Exploring the Mechanism of Edaravone for Oxidative Stress in Rats with Cerebral Infarction Based on Quantitative Proteomics Technology

Objective. To explore the mechanism of edaravone in the treatment of oxidative stress in rats with cerebral infarction based on quantitative proteomics technology. Method. The modified Zea Longa intracavitary suture blocking method was utilized to make rat CI model. After modeling, the rat was intragastrically given edaravone for 7 days, once a day. After the 7-day intervention, the total proteins of serum were extracted. After proteomics analysis, the differentially expressed proteins are analyzed by bioinformatics. Then chemoinformatics methods were used to explore the biomolecular network of edaravone intervention in CI. Result. The neurological scores and pathological changes of rats were improved after the intervention of edaravone. Proteomics analysis showed that in the model/sham operation group, 90 proteins in comparison group were upregulated, and 26 proteins were downregulated. In the edaravone/model group, 21 proteins were upregulated, and 41 proteins were downregulated. Bioinformatics analysis and chemoinformatics analysis also show that edaravone is related to platelet activation and aggregation, oxidative stress, intercellular adhesion, glycolysis and gluconeogenesis, iron metabolism, hypoxia, inflammatory chemokines, their mediated signal transduction, and so on. Conclusion. The therapeutic mechanism of edaravone in the treatment of CI may involve platelet activation and aggregation, oxidative stress, intercellular adhesion, glycolysis and gluconeogenesis, iron metabolism, hypoxia, and so on. This study revealed the serum protein profile of edaravone in the treatment of cerebral infarction rats through serum TMT proteomics and discovered the relevant mechanism of edaravone regulating iron metabolism in cerebral infarction, which provides new ideas for the study of edaravone intervention in cerebral infarction and also provides reference information for future research on the mechanism of edaravone intervention in iron metabolism-related diseases.

Prediction of Peptide Detectability Based on CapsNet and Convolutional Block Attention Module

According to proteomics technology, as impacted by the complexity of sampling in the experimental process, several problems remain with the reproducibility of mass spectrometry experiments, and the peptide identification and quantitative results continue to be random. Predicting the detectability exhibited by peptides can optimize the mentioned results to be more accurate, so such a prediction is of high research significance. This study builds a novel method to predict the detectability of peptides by complying with the capsule network (CapsNet) and the convolutional block attention module (CBAM). First, the residue conical coordinate (RCC), the amino acid composition (AAC), the dipeptide composition (DPC), and the sequence embedding code (SEC) are extracted as the peptide chain features. Subsequently, these features are divided into the biological feature and sequence feature, and separately inputted into the neural network of CapsNet. Moreover, the attention module CBAM is added to the network to assign weights to channels and spaces, as an attempt to enhance the feature learning and improve the network training effect. To verify the effectiveness of the proposed method, it is compared with some other popular methods. As revealed from the experimentally achieved results, the proposed method outperforms those methods in most performance assessments.

Evaluation of the anti-atherosclerosis effect of Shanhuaxiaozhi Formulation by combination of GC–MS-based metabolomics and TMT-based proteomics technology

Objective Shanhuaxiaozhi formulation (SHXZF) is a traditional Chinese medicine preparation composed of Saffron, Crataegi Fructus, Chrysanthemi Flos, Tangerine Peel and Fructus Lycii. It is used in clinics for treating atherosclerosis with promising evidence of efficacy. Although some of the drugs in SHXZF have been reported to have significant therapeutic effects on atherosclerosis, the metabolic regulation and underlying mechanism of SHXZF during the remission of atherosclerosis are still unclear. This study aimed to integrate proteome and metabolome data sets for a holistic view of the molecular mechanisms of SHXZF in treating atherosclerosis. Methods Serum samples and aortic arch tissue from male ApoE−/− mice and C57BL/6L mice were analyzed respectively using gas chromatography–mass spectrometry (GC–MS) based metabolomics technology and Tandem Mass Tags (TMT) based quantitative proteomics technology. Metabonomics and proteomics data were integrated to analyze the mechanism of SHXZF in the treatment of atherosclerosis. Results A total of 24 potential biomarkers and 70 differential proteins were identified. These substances were mainly involved in three biological pathways: the cAMP signaling pathway, the lipid metabolism pathway, and the myocardial contraction pathway. Conclusions The results suggested that SHXZF could effectively treat atherosclerosis, partially by regulating the above three metabolic pathways. The combination of proteomics and metabolomics provided a feasible method to uncover the underlying interventional effect and therapeutic mechanism of SHXZF on atherosclerosis.

Brucella melitensis UGPase inhibits the activation of NF-κB by modulating the ubiquitination of NEMO

Background UTP-glucose-1-phosphoryl transferase (UGPase) catalyzes the synthesis of UDP-glucose, which is essential for generating the glycogen needed for the synthesis of bacterial lipopolysaccharide (LPS) and capsular polysaccharide, which play important roles in bacterial virulence. However, the molecular function of UGPase in Brucella is still unknown. Results In this study, the ubiquitination modification of host immune-related protein in cells infected with UGPase-deleted or wild-type Brucella was analyzed using ubiquitination proteomics technology. The ubiquitination modification level and type of NF-κB Essential Modulator (NEMO or Ikbkg), a molecule necessary for NF-κB signal activation, was evaluated using Coimmunoprecipitation, Western blot, and dual-Luciferase Assay. We found 80 ubiquitin proteins were upregulated and 203 ubiquitin proteins were downregulated in cells infected with B. melitensis 16 M compared with those of B. melitensis UGPase-deleted strain (16 M-UGPase−). Moreover, the ubiquitin-modified proteins were mostly enriched in the categories of regulation of kinase/NF-κB signaling and response to a bacterium, suggesting Brucella UGPase inhibits ubiquitin modification of related proteins in the host NF-κB signaling pathway. Further analysis showed that the ubiquitination levels of NEMO K63 (K63-Ub) and Met1 (Met1-Ub) were significantly increased in the 16 M-UGPase−-infected cells compared with that of the 16 M-infected cells, further confirming that the ubiquitination levels of NF-κB signaling-related proteins were regulated by the bacterial UGPase. Besides, the expression level of IκBα was decreased, but the level of p-P65 was significantly increased in the 16 M-UGPase−-infected cells compared with that of the 16 M- and mock-infected cells, demonstrating that B. melitensis UGPase can significantly inhibit the degradation of IκBα and the phosphorylation of p65, and thus suppressing the NF-κB pathway. Conclusions The results of this study showed that Brucella melitensis UGPase inhibits the activation of NF-κB by modulating the ubiquitination of NEMO, which will provide a new scientific basis for the study of immune mechanisms induced by Brucella.

Further Theoretical Considerations for Next-Generation Proteomics

In a recent Journal of Proteome Research paper, I described some general properties and constraints of a hypothetical next generation of proteomics technology based on single-molecule peptide sequencing. This work prompted many interesting questions, both from the reviewers of the initial manuscript and later from readers and colleagues. This follow-up paper addresses some of questions by clarifying the original results, considering alternative metrics, and a number of new simulations. Specifically, the discriminative power of individual amino acids is revisited, simulating additional proteolytic agents. These simulations show allowing missed cleavages generally increases the discriminative power of the amino acids in the proteolytic motif. Additional simulations show the effect of non-ideal conditions modelled on the number of proteins lacking proteotypic reads is very small, and that the average number of proteotypic reads per protein follow the same rule on the performance of the optimal choice of labeled amino acids as the number of distinguishable proteins in NeXtProt. The goal of this paper is to expand prior results and continue the scientific discussion on the possibilities of future proteomics technologies.

Integrating transcriptome and proteome analysis to determine the lignin synthesis pathway involved in Panax notoginseng in fungal stress

Background Plants are constantly threatened by various pathogens in a challenging environment. Altemaria panax Whetzel is a destructive pathogen that affects many plants, including Panax notoginseng, and significantly reduces the yield and product quality of Panax notoginseng. It is not clear how Panax notoginseng responds to pathogen infection.Methods Using the advanced advantages of transcriptome and proteomics technology, we studied the response of Panax notoginseng to Altemaria panax stress.Results Compared with the control, fungal infection caused significant changes in the Panax notoginseng transcriptome and proteome. Specifically, a total of 136,100 transcripts and 4,468 proteins were identified. The integration of transcriptome and proteome profiles revealed many candidate transcripts/proteins, which may be involved in lignin synthesis during the activation of defense responses by Panax notoginseng. Many genes and proteins are induced or inhibited by fungi. Among them, the expression levels of genes PAL, 4CL, COMT, CAD and POX in the lignin synthesis pathway are significantly increased, which indicates that the fungus activates the defense response of Panax notoginseng.Conclusions As far as we know, this is the first time that transcriptome and proteome analysis have been combined to study the response of Panax notoginseng to disease. This study provides a wide range of new information about the transcriptome, proteome and their correlation of Panax notoginseng in response to fungal stress. The analysis of this resource allows us to examine the mechanisms of transcription and protein diversification, which expands the knowledge of the complexities of the transcriptome and proteome in traditional Chinese medicines.

Acute Noise Causes Down-Regulation of ECM Protein Expression in Guinea Pig Cochlea

Background: Proteomics technology reveals the marker proteins, potential pathogenesis and intervention targets after noise-induced hearing loss.To study the differences in cochlea protein expression before and after noise exposure using proteomics to reveal the pathological mechanism of noise-induced hearing loss (NIHL).Methods: A guinea pig NIHL model was established to test the ABR thresholds before and after noise exposure. The proteomics technology was used to study the mechanism of differential protein expression in the cochlea by noise stimulation.Results: The average hearing threshold of guinea pigs on the first day after noise exposure was 57.00±6.78dB SPL; the average hearing threshold on the seventh day after noise exposure was 45.83±6.07dB SPL,. The proteomics technology identified 3122 different inner ear proteins, of which six proteins related to the hearing were down-regulation: TenascinC, Collagen type XI alpha two chains, Collagen type II alpha one chain, Thrombospondin 2, Collagen type XI alpha one chain and Ribosomal protein L38, and are enriched in protein absorption, focal adhesion, and extracellular matrix receptor pathways.Conclusion: Impulse noise can affect the expression of differential proteins through focal adhesion pathways. This data can provide an experimental basis for the research on the prevention and treatment of NIHL.Trial registration: Not applicable.