resistant elution of phosphopeptides from the biDZMOF can be directly coupled to a tandem mass spectrometry system for peptide analysis without desalting treatment. 425 phosphopeptides in total in 3 independent samples were identified from 10 µL human saliva after enrichment with biDZMOF. The improvement in alkali resistance and successful post-modification of biUIO-66-NH2NO2 suggest an efficient strategy to develop new types of MOF materials for application.

Molecular insights into the catalytic oxidation of methanol-to-olefins wastewater with phosphoric acid modified sludge biochar.

With the development of methanol-to-olefin (MTO) process, the effective disposal of wastewater was one key factor for the long-period and benign development of this technology. Herein, a sludge-based biochar catalyst (GSC-P) was synthesized and used in photo-Fenton reaction for the degradation of MTO wastewater from the outlet of a biological aerated filter. More iron was distributed on the surface of GSC-P catalyst, facilitating the photo-Fenton oxidation of MTO wastewater, with chemical oxygen demand (COD) removal rate of 75.4% and total organic carbon (TOC) removal rate of 62.5%. The 2223 unique molecular formulas assigned by a Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in the original MTO wastewater showed that CHO compounds shared the lowest peak numbers (20.2%) but the highest peak abundance (51.6%) among the four groups. Besides, lipids, unsaturated hydrocarbons, lignins and proteins were the main structural types. After photo-Fenton treatment of 60 min, there were 56.7%-74.0% of compounds removed by the analysis of van Krevelen diagram, indicating that the MTO wastewater was degraded efficiently. Three possible evolution processes of dissolved organic matters during the photo-Fenton reaction were disclosed at the molecular-level.

Self-assembly of MoS2 nanosheet adhered on Fe-MOF heterocrystals for peroxymonosulfate activation via interfacial interaction.

A novel heterogeneous catalyst PB@MoS2 was successfully synthesized via facile hydrothermal processes and identified as a superior peroxymonosulfate (PMS) activator for organic pollutants degradation under visible light irradiation. The MoS2 nanosheet is uniformly adhered to the surface of iron-based metal-organic framework Prussian blue (PB) cube, exhibiting a tightly hydrangeas-like structure. Benefiting from strongly interfacial interaction (FeMo-sulfide) between PB and MoS2, as confirmed by 57Fe M̈össbauer spectra and electrochemical measurement, the PB@MoS2 catalyst significantly accelerate the charge carrier transfer via interfacial FeMo-sulfide and thereby improve PMS activation ability to generate abundant reactive radicals. Moreover, the crucial iron active site was steadily validated by introduction of sodium oxalate trapping agent and visible light. In summary, the visible light induced Fenton-like reaction over PB@MoS2 catalyst promoted the FeII/FeIII cycling and electron transport and further triggered the reactive species (SO4-, OH, O2- and h+) productivity, realizing an extraordinarily high degradation and mineralization efficiency for various refractory organic pollutants. This work would provide a deep insight into develop heterogeneous Fe-based metal organic framework/MoS2 catalyst for environmental restoration and remediation by photo-Fenton reaction.

Microorganisms as bio-filters to mitigate greenhouse gas emissions from high-altitude permafrost revealed by nanopore-based metagenomics.

The distinct climatic and geographical conditions make high-altitude permafrost on the Tibetan Plateau suffer more severe degradation than polar permafrost. However, the microbial responses associated with greenhouse gas production in thawing permafrost remain obscured. Here we applied nanopore-based long-read metagenomics and high-throughput RNA-seq to explore microbial functional activities within the freeze-thaw cycle in the active layers of permafrost at the Qilian Mountain. A bioinformatic framework was established to facilitate phylogenetic and functional annotation of the unassembled nanopore metagenome. By deploying this strategy, 42% more genera could be detected and 58% more genes were annotated to nitrogen and methane cycle. With the aid of such enlarged resolution, we observed vigorous aerobic methane oxidation by Methylomonas, which could serve as a bio-filter to mitigate CH4 emissions from permafrost. Such filtering effect could be further consolidated by both on-site gas phase measurement and incubation experiment that CO2 was the major form of carbon released from permafrost. Despite the increased transcriptional activities of aceticlastic methanogenesis pathways in the thawed permafrost active layer, CH4 generated during the thawing process could be effectively consumed by the microbiome. Additionally, the nitrogen metabolism in permafrost tends to be a closed cycle and active N2O consumption by the topsoil community was detected in the near-surface gas phase. Our findings reveal that although the increased thawed state facilitated the heterotrophic nitrogen and methane metabolism, effective microbial methane oxidation in the active layer could serve as a bio-filter to relieve the overall warming potentials of greenhouse gas emitted from thawed permafrost.

One-pot hydrothermal cross-linking preparation of poly(vinylpyrrolidone) immobilized silica stationary phase for hydrophilic interaction chromatography.

Hydrothermally cross-linked polyvinylpyrrolidone (PVP) immobilized SiO2 stationary phase (CPVP-Sil) was prepared via a green and facile one-pot method which was demonstrated for hydrophilic interaction liquid chromatography (HILIC) as well as reverse phase chromatography(RP). A water or organic solvent-insoluble permanent CPVP immobilizing on the silica particle surface can be formed simply by dipping silica particles into PVP solution and low temperature hydrothermal treatment. The cross-linked PVP network coating on SiO2 endow it ring lactam functional groups which exhibited excellent separation ability of polar compounds by a typical HILIC retention mechanism at higher organic solvent contents (>55% ACN) and additionally polyvinyl groups for separation of alkylbenzenes in RP mode(<25% ACN). A high column efficiency of about 7 × 104 plates per meter was obtained for the test catechol compound. Remarkably, the CPVP-Sil packing materials showed good stability in acid (at pH 3.5) or basic (at pH 9.5) conditions, with 5400-fold column volumes and 3500-fold column volumes respectively.

The synthesis and structure of the [PdAu13(PPh3)3(SR)7]+ nanocluster.

Metal alloy nanoclusters have attracted increasing attention due to the synergistic effect of the foreign atoms. For the first time the synthesis and crystal structure of the [PdAu13(PPh3)3(SR)7]+ nanocluster is reported. The crystal structure of the nanocluster was determined by single crystal X-ray diffraction. The [PdAu13(PPh3)3(SR)7]+ nanocluster has a concave polyhedron Au9Pd kernel, which looks like a girl dancing ballet. The structure shows that [PdAu13(PPh3)3(SR)7]+ has an open shell. Meanwhile, we also carried out ultraviolet-visible (Uv-vis) absorption spectroscopy and fluorescence spectroscopy to study the optical properties of the [PdAu13(PPh3)3(SR)7]+ nanocluster.

A multi-omics investigation of the molecular characteristics and classification of six metabolic syndrome relevant diseases.

Metabolic syndrome (MTS) is a cluster of concurrent metabolic abnormal conditions. MTS and its component metabolic diseases are heterogeneous and closely related, making their relationships complicated, thus hindering precision treatment. Methods: We collected seven groups of samples (group a: healthy individuals; group b: obesity; group c: MTS; group d: hyperglycemia, group e: hypertension, group f: hyperlipidemia; group g: type II diabetes, n=7 for each group). We examined the molecular characteristics of each sample by metabolomic, proteomic and peptidomic profiling analysis. The differential molecules (including metabolites, proteins and peptides) between each disease group and the healthy group were recognized by statistical analyses. Furthermore, a two-step clustering workflow which combines multi-omics and clinical information was used to redefine molecularly and clinically differential groups. Meanwhile, molecular, clinical, network and pathway based analyses were used to identify the group-specific biological features. Results: Both shared and disease-specific molecular profiles among the six types of diseases were identified. Meanwhile, the patients were stratified into three distinct groups which were different from original disease definitions but presented significant differences in glucose and lipid metabolism (Group 1: relatively favorable metabolic conditions; Group 2: severe dyslipidemia; Group 3: dysregulated insulin and glucose). Group specific biological signatures were also systematically described. The dyslipidemia group showed higher levels in multiple lipid metabolites like phosphatidylserine and phosphatidylcholine, and showed significant up-regulations in lipid and amino acid metabolism pathways. The glucose dysregulated group showed higher levels in many polypeptides from proteins contributing to immune response. The another group, with better glucose/lipid metabolism ability, showed higher levels in lipid regulating enzymes like the lecithin cholesterol acyltransferase and proteins involved in complement and coagulation cascades. Conclusions: This multi-omics based study provides a general view of the complex relationships and an alternative classification for various metabolic diseases where the cross-talk or compensatory mechanism between the immune and metabolism systems plays a critical role.

[Research progress in hydrothermal carbon materials for separation and analysis].

Hydrothermal carbon materials are new functional materials prepared by the hydrothermal reaction of sugars or carbonaceous organic compounds. They have many advantages such as abundant resources of raw materials, environmental-friendliness, hydrophilicity, and easy of modify and so on. These carbon materials have been widely used as catalyst carriers, energy electrode materials, environmental adsorbents, etc. Among these, the application of hydrothermal carbon materials as absorbents reveals their ability to show strong interactions with specific molecules. In recent years, the application of these materials has been gradually extended to the field of chromatography, as stationary phases for solid-phase separation as well as for the enrichment of complex biological samples. In this paper, the recent applications of hydrothermal carbon materials for the analysis of ionic compounds, polar compounds, phosphorylated peptides, and glycopeptides are presented. Finally, the future scope of these materials in separation and enrichment is also discussed.

[Preparation of core-shell silica-carbon composite microspheres stationary phase and application in saccharide separation].

In this study, core-shell mesoporous silica-carbon composite microspheres (Sil@MC) were prepared by one-step coating of the phenol formaldehyde polymer (PF) on SiO2 surface and by carbonizing the PF polymer under nitrogen atmosphere. The morphology observation of the Sil@MC stationary phase showed that it had good monodispersity. Surface area (302 m2/g), mean pore diameter (9.5 nm), and pore volume (0.63 cm3/g) of Sil@MC materials were also measured by pore structure analysis. The results showed that the Sil@MC was successfully immobilized on the silica particles via copolymerization and carbonization. As a stationary phase of HPLC, the Sil@MC column was filled by a slurry method. The Sil@MC materials formed after calcination of SiO2 coated with phenolic resin could be used for the separation of four polar sugar compounds (D-(+)-glucosamine hydrochloride, glucose, D-(+)-trehalose dihydrat and raffinose) with the mobile phase of acetonitrile-water (containing 0.1% (v/v) formic acid). However, the material formed by calcinating SiO2 without coating phenolic resin could not separate these polar sugar compounds by HPLC-MS. Finally, the representative oligosaccharide isomers of raffinose, melezitose and stachyose, nystose, and human milk oligosaccharide isomers, such as 3'-sialyllactose, 6'-sialyllactose and lacto-N-newtetraose, lacto-N-tetraose, were successfully separated by the Sil@MC column with good peak shapes. The results demonstrates that silica-carbon composites derived from phenolic resin have potential application in polar compounds chromatographic separation.

Two-Dimensional Tin Selenide (SnSe) Nanosheets Capable of Mimicking Key Dehydrogenases in Cellular Metabolism.

While dehydrogenases play crucial roles in tricarboxylic acid (TCA) cycle of cell metabolism, which are extensively explored for biomedical and chemical engineering uses, it is a big challenge to overcome the shortcomings (low stability and high costs) of recombinant dehydrogenases. Herein, it is shown that two-dimensional (2D) SnSe is capable of mimicking native dehydrogenases to efficiently catalyze hydrogen transfer from 1-(R)-2-(R')-ethanol groups. In contrary to susceptible native dehydrogenases, lactic dehydrogenase (LDH) for instance, SnSe is extremely tolerant to reaction condition changes (pH, temperature, and organic solvents) and displays extraordinary reusable capability. Structure-activity analysis indicates that the single-atom structure, Sn vacancy, and hydrogen binding affinity of SnSe may be responsible for their catalytic activity. Overall, this is the first report of a 2D SnSe nanozyme to mimic key dehydrogenases in cell metabolism.

[Quantitative endogenous peptidomics analysis of the type-2 diabetic clinical serum samples].

Diabetes is a systemic metabolic disorder syndrome, mainly characterized by hyperglycemia, and is associated with the dysfunction of various organs, such as liver, pancreas, intestine, adipose muscle tissue, kidney and brain. It has become a global epidemic disease that seriously threatens human health. Therefore, mapping the global molecular signatures of diabetes-related disease spectrum can provide more comprehensive data to understand early clinical diagnosis, molecular typing, and pathological processes involved in diabetes mellitus. In this study, we performed a quantitative differential analysis on the endogenous peptidome of the serum samples obtained from healthy, prediabetes and type 2 diabetes groups to explore the peptidomics evolution in the development of diabetes. Partial least squares-discriminant analysis (PLS-DA) was used for pattern recognition. A nonparametric test was examined to find out the significantly changed endogenous peptides. As a result, 690 serum endogenous peptides were identified totally, among which 163 endogenous peptides were statistically different among the three groups. This could be promising quantitative peptidomics data for early screening, diagnosis and molecular typing of type 2 diabetes mellitus.

The efficient profiling of serum N-linked glycans by a highly porous 3D graphene composite.

In this work, an enrichment approach for the profiling of N-linked glycans was developed by utilizing a highly porous 3D graphene composite fabricated from graphene oxide nanosheets and a phenol-formaldehyde polymer via graphitization and KOH activation. In tailoring the large surface area (ca. 2213 m2 g-1) and 3D-layered mesoporous structure, the 3D graphene composite demonstrated not only high efficiency in glycan enrichment but also the size-exclusion effect against residual protein interference. For a standard protein ovalbumin digest, 26 N-linked glycans were identified with good repeatability, and the detection limit was as low as 0.25 ng µL-1 with the identification of 13 N-linked glycans (S/N > 10). When the mass ratio of the ovalbumin digest to the interfering proteins, i.e., bovine serum albumin and ovalbumin was 1 : 2000 : 2000, 18 N-linked glycans could still be detected with sufficient signal intensities. From a 60 nL minute complex human serum sample, up to 53 N-linked glycans with S/N > 10 were identified after the 3D graphene enrichment, while only 20 N-linked glycans were identified by the porous graphitized carbon material used for comparison. In addition, the application of the 3D graphene composite in profiling the up-regulated and down-regulated N-linked glycans from the real clinical serum samples of ovarian cancer patients confirmed the potential of the 3D graphene composite for analyzing minute and complicated biological samples.

High Anti-Interfering Profiling of Endogenous Glycopeptides for Human Plasma by the Dual-Hydrophilic Metal-Organic Framework.

Glycopeptidome profiling provides large-scale information about the glycosylation level of endogenous peptides, reflecting the dynamic processes of disease occurrences and developments. However, endogenous glycopeptides are usually submerged in complex fluids containing a wide variety of interference molecules, such as high concentration proteins, nonglycopeptides, and salts, which confounds attempts to identify glycopeptidome. Here, a dual-hydrophilic metal-organic framework is developed to selectively capture endogenous glycopeptides in complex biological fluid. The hydrophilic matrix material provides specific selectivity toward glycopeptides, while the deliberate surface regulation using hydrophilic species enhances its interaction with glycopeptides. This hydrophilic probe presents an extremely high performance in anti-interfering enrichment of glycopeptides from mimic complex samples, even when the molar ratio of immunoglobulin G versus bovine serum albumin was up to about 1:5000. More excitingly, in the practical application of glycopeptidome analysis, a total of 380 endogenous N-glycopeptides with 180 unique N-glycopeptide sites were identified from human plasma. This strategy is expected to broaden the application of dual-hydrophilic MOF-based materials, especially in dealing with the challenges of extremely complex biological samples.

Facile one-pot synthesized hydrothermal carbon from cyclodextrin: A stationary phase for hydrophilic interaction liquid chromatography.

A new hydrothermal carbon was prepared by a "one-pot" hydrothermal transformation of ß-cyclodextrin on silica microspheres (noted as silica@HTC microspheres), which was featuring as a new stationary phase for the hydrophilic interaction liquid chromatography (HILIC). The synthesized silica@HTC possessed polar groups of hydroxyl, carbonyl and carboxyl groups arising from the carbonization transformation of ß-cyclodextrin. As demonstrating great hydrophilicity, the silica@HTC was applied as an excellent HILIC stationary phase for the separation of polar compounds including phenols and the endocrine disrupting chemicals (EDCs). In comparison with commercial available HILIC stationary phases, the separation performance of the silica@HTC stationary phase was superior in the separation of phenols and EDCs. The mild hydrothermal carbon transformation of the ß-cyclodextrin on the silica microspheres in the "one-pot" manner would represent a new and simple approach to prepare a new class of saccharide-derived stationary phases by using saccharides as precursors.