Spatial proteomics of vesicular trafficking: coupling mass spectrometry and imaging approaches in membrane biology.

In plants, membrane compartmentalization requires vesicle trafficking for communication among distinct organelles. Membrane proteins involved in vesicle trafficking are highly dynamic and can respond rapidly to changes in the environment and to cellular signals. Capturing their localization and dynamics is thus essential for understanding the mechanisms underlying vesicular trafficking pathways. Quantitative mass spectrometry and imaging approaches allow a system-wide dissection of the vesicular proteome, the characterization of ligand-receptor pairs and the determination of secretory, endocytic, recycling and vacuolar trafficking pathways. In this review, we highlight major proteomics and imaging methods employed to determine the location, distribution and abundance of proteins within given trafficking routes. We focus in particular on methodologies for the elucidation of vesicle protein dynamics and interactions and their connections to downstream signalling outputs. Finally, we assess their biological applications in exploring different cellular and subcellular processes.

Antioxidant properties of polyphenols from snow chrysanthemum (Coreopsis tinctoria) and the modulation on intestinal microflora in vitro.

CONTEXT: Coreopsis tinctoria Nutt (Asteraceae), named snow chrysanthemum, is known to have a high level of polyphenols. However, the potential prebiotic effect on modulating intestinal microflora is still unclear. OBJECTIVE: The chemical composition, antioxidant properties of snow chrysanthemum polyphenols (SCPs) and their effects on human intestinal microbiota were investigated. MATERIALS AND METHODS: SCPs were extracted using ultrasonic-assisted extraction, and further determined using UPLC-QE Orbitrap/MS. Five assays were used to investigate the antioxidant activities of SCPs. Subsequently, the effects of SCPs on intestinal microbiota in vitro were determined by high throughput sequencing and bioinformatics analysis. RESULTS: Marein, isookanin and cymaroside were the major phenolic compounds, which accounted for 42.17%, 19.53% and 12.25%, respectively. Marein exhibited higher scavenging capacities in DPPH (EC50 = 8.84 µg/mL) and super anion radical assay (EC50 = 282.1 µg/mL) compared to cymaroside and isookanin. The antioxidant capacity of cymaroside was weakest among the three phenolic compounds due to the highest EC50 values, especially for superoxide anion radical assay, EC50 > 800 µg/mL. The result of in vitro fermentation showed that the three phenolic compounds increased the relative abundances of Escherichia/Shigella, Enterococcus, Klebsiella, etc., and isookanin notably increased the relative abundance of Bifidobacterium and Lactobacillus. DISCUSSION AND CONCLUSIONS: SCPs exhibited antioxidant properties and potential prebiotic effects on modulating the gut microbiota composition. The findings indicated that SCPs consumption could exert prebiotic activity that is beneficial for human health.

Visualizing calcium-dependent signaling networks in plants.

Calcium-dependent protein kinases (CDPKs) are a multigene protein kinase family that have key regulatory roles in plants. However, imaging CDPK signals in plant cells remains challenging. The recently developed genetically encoded CDPK-Förster resonance energy transfer (FRET) reporter developed by Liese et al. allows visualization of calcium (Ca2+)-dependent conformational changes during activation or inactivation of CDPKs, providing a powerful tool for real-time monitoring of calcium decoding in plants.

Mass spectrometric exploration of phytohormone profiles and signaling networks.

Phytohormones have crucial roles in plant growth, development, and acclimation to environmental stress; however, measuring phytohormone levels and unraveling their complex signaling networks and interactions remains challenging. Mass spectrometry (MS) has revolutionized the study of complex biological systems, enabling the comprehensive identification and quantification of phytohormones and their related targets. Here, we review recent advances in MS technologies and highlight studies that have used MS to discover and analyze phytohormone-mediated molecular events. In particular, we focus on the application of MS for profiling phytohormones, elucidating phosphorylation signaling, and mapping protein interactions in plants.

Cell plasticity in patients with NSCLC: The controversial origins of transformed SCLC.

In recent years, the application of targeted therapy has greatly improved the survival of NSCLC patients with known tumor mutations. However, the plasticity of tumor cells can drive them to transform into a phenotypic state that is no longer targeted by drugs. One of the mechanisms by which drug resistance occurs is the transformation from NSCLC to SCLC. This seems to occur because of the selection pressure exerted by the drugs. However, the transformation has also been observed in non-targeted patients, which challenges the origin of transformed SCLC. In the present study, the current clinical understanding of transformed SCLC is summarized along with the current understanding of its genome status and cloning history in cancer progression. This was done to explore the origins of transformed SCLC, find key molecular markers to predict the occurrence of the transformation, and permit timely adjustment of patients' treatment plans. Besides, the current clinical trials on transformed SCLC are discussed. Finally, recommendations are made on the problems that need to be solved to improve the diagnosis and treatment of patients with transformed SCLC.

Mapping Plant Phosphoproteome with Improved Tandem MOAC and Label-Free Quantification.

Protein phosphorylation represents a fundamental and evolutionarily conserved type of posttranslational modification that regulates protein functions and cellular signal transmission. Due to the dynamic nature of protein phosphorylation processes in plant cells, large-scale studies of phosphoproteins face several challenges such as low stoichiometry in the modified peptides in a proteome, as well as heterogeneity of the phosphopeptides of a given protein. Here we describe an updated tandem MOAC combined phosphoprotein and phosphopeptide enrichment strategy, a scalable phosphoproteomics approach that allows identification of thousands of phophopeptides in plant materials in one LC-MS analysis. We implemented modifications to several steps of the original tandem MOAC procedure to increase the identification and quantification of phosphopeptides in a sample beginning with less amount of tissue and a smaller amount of extracted protein.

[Prospective study of cystatin C for diagnosis of acute kidney injury after cardiac surgery].

OBJECTIVE: To prospectively study the value of cystatin C in diagnosis of acute kidney injury (AKI) in patients after cardiac surgery. METHODS: A total of 132 patients undergoing cardiopulmonary bypass were enrolled in this prospectively study. From each patient, blood samples were collected everyday before and after operation to detect the serum creatinine (Scr) and cystatin C levels by enzymatic method and particle-enhanced turbidimetric immunoassay (PETIA), respectively, and the glomerular filtration rate (eGFR) was estimated using MDRD equation. AKI diagnosis was made according to the RIFLE criteria of the Acute Dialysis Quality Initiative (ADQI) (R: Scr increased by > or =50%; I: Scr increased by > or =100%; F: Scr increased by > or =200%; L: Loss of kidney function; E: End-stage renal disease). Another AKI diagnostic criterion was also adopted according to the levels of cystatin C increment, namely an increase by > or =50%, > or =100%, and > or =200%. RESULTS: Twenty-nine patients (21.9%) developed AKI of varied severities, including 10 meeting the R-criteria, 12 the I-criteria, 7 the F-criteria, with the other 103 patients without AKI serving as the control group. Cystatin C of the 29 AKI patients was drastically increased in comparison with that of the control group (P<0.001). Significant linear correlation was found between cystatin C and Scr (r=0.732, P<0.001) and between [cystatin C]-1 and estimated GFR (R=0.803, P<0.001). By the two diagnostic criteria based on cystatin C and Scr levels, respectively, the median diagnostic time of AKI was 2 days (range 1-4 days) and 3 days (range 2-5 days) for R criteria (10 patients, P=0.014), 3.5 days (range 1-6 days) and 5 days (range 2-8 days) for I criteria (12 patients, P=0.008), and 5 days (range 3-7 days) and 6.5 days (range 4-9 days) for F criteria (7 patients, P=0.02), respectively. ROC analysis confirmed excellent accuracy of cystatin C in AKI diagnosis (AUC=0.992). With the cut-off value of cystatin C increment by > or =50%, the diagnostic sensitivity and specificity of AKI was 92% and 95%, respectively. CONCLUSION: Cystatin C can serve as a good indicator for AKI diagnosis to allow earlier detection of AKI than Scr-based diagnosis in patients after cardiac surgery.