Exosomal circRNAs in the plasma serve as novel biomarkers for IPF diagnosis and progression prediction.

BACKGROUND: Idiopathic Pulmonary Fibrosis (IPF) is a type of chronic interstitial pneumonia, often fatal, with elusive causes and a bleak prognosis. Its treatment options are limited and largely ineffective. Early detection and precise diagnosis are pivotal in managing the disease effectively and enhancing patient survival rates. Recently, the quest for trustworthy biomarkers for IPF has gained momentum. Notably, emerging studies indicate that circular RNAs (circRNAs) found in exosomes may hold significant potential as valuable diagnostic markers. METHODS: In this study, we initially explored the expression profile of circRNAs in exosomes sourced from the blood of IPF patients and healthy volunteers, employing a human circRNA microarray. We then utilized RT-qPCR to corroborate the dysregulated circRNAs identified by the microarray during the training phase. Next, the circRNAs that displayed a significant increase during the training phase were selected for further validation in a larger cohort encompassing 113 IPF patients and 76 healthy volunteers. Ultimately, the expression level and function of hsa_circ_0044226 were substantiated through a series of in vivo and in vitro experiments. RESULTS: Utilizing a human circRNA microarray, we identified 11 dysregulated circRNAs in the exosomes derived from the blood of IPF patients and control volunteers. Subsequent RT-qPCR analysis revealed significant increases in three circRNAs (hsa_circ_0044226, hsa_circ_0004099, hsa_circ_0008898) within the IPF patients. Notably, hsa_circ_0044226 was markedly elevated in patients experiencing acute exacerbation of IPF (AE-IPF) compared to those with stable IPF (S-IPF). Additionally, an upregulation of hsa_circ_0044226 was observed in the blood exosomes derived from a bleomycin-induced IPF mouse model. CONCLUSION: The expression levels of hsa_circ_0044226, hsa_circ_0004099, and hsa_circ_0008898 in plasma exosomes introduce a new paradigm of biomarkers for the diagnosis and progression of IPF.

Characterization of the key odor-active compounds in different aroma types of Fu brick tea using HS-SPME/GC-MSO combined with sensory-directed flavor analysis.

Fu brick tea (FBT) is popular for its unique 'fungal flower' aroma, however, its key odor-active compounds are essentially unknown. In this study, the odor-active compounds of "stale-fungal" aroma (CJX), "fresh-fungal" aroma (QJX), and "fermentation-fungal" aroma (FJX) types FBT were extracted and examined by headspace solid phase microextraction (HS-SPME) combined with gas chromatography-mass spectrometry (GC-MS) and gas chromatographyolfactometry (GC-O). A total of 43 volatile and 38 odor-active compounds were identified by these methods. Among them, the content of dihydroactindiolide (4596-13189 µg/L), (E)-linalool oxide (2863-6627 µg/L), and benzyl alcohol (4992-6859 µg/L) were highest. Aroma recombination experiments further verified that these odor-active compounds could be simulated the overall aroma profile of FBT successfully. Furthermore, omission experiments confirmed that 15, 20, and 15 key odor-active compounds in CJX, QJX, and FJX FBT, respectively. This study will provide a theoretical basis for comprehensively understanding the formation of characteristic aromas in FBT.

Characterization of key aroma compounds and core functional microorganisms in different aroma types of Liupao tea.

Liupao tea is a representative Chinese dark tea. Stale-aroma type, betelnut-aroma type and fungal-aroma type were the main aroma types of Liupao tea. In this study, aroma profiles and fungal communities of the three aroma types of Liupao tea were examined by HS-SPME/GC-MS and Illumina MiSeq analysis. A total of 102 volatiles were identified and quantified in Liupao tea. Indicated by OPLS-DA analysis, six aroma compounds with stale, woody, roasted notes in stale-aroma type samples, five aroma compounds possessing smoky, minty, pungent notes in betelnut-aroma type samples, and nine aroma compounds owned minty, floral, fruity, woody, green notes in fungal-aroma type samples were responsible for the different aroma characteristics formation of Liupao tea. In addition, a total of 60 fungal genera were identified in Liupao tea. Aspergillus, Wallemia, Xeromyces were the predominant fungal genera in Liupao tea. Ten fungal genera, including Wallemia, Tritirachium, Debaryomyces, Trichomonascus, unclassified_o_Hypocreales in betelnut-aroma type, Rasamsonia, Candida, Blastobotrys, Acremonium in stale-aroma type, and Xeromyces in fungal-aroma type, were identified as the biomarkers in the three aroma types of Liupao tea. Furthermore, fungal genera including Aspergillus, Wallemia, Xeromyces, and Blastobotrys were identified as the core functional microorganisms contributing to the variation of volatile profiles based on O2PLS analysis. This study provided useful information on the key aroma compounds and core functional microorganisms that drive the different aroma characteristics formation of Liupao tea.

Characterization of the Key Aroma Compounds in Different Aroma Types of Chinese Yellow Tea.

Yellow tea is one of the six major tea categories in China. The floral fragrance type, high-fired fragrance type, fresh fragrance type, and corn-like fragrance type were the main aroma types of yellow tea screened by QDA. A total of 103 volatiles were identified in yellow teas by HS-SPME/GC-MS analysis. Using multivariate analysis and OAVs, forty-seven aroma compounds were identified as key aroma compounds for the formation of different aroma types of yellow teas. Among them, 8, 14, 7, and 18 key aroma compounds played an important role in the formation of aroma characteristics of floral fragrance, high-fired fragrance, fresh fragrance, and corn-like fragrance types of yellow teas, respectively. Furthermore, PLS analysis revealed that 12 aroma compounds were the key contributors to the 'floral and fruity' and 'sweet' attributes, five aroma compounds contributed to the 'roasted' attribute, and four aroma compounds related to the 'fresh' and 'grassy' attributes. This study provides new insights into the aroma characteristics formation of different aroma types of yellow teas and will provide a valuable theoretical basis for improving the flavor quality of yellow tea during the manufacturing process.

The proteome of Shigella flexneri 2a 2457T grown at 30 and 37 degrees C.

To upgrade the proteome reference map of Shigella flexneri 2a 2457T, the protein expression profiles of log phase and stationary phase cells grown at 30 and 37 degrees C were thoroughly analyzed using multiple overlapping narrow pH range (between pH 4.0 and 11.0) two-dimensional gel electrophoresis. A total of 723 spots representing 574 protein entries were identified by MALDI-TOF/TOF MS, including the majority of known key virulence factors. 64 hypothetical proteins and six misannotated proteins were also experimentally identified. A comparison between the four proteome maps showed that most of the virulence-related proteins were up-regulated at 37 degrees C, and the differences were more notable in stationary phase cells, suggesting that the expressions of these virulence factors were not only controlled by temperature but also controlled by the nutrients available in the environment. The expression patterns of some virulence-related genes under the four different conditions suggested that they might also be regulated at the post-transcriptional level. A further significant finding was that the expression of the protein ArgT was dramatically up-regulated at 30 degrees C. The results of semiquantitative RT-PCR analysis showed that expression of argT was not regulated at the transcriptional level. Therefore, we carried out a series of experiments to uncover the mechanism regulating ArgT levels and found that the differential expression of ArgT was due to its degradation by a periplasmic protease, HtrA, whose activity, but not its synthesis, was affected by temperature. The cleavage site in ArgT was between position 160 (Val) and position 161 (Ala). These results may provide useful insights for understanding the physiology and pathogenesis of S. flexneri.

Global analysis of a plasmid-cured Shigella flexneri strain: new insights into the interaction between the chromosome and a virulence plasmid.

Shigella flexneri is an important human pathogen that causes dysentery, and remains a significant threat to public health, particularly in developing countries. The virulence of this pathogen is dependent on an acquired virulence plasmid. To investigate the crosstalk between the bacterial chromosome and the exogenous virulence plasmid, a virulence plasmid-cured strain was constructed using plasmid incompatibility. The global patterns of gene expression of this strain compared with the wild-type strain were analyzed using 2-DE combined with MALDI-TOF MS. Most known virulence factors of S. flexneri were identified in the 2-DE gels. Interestingly, the expression of the glycerol 3-phosphate (glp) regulon-encoded proteins was increased when the virulence plasmid was absent. Microarray analysis confirmed that regulation occurred at the transcriptional level. Purification and identification of DNA binding proteins with affinity for the regulatory region of the glp genes revealed that regulation mediated by the virulence plasmid to control the expression of the glp regulon might in turn be mediated by protein GlpR. To our knowledge, this is the first study analyzing the interaction between a pathogen chromosome and a virulence plasmid at the proteomic level.