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.

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.

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.

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.

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.

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.

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.

In Situ and Timed Extraction of Cellular Peptides from Live HeLa Cells by Photo-Switchable Mesoporous Silica Nanocarriers.

In situ and timed extraction of cellular peptides is a great challenge for dynamic and global proteomic investigation of live cells. In this work, a mesoporous silica nanocarrier with photoswitchable off/on coumarin gates (MSNcg) was developed for capturing peptides from the cytosol of living HeLa cells. The MSNcg was constructed from mesoporous silica nanoparticle (MSN) and its subsequent modifications with TAT peptides and coumarin, to endow the features of the size-exclusion effect of the mesoporous silica and the localization of nanocarrier at cytosol by TAT peptide and to control the closing and opening of the coumarin gates by reversible photodimerization and photocleavage. With the pre-endocytosing of MSNcg, 126 cytosol peptides were harvested and identified from living HeLa cells. Moreover, 3 peptides were captured containing dynamic and changeable information. The extraction strategy of using MSNcg exhibited promising potentials in the in situ and dynamic extraction of endogenous peptides and/or proteins from living systems.

Nano LC-MS Based Proteomic Analysis as a Predicting Approach to Study Cellular Responses of Carbon Nanotubes.

Nano-bio interface has been paid much attention recently, though with the lack of methodology to predict the potential responses in biological systems such as cells induced by nanomaterials. In this study, we described a proteomic approach to investigate the proteome change in K562 cells exposed to oxidized single-walled carbon nanotubes (o-SWCNTs). 605 proteins were identified by semi-quantitative proteomic analysis (SQPA), including 29 significantly changed proteins with spectra count (SpC) ratios lager than 2 or less than 0.5. Three of them including HBA, CFL1 and LMAN2 were further validated by western blotting. The differential proteins were further classified by Ingenuity Pathways Analysis (IPA) to integrate them into a signaling network. Based on the information by this network, we predict that o-SWCNT treatment activated cell aggregation, decreased cell migration, but had no effect on cell death. And these cellular responses were further experimentally demonstrated. The protein signaling network established in this study would greatly benefit the studies on the bio-applications of o-SWCNTs and their toxicity studies. Our study demonstrated that proteomics could be used as a predicting tool to study nano-bio interface at cellular level.

Biological characteristics of adipose tissue-derived stem cells labeled with amine-surface-modified superparamagnetic iron oxide nanoparticles.

Cell labeling and tracking are becoming increasingly important areas within the field of stem cell transplantation. The ability to track the migration and distribution of implanted cells is critical to understanding the beneficial effects and mechanisms of stem cell therapy. The present study investigated the effects of amine-surface-modified superparamagnetic iron oxide (SPIO) nanoparticles on the biological properties of human adipose tissue-derived stem cells (hADSCs). Monodisperse hydrophobic magnetite (Fe3 O4 ) nanoparticles were prepared using silicon and surface-modified with amine coating. Cell viability, proliferation, differentiation potential, and surface marker expression were evaluated. The magnetic particles (10-18 nm) displayed high labeling efficiency and stability in hADSCs. SPIO-labeled cells produced a hypointense signal and were effectively visualized by MRI for up to 21 days. The results of MTT proliferation assays and flow cytometry analysis demonstrated that SPIOs were biocompatible, viz. the labeling process did not cause cell death or apoptosis and had no side effects on cell proliferation. In vivo experiments showed that the magnetic particles did not affect liver and kidney function. The successful and stable labeling of hADSCs combined with efficient magnetic tropism demonstrates that SPIOs are promising candidates for hADSC tracking in hADSC-based cell therapy applications.

Spatial blockage of ionic current for electrophoretic translocation of DNA through a graphene nanopore.

Graphene nanopore has been promising the ultra-high resolution for DNA sequencing due to the atomic thickness and excellent electronic properties of the graphene monolayer. The dynamical translocation phenomena and/or behaviors underneath the blocked ionic current, however, have not been well unveiled to date for the translocation of DNA electrophoretically through a graphene nanopore. In this report, the assessment on the sensitivity of ionic current to instantaneous statuses of DNA in a 2.4 nm graphene nanopore was carried out based on the all-atom molecular dynamics simulations. By filtering out the thermal noise of ionic current, the instantaneous conformational variations of DNA in a graphene nanopore have been unveiled from the fluctuations of ionic current, because of the spatial blockage effect of DNA against ionic current. Interestingly, the neighborhood effect of DNA against ionic current was also observed within a distance of 1.5 nm nearby the graphene nanopore, suggesting the further precise control for DNA translocation through a graphene nanopore in gene sequencing. Moreover, the sensitivity of the blocked ionic current toward the instantaneous conformations of DNA in a graphene nanopore demonstrates the great potential of graphene nanopores in the dynamics analysis of single molecules.

In vivo detection of magnetic labeled oxidized multi-walled carbon nanotubes by magnetic resonance imaging.

Functionalized carbon nanotubes (f-CNTs) have been widely used in bio-medicine as drug carriers, bio-sensors, imaging agents and tissue engineering additives, which demands better understanding of their in vivo behavior because of the increasing exposure potential to humans. However, there are limited studies to investigate the in vivo biodistribution and elimination of f-CNTs. In this study, superparamagnetic iron oxides (SPIOs) were used to label oxidized multiwalled carbon nanotubes (o-MWCNTs) for in vivo distribution study of o-MWCNTs by magnetic resonance imaging (MRI). SPIO labeled o-MWCNTs (((SPIO))o-MWCNTs) were prepared by a hydrothermal reaction process, and characterized by TEM, XRD and magnetometer. ((SPIO))o-MWCNTs exhibited superparamagnetic property, excellent biocompatibility and stability. The intravenously injected ((SPIO))o-MWCNTs were observed in liver, kidney and spleen, while the subcutaneously injected ((SPIO))o-MWCNTs could be only detected in sub mucosa. Most of the intravenously injected ((SPIO))o-MWCNTs could be eliminated from liver, spleen, kidney and sub mucosa on 4 d post injection (P.I.). However, the residual o-MWCNTs could induce 30-40% MRI signal-to-noise ratio changes in these tissues even on 30 d P.I. This in vivo biodistribution and elimination information of o-MWCNTs will greatly facilitate the application of f-CNT based nanoproducts in biomedicine. In addition, the magnetic labeling method provides an approach to investigate the in vivo biodistribution and clearance of other nanomaterials.

Cell nucleus targeting for living cell extraction of nucleic acid associated proteins with intracellular nanoprobes of magnetic carbon nanotubes.

Since nanoparticles could be ingested by cells naturally and target at a specific cellular location as designed, the extraction of intracellular proteins from living cells for large-scale analysis by nanoprobes seems to be ideally possible. Nucleic acid associated proteins (NAaP) take the crucial position during biological processes in maintaining and regulating gene structure and gene related behaviors, yet there are still challenges during the global investigation of intracellular NAaP, especially from living cells. In this work, a strategy to extract intracellular proteins from living cells with the magnetic carbon nanotube (oMWCNT@Fe3O4) as an intracellular probe is developed, to achieve the high throughput analysis of NAaP from living human hepatoma BEL-7402 cells with a mass spectrometry-based proteomic approach. Due to the specific intracellular localization of the magnetic carbon nanotubes around nuclei and its strong interaction with nucleic acids, the highly efficient extraction was realized for cellular NAaP from living cells, with the capability of identifying 2383 intracellular NAaP from only ca. 10,000 living cells. This method exhibited potential applications in dynamic and in situ analysis of intracellular proteins.

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.

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.

Highly efficient extraction of cellular nucleic acid associated proteins in vitro with magnetic oxidized carbon nanotubes.

Nucleic acid associated proteins (NAaP) play the essential roles in gene regulation and protein expression. The global analysis of cellular NAaP would give a broad insight to understand the interaction between nucleic acids and the associated proteins, such as the important proteinous regulation factors on nucleic acids. Proteomic analysis presents a novel strategy to investigate a group of proteins. However, the large scale analysis of NAaP is yet impossible due to the lack of approaches to harvest target protein groups with a high efficiency. Herein, a simple and efficient method was developed to collect cellular NAaP using magnetic oxidized carbon nanotubes based on the strong interaction between carbon nanotubes and nucleic acids along with corresponding associated proteins. We found that the magnetic oxidized carbon nanotubes demonstrated a nearly 100% extraction efficiency for intracellular nucleic acids from cells in vitro. Importantly, the proteins associated on nucleic acids could be highly efficiently harvested using magnetic oxidized carbon nanotubes due to the binding of NAaP on nucleic acids. 1594 groups of nuclear NAaP and 2595 groups of cellular NAaP were extracted and identified from about 1,000,000 cells, and 803 groups of NAaP were analyzed with only about 10,000 cells, showing a promising performance for the proteomic analysis of NAaP from minute cellular samples. This highly efficient extraction strategy for NAaP is a simple approach to identify cellular nucleic acid associated proteome, and we believed this strategy could be further applied in systems biology to understand the gene expression and regulation.

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.

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.

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.