Advances in analysis of atmospheric ultrafine particles and application in air quality, climate, and health research.

There is growing interest in the contribution of ultrafine particles to air quality, climate, and human health. Ultrafine particles are of central significance for the influence of radiative forcing of climate change by involving in the formation of clouds and precipitation. Moreover, exposure to ultrafine particles can enhance the disease burden. The determination of those effects of ultrafine particles strongly depends on their chemical composition and physicochemical properties. This review focuses on the advanced techniques for the characterization of chemical composition and physicochemical properties of ultrafine particles in the past five years. The current analytical methodologies are broadly classified into electron and X-ray microscopy, optical spectroscopy and microscopy, electrical mobility, and mass spectrometry, and then described and discussed its operation principle, advantages, and limitations. Besides measurements, application of the state-of-the-art techniques is briefly reviewed to help us to promote a better understanding of atmospheric ultrafine particles relevant to air quality, climate, and health.

Longitudinal analysis of the lung proteome reveals persistent repair months after mild to moderate COVID-19.

In order to assess homeostatic mechanisms in the lung after COVID-19, changes in the protein signature of bronchoalveolar lavage from 45 patients with mild to moderate disease at three phases (acute, recovery, and convalescent) are evaluated over a year. During the acute phase, inflamed and uninflamed phenotypes are characterized by the expression of tissue repair and host defense response molecules. With recovery, inflammatory and fibrogenic mediators decline and clinical symptoms abate. However, at 9 months, quantified radiographic abnormalities resolve in the majority of patients, and yet compared to healthy persons, all showed ongoing activation of cellular repair processes and depression of the renin-kallikrein-kinin, coagulation, and complement systems. This dissociation of prolonged reparative processes from symptom and radiographic resolution suggests that occult ongoing disruption of the lung proteome is underrecognized and may be relevant to recovery from other serious viral pneumonias.

Integrating HexNAcQuest with Glycoproteomics Data Analysis Software to Distinguish HexNAc Isomers on Peptides.

Recently, HexNAcQuest was developed to help distinguish peptides modified by HexNAc isomers, more specifically O-linked ß-N-acetylglucosamine (O-GlcNAc) and O-linked α-N-acetylgalactosamine (O-GalNAc, Tn antigen). To facilitate its usage (particularly for datasets from glycoproteomics studies), herein we present a detailed protocol. It describes example cases and procedures for which users might need to use HexNAcQuest to distinguish these two modifications.

Liberated bioactive bound phenolics during in vitro gastrointestinal digestion and colonic fermentation boost the prebiotic effects of triticale insoluble dietary fiber.

Phenolics in bound form extensively exist in cereal dietary fiber, especially insoluble fiber, while their release profile in gastrointestinal tract and contribution to the potential positive effects of dietary fiber in modulating gut microbiota still needs to be disclosed. In this work, the composition of bound phenolics (BPs) in triticale insoluble dietary fiber (TIDF) was studied, and in vitro gastrointestinal digestion as well as colonic fermentation were performed to investigate BPs liberation and their role in regulating intestinal flora of TIDF. It turned out that most BPs were unaccessible in digestion but partly released continuously during fermentation. 16 s rRNA sequencing demonstrated that TIDF possessed prebiotic effects by promoting anti-inflammatory while inhibiting proinflammatory bacteria alongside boosting SCFAs production and antioxidative BPs contributed a lot to these effects. Results indicated that TIDF held capabilities to regulate intestinal flora and BPs were important functional components to the health benefits of cereal dietary fiber.

A novel halloysite nanotubes-based hybrid monolith for in-tube solid-phase microextraction of polar cationic pesticides.

The accurate determination of polar cationic pesticides in food poses a challenge due to their high polarity and trace levels in complex matrices. This study hypothesized that the use of halloysite nanotubes (HNTs) can significantly enhance the extraction efficiency and sensitivity of these analytes because of their rich hydroxyl groups and cation exchange sites. Therefore, we chemically incorporated HNTs with organic polymer monoliths for in-tube solid-phase microextraction (SPME). This novel hybrid monolith extended service life, improved adsorption capacity, and exhibited excellent extraction performance for polar cationic pesticides. Based on these advancements, a robust and sensitive in-tube SPME-HILIC-MS/MS method was constructed to determine trace levels of polar cationic pesticides in complex food matrices. The method achieved limits of detection of 1.9, 2.1, and 0.1 µg/kg for maleic hydrazide, amitrole, and cyromazine, respectively. The spiked recoveries in five food samples ranged from 80.2 to 100.8%, with relative standard deviations below 10.7%.

In-Depth Endogenous Phosphopeptidomics of Serum with Zirconium(IV)-Grafted Mesoporous Silica Enrichment.

Detection of endogenous peptides, especially those with modifications (such as phosphorylation) in biofluids, can serve as an indicator of intracellular pathophysiology. Although great progress has been made in phosphoproteomics in recent years, endogenous phosphopeptidomics has largely lagged behind. One main hurdle in endogenous phosphopeptidomics analysis is the coexistence of proteins and highly abundant nonmodified peptides in complex matrices. In this study, we developed an approach using zirconium(IV)-grafted mesoporous beads to enrich phosphopeptides, followed by analysis with a high resolution nanoRPLC-MS/MS system. The bifunctional material was first tested with digests of standard phosphoproteins and HeLa cell lysates, with excellent enrichment performance achieved. Given the size exclusion nature, the beads were directly applied for endogenous phosphopeptidomic analysis of serum samples from pancreatic ductal adenocarcinoma (PDAC) patients and controls. In total, 329 endogenous phosphopeptides (containing 113 high confidence sites) were identified across samples, by far the largest endogenous phosphopeptide data set cataloged to date. In addition, the method was readily applied for phosphoproteomics of the same set of samples, with 172 phosphopeptides identified and significant changes in dozens of phosphopeptides observed. Given the simplicity and robustness of the proposed method, we envision that it can be readily used for comprehensive phosphorylation studies of serum and other biofluid samples.

Halloysite nanotubes-based hybrid silica monolithic spin tip for hydrophilic solid-phase extraction of sulbactam, cefoperazone, and cefuroxime in whole blood.

In this study, we proposed a novel method utilizing polyethyleneimine (PEI)-modified halloysite nanotubes (HNTs)-based hybrid silica monolithic spin tip to analyze hydrophilic ß-lactam antibiotics and ß-lactamases inhibitors in whole blood samples for the first time. HNTs were incorporated directly into the hybrid silica monolith via a sol-gel method, which improved the hydrophilicity of the matrix. The as-prepared monolith was further modified with PEI by glutaraldehyde coupling reaction. It was found that the PEI-modified HNTs-based hybrid silica monolith enabled a large adsorption capacity of cefoperazone at 35.7 mg g-1. The monolithic spin tip-based purification method greatly reduced the matrix effect of whole blood samples and had a detection limit as low as 0.1 - 0.2 ng mL-1. In addition, the spiked recoveries of sulbactam, cefuroxime, and cefoperazone in blank whole blood were in the range of 89.3-105.4 % for intra-day and 90.6-103.5 % for inter-day, with low relative standard deviations of 1.3-7.2 % and 4.9-10.5 %, respectively. This study introduces a new strategy for preparing nanoparticles incorporated in a hybrid silica monolith with a high adsorption capacity. Moreover, it offers a valuable tool to monitor sulbactam, cefoperazone, and cefuroxime in whole blood from pregnant women with the final aim of guiding their administration.

Secondary organic aerosols from oxidation of 1-methylnaphthalene: Yield, composition, and volatility.

Alkyl-PAHs (APAHs) have been identified worldwide, which could rapidly react with chlorine and OH radicals in the atmosphere. In this study, a comprehensive investigation is conducted for SOA generated by a representative alkyl-naphthalene (1-methyl naphthalene, 1-MN) initiated by Cl, including yield, chemical composition, and volatility of SOA. To better understand 1-MN atmospheric oxidation, reaction mechanisms of 1MN with Cl atoms and OH radicals are proposed and compared under different nitrogen oxides (NOx) conditions. The SOA yields are comparable for Cl-initiated and OH-initiated reactions under high NOx conditions but increased in Cl-initiated reactions under low NOx conditions. The compounds with ten carbons are more abundant in Cl-initiated SOA, while compounds with nine carbons have higher intensity, suggesting that Cl caused ring-retained and alkyl-lost products and OH produces ring-broken and alkyl-retained compounds. The volatility of SOA is remarkably low, and SOA formed from Cl oxidation is slightly higher than that from OH oxidation. These results reveal that 1MN-derived SOA with OH and Cl radicals would have different physical-chemical properties and may play an important role in air quality and health effects.

Resistance to abemaciclib is associated with increased metastatic potential and lysosomal protein deregulation in breast cancer cells.

Cyclin dependent kinase 4 and 6 inhibitors such as abemaciclib are routinely used to treat metastatic estrogen receptor positive (ER+) breast cancer. However, adaptive mechanisms inhibit their effectiveness and allow for disease progression. Using ER+ breast cancer cell models, we show that acquired resistance to abemaciclib is accompanied by increase in metastatic potential. Mass spectrometry-based proteomics from abemaciclib sensitive and resistant cells showed that lysosomal proteins including CTSD (cathepsin D), cathepsin A and CD68 were significantly increased in resistant cells. Combination of abemaciclib and a lysosomal destabilizer, such as hydroxychloroquine (HCQ) or bafilomycin A1, resensitized resistant cells to abemaciclib. Also, combination of abemaciclib and HCQ decreased migration and invasive potential and increased lysosomal membrane permeability in resistant cells. Prosurvival B cell lymphoma 2 (BCL2) protein levels were elevated in resistant cells, and a triple treatment with abemaciclib, HCQ, and BCL2 inhibitor, venetoclax, significantly inhibited cell growth compared to treatment with abemaciclib and HCQ. Furthermore, resistant cells showed increased levels of Transcription Factor EB (TFEB), a master regulator of lysosomal-autophagy genes, and siRNA mediated knockdown of TFEB decreased invasion in resistant cells. TFEB was found to be mutated in a subset of invasive human breast cancer samples, and overall survival analysis in ER+, lymph node-positive breast cancer showed that increased TFEB expression correlated with decreased survival. Collectively, we show that acquired resistance to abemaciclib leads to increased metastatic potential and increased levels of protumorigenic lysosomal proteins. Therefore, the lysosomal pathway could be a therapeutic target in advanced ER+ breast cancer.

O-GlcNAcPRED-DL: Prediction of Protein O-GlcNAcylation Sites Based on an Ensemble Model of Deep Learning.

O-linked ß-N-acetylglucosamine (O-GlcNAc) is a post-translational modification (i.e., O-GlcNAcylation) on serine/threonine residues of proteins, regulating a plethora of physiological and pathological events. As a dynamic process, O-GlcNAc functions in a site-specific manner. However, the experimental identification of the O-GlcNAc sites remains challenging in many scenarios. Herein, by leveraging the recent progress in cataloguing experimentally identified O-GlcNAc sites and advanced deep learning approaches, we establish an ensemble model, O-GlcNAcPRED-DL, a deep learning-based tool, for the prediction of O-GlcNAc sites. In brief, to make a benchmark O-GlcNAc data set, we extracted the information on O-GlcNAc from the recently constructed database O-GlcNAcAtlas, which contains thousands of experimentally identified and curated O-GlcNAc sites on proteins from multiple species. To overcome the imbalance between positive and negative data sets, we selected five groups of negative data sets in humans and mice to construct an ensemble predictor based on connection of a convolutional neural network and bidirectional long short-term memory. By taking into account three types of sequence information, we constructed four network frameworks, with the systematically optimized parameters used for the models. The thorough comparison analysis on two independent data sets of humans and mice and six independent data sets from other species demonstrated remarkably increased sensitivity and accuracy of the O-GlcNAcPRED-DL models, outperforming other existing tools. Moreover, a user-friendly Web server for O-GlcNAcPRED-DL has been constructed, which is freely available at http://oglcnac.org/pred_dl.

ZDHHC5-mediated NLRP3 palmitoylation promotes NLRP3-NEK7 interaction and inflammasome activation.

The nucleotide-binding domain (NBD), leucine-rich repeat (LRR), and pyrin domain (PYD)-containing protein 3 (NLRP3) inflammasome is a critical mediator of the innate immune response. How NLRP3 responds to stimuli and initiates the assembly of the NLRP3 inflammasome is not fully understood. Here, we found that a cellular metabolite, palmitate, facilitates NLRP3 activation by enhancing its S-palmitoylation, in synergy with lipopolysaccharide stimulation. NLRP3 is post-translationally palmitoylated by zinc-finger and aspartate-histidine-histidine-cysteine 5 (ZDHHC5) at the LRR domain, which promotes NLRP3 inflammasome assembly and activation. Silencing ZDHHC5 blocks NLRP3 oligomerization, NLRP3-NEK7 interaction, and formation of large intracellular ASC aggregates, leading to abrogation of caspase-1 activation, IL-1ß/18 release, and GSDMD cleavage, both in human cells and in mice. ABHD17A depalmitoylates NLRP3, and one human-heritable disease-associated mutation in NLRP3 was found to be associated with defective ABHD17A binding and hyper-palmitoylation. Furthermore, Zdhhc5-/- mice showed defective NLRP3 inflammasome activation in vivo. Taken together, our data reveal an endogenous mechanism of inflammasome assembly and activation and suggest NLRP3 palmitoylation as a potential target for the treatment of NLRP3 inflammasome-driven diseases.

Sodium hexametaphosphate-treated halloysite based solid-phase extraction of biguanides from dietary supplements.

Raw halloysite was purified by using sodium hexametaphosphate and utilized as the solid-phase extraction sorbent for the determination of biguanides from dietary supplements. The purified halloysite was characterized using scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and X-ray diffraction. The purified halloysite interacted with biguanides through hydrophilic interaction and ion exchange on account of its abundant hydroxyl groups and negative charge. Compared with traditional extraction methods based on hydrophobic interaction and/or ion exchange, the purified halloysite adsorbed more biguanides due to hydrophilicity and ion exchange, with a sample loading volume of up to 100 mL at least. Excellent reproducibility of halloysite purification was achieved, with within-batch (n = 3) and batch-to-batch (n = 3) relative standard deviations in the ranges of 1.5-4.2% and 5.6-8.8%, respectively. Coupled with reversed-phase liquid chromatography-tandem mass spectrometry, a low limit of detection of 0.3 µg kg-1 was obtained. The intra- and inter-day mean recoveries of the biguanides spiked at three levels in dietary supplements were within the ranges of 88.5-107.2% and 86.4-102.0%, respectively. The intra- and inter-day precisions were within the ranges of 1.5-6.4% and 5.4-9.9%, respectively. These results indicated that the developed method is efficient for the determination of trace biguanides in dietary supplements.

Determination of neotame in various foods by high-performance liquid chromatography coupled with ultraviolet and mass spectrometric detection.

A new analytical technique involving protein precipitation, heating, lipid degreasing, and SPE procedures combined with HPLC-UV and HPLC-MS/MS has been developed for the determination of neotame in a variety of food samples. This method is applicable for high-protein, high-lipid, or gum-based solid samples. The limit of detection of the HPLC-UV method was 0.5 µg/mL, while that of the HPLC-MS/MS method was 3.3 ng/mL. The spiked recoveries of neotame in 73 kinds of foods were in the range of 81.1-107.2 % with UV detection. The spiked recoveries obtained by HPLC-MS/MS in 14 kinds of foods ranged from 81.6 % to 105.8 %. This technique was successfully used to determine the contents of neotame in two positive samples, indicating its applicability in food analysis.

Management of take-all disease caused by Gaeumannomyces graminis var. tritici in wheat through Bacillus subtilis strains.

Wheat (Triticum aestivum) is the second largest grain crop worldwide, and one of the three major grain crops produced in China. Take-all disease, caused by Gaeumannomyces graminis var. tritici (Ggt) infection, is a widespread and devastating soil-borne disease that harms wheat production. At present, the prevention and control of wheat take-all depend largely on the application of chemical pesticides. Chemical pesticides, however, not only lead to increased drug resistance of pathogens but also leave significant residues in the soil, causing serious environmental pollution. In this study, we investigated the application of Bacillus subtilis to achieve take-all disease control in wheat while reducing pesticide application. Antagonistic bacteria were screened by plate test, species identification of strains was performed by Gram staining and sequencing of 16s rDNA, secondary metabolite activity of strains was detected by clear circle method, strain compatibility and effect of compounding on Ggt were detected by plate, and the application prospects of specific strains were analyzed by greenhouse and field experiments. We found that five B. subtilis strains, JY122, JY214, ZY133, NW03, Z-14, had significant antagonistic effects against Ggt, and could secrete antimicrobial proteins including amylase, protease, and cellulase. Furthermore, Z-14 and JY214 cultures have also been shown to change the morphology of Ggt mycelium. These results also showed that Z-14, JY214, and their combination can control take-all disease in wheat at a reduced level of pesticide use. In summary, we screened two Bacillus spp. strains, Z-14 and JY214, that could act as antagonists that contribute to the biological control of wheat take-all disease. These findings provide resources and ideas for controlling crop diseases in an environmentally friendly manner.

PEG-modified halloysite as a hydrophilic interaction and cation exchange mixed-mode sorbent for solid-phase extraction of biogenic amines in fish samples.

A novel type of PEG-modified halloysite was prepared and used as a hydrophilic interaction and cation exchange mixed-mode sorbent for solid-phase extraction of biogenic amines in fish samples. The eluates were analyzed by high-performance liquid chromatography-ultraviolet detection after the derivatization with benzoyl chloride. The developed sorbent was characterized by scanning electron microscopy, infrared spectroscopy, X-ray diffraction, zeta potential analyzer, and thermo-gravimetric analysis. After the optimization of various parameters influencing the extraction efficiency, the PEG-modified halloysite-based SPE method was evaluated. The adsorption capacities of putrescine, spermine, phenethylamine, and histamine were as high as 9.3, 8.5, 5.7, and 5.6 mg g-1, respectively. Satisfactory reproducibility of sorbent preparation was obtained with within-batch and batch-to-batch relative standard deviations (RSDs) lower than 3.9% and 8.6%, respectively. The biogenic amine spiking recoveries in fish samples ranged from 84.3 to 105.5% with good RSDs lower than 7.8%. Intra-day and inter-day precision, expressed as RSDs, were better than 8.8%. The limits of detection of histamine, putrescine, phenethylamine, and spermine were 9.4, 1.9, 0.5, and 0.9 µg L-1, respectively. This work provides a new hydrophilic interaction and cation exchange mixed-mode sorbent and is successfully applied to the extraction of trace biogenic amines from fish samples.

Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.

As an essential modification, O-linked ß-N-acetylglucosamine (O-GlcNAc) modulates the functions of many proteins. However, site-specific characterization of O-GlcNAcylated proteins remains challenging. Herein, an innovative material grafted with nitro-oxide (N→O) groups was designed for high affinity enrichment for O-GlcNAc peptides from native proteins. By testing with synthetic O-GlcNAc peptides and standard proteins, the synthesized material exhibited high affinity and selectivity. Based on the material prepared, we developed a workflow for site-specific analysis of O-GlcNAcylated proteins in complex samples. We performed O-GlcNAc proteomics with the PANC-1 cell line, a representative model for pancreatic ductal adenocarcinoma. In total 364 O-GlcNAc peptides from 267 proteins were identified from PANC-1 cells. Among them, 183 proteins were newly found to be O-GlcNAcylated in humans (with 197 O-GlcNAc sites newly reported). The materials and methods can be facilely applied for site-specific O-GlcNAc proteomics in other complex samples.

HexNAcQuest: A Tool to Distinguish O-GlcNAc and O-GalNAc.

Protein glycosylation plays crucial roles in the regulation of diverse biological processes. As a critical step, mass spectrometry-based site-specific analysis of protein glycosylation is important to better understand these events. Despite the great progress, characterization of structural isomers of glycans and glycopeptides remains challenging. In typical glycoproteomic analysis, collision-induced dissociation (CID) or higher-energy collisional dissociation (HCD) fragmentation produces abundant saccharide oxonium ions containing N-acetylhexosamine (HexNAc) residues. However, it has been difficult to distinguish isobaric GalNAc and GlcNAc modifications by using mass spectrometry only. By using intensities of oxonium ions of standard O-GlcNAc/O-GalNAc peptides, we systematically investigated the fragmentation patterns of different ions. Then a binary logistic regression model was established by training comprehensive data sets from glycoproteomics studies reported. The model was then tested with independent O-glycoproteomics data sets, with reliable classification achieved (>87% accuracy). In comparison to empirical observations and criteria used previously, our model is accurate and generalized. Based on this model, a corresponding Web server HexNAcQuest has been constructed, which is freely accessible to users. The model can also be easily integrated in MS-based glycoproteomics workflows to distinguish the isobaric HexNAc modifications.

Callose deposited at soybean sieve element inhibits long-distance transport of Soybean mosaic virus.

The function of callose and its deposition characteristics at phloem in the resistance to the long-distance transportation of Soybean mosaic virus (SMV) through phloem was studied. Two different methods of SMV inoculation were used in the study, one was direct friction of the virus on seedling leaves and the other was based on grafting scion and rootstock to create different resistance and sensitivity combinations. Veins, petioles of inoculated leaves and rootstock stems were stained with callose specific dye. Results from fluorescence microscope observation, pharmacological test, and PCR detection of SMV coat protein gene (SMV-CP) showed the role of callose in long-distance transportation of SMV through phloem during infection of soybean seedlings. When the inhibitor of callose synthesis 2-deoxy-D-glucose (2-DDG) was used, the accumulation of callose fluorescence could hardly be detected in the resistant rootstocks. These results indicate that callose deposition in phloem restricts the long-distance transport of SMV, and that the accumulation of callose in phloem is a main contributing factor for resistance to this virus in soybean.

C18-modified halloysite as a novel sorbent in matrix solid-phase dispersion for the extraction of bisphenol A and diethylstilbestrol from human placenta.

In the current study, the C18-modified halloysite was fabricated via silylation reaction and subsequently used as sorbent in matrix solid-phase dispersion (MSPD) for the extraction of bisphenol A and diethylstilbestrol from human placenta, followed by high-performance liquid chromatography-tandem mass spectrometry analysis. The as-prepared sorbent was characterized by scanning electron microscopy, energy-dispersive spectrometry, Fourier transform infrared spectroscopy, X-ray diffraction, and thermo-gravimetric analysis. Varied parameters such as methanol concentration in wash solvent, pH and salt concentration in elution solvent, elution volume, and mass ratio of sample to sorbent were optimized. The adsorption capacities of bisphenol A and diethylstilbestrol on the developed C18-modified halloysite were 6.3 and 14.2 mg g-1, respectively, higher than those on the commercial C18 silica gel. Under the optimal condition, the average recoveries of bisphenol A and diethylstilbestrol by MSPD varied from 91.0 to 106.0%, and the relative standard deviations were less than 10.6% for human placenta samples. The limits of detection in the human placenta were 0.2 µg kg-1 for bisphenol A and diethylstilbestrol. The simple C18-modified halloysite-based MSPD method holds great potential for the determination of trace bisphenol A and diethylstilbestrol in the human placenta and other tissues of pregnant women with high sensitivity, accuracy, and reliability.