Journal: International Journal of Surgery (London, England)

Article Title: Tibial cortex transverse transport surgery improves wound healing in patients with severe type 2 DFUs by activating a systemic immune response: a cross-sectional study

doi: 10.1097/JS9.0000000000001897

Figure Lengend Snippet: The design and workflow of this study. This study mainly contained four parts. First, 68 patients with unilateral or bilateral DFUs were treated with TTT surgery, and samples at six key time points were collected for the study. Second, label-free proteomic analysis of immunomodulatory proteins and regulatory pathways ( N =30, TTT 0 , TTT 3 , TTT 7 , TTT 14 , TTT 21 , and TTT 35 ) was performed. Third, skin tissue samples from three key time points were collected for spatial metabolomics to validate the immunological metabolites ( N =7, TTT 0 , TTT 14, and TTT 21 ). Next, the specific immune biomarkers were validated in the clinical laboratory (TTT 0 , TTT 3 , TTT 7 , TTT 14 , TTT 21 , and TTT 35 ). In addition, transcriptomics analysis for skin tissue samples was applied to screen out differential genes and signal pathways in regulating the immune response and wound healing ( N =3, TTT 0 , TTT 14 , and TTT 21 ). Finally, the integration of data from multiomic and clinical immune biomarker analyses was applied to investigate possible immune responses. N, the number of patients; TTT 0 , 1 day before the TTT external fixator was fixed; TTT 3 , 3 days after the TTT external fixator was fixed; TTT 7 , 7 days after the TTT external fixator was fixed; TTT 14 , the day at which the upward movement was completed; TTT 21 , the day at which the downward transfer was completed; TTT 35 , the second day after the TTT external fixator was removed. DFU, diabetic foot ulceration; TTT, tibial cortex transverse transport.

Article Snippet: The analytical platform used for proteomic analysis was from Dashuo Biotech Co. Ltd (Dalian, China), the spatially resolved metabolomics platform was from MetWare Co. Ltd (Wuhan, China), and the transcriptomics platform was from Kangxiang Biotechnology Co. Ltd (Shanghai, China).

Techniques: Biomarker Assay

Journal: International Journal of Surgery (London, England)

Article Title: Tibial cortex transverse transport surgery improves wound healing in patients with severe type 2 DFUs by activating a systemic immune response: a cross-sectional study

doi: 10.1097/JS9.0000000000001897

Figure Lengend Snippet: Spatially resolved metabolomics analysis of DFU skin tissues. (A) Crucial processing of skin tissue samples for spatial metabolomics analysis, including H&E staining of skin tissue sections, DHB matrix spraying of frozen sections, and metabolite spatial distribution with Gaussian smoothing. (B and C) OPLS-DA of spatial metabolomics datasets. (D–F) Representative mass spectra of DFU skin tissue (TTT 0 , TTT 14 , and TTT 21 ). (G–I) The bar diagram shows the expression levels of differentially abundant metabolites in glycerophospholipid, fatty acid, and glycerophospholipid metabolism pathways at TTT 14 and TTT 21 compared with TTT 0 . A total of eight differentially abundant metabolites were identified in TTT 0 , TTT 14 , and TTT 21 , and their change trends were statistically analyzed. (J–L) Bar plot of KEGG pathway enrichment analysis for the differentially abundant metabolites. The glycerophospholipid metabolism pathway was validated in DFU skin tissues. ** P value <0.005; * P value <0.05. DFU, diabetic foot ulceration; KEGG, Kyoto Encyclopedia of Genes and Genomes; TTT, tibial cortex transverse transport.

Article Snippet: The analytical platform used for proteomic analysis was from Dashuo Biotech Co. Ltd (Dalian, China), the spatially resolved metabolomics platform was from MetWare Co. Ltd (Wuhan, China), and the transcriptomics platform was from Kangxiang Biotechnology Co. Ltd (Shanghai, China).

Techniques: Staining, Expressing

Journal: International Journal of Surgery (London, England)

Article Title: Tibial cortex transverse transport surgery improves wound healing in patients with severe type 2 DFUs by activating a systemic immune response: a cross-sectional study

doi: 10.1097/JS9.0000000000001897

Figure Lengend Snippet: Spatial expression images of differentially abundant metabolites in DFU tissue sections based on spatially resolved metabolomics data (intensity in color scale is relative value). (A) Expression and spatial distributions of theobromine, levocarnitine propionate, canthaxanthin A, and triacetin at TTT 14 compared with those at TTT 0 . (B) Expression and spatial distributions of elemonic acid and camelliagenin at TTT 21 compared with those at TTT 0 . (C) Decreased concentrations of L-palmitoylcarnitine and stearoylcarnitine in DFU tissues from TTT 14 and TTT 21 patients compared with those of TTT 0 patients. * P value <0.05, ** P value <0.01. DFU, diabetic foot ulceration; TTT, tibial cortex transverse transport.

Article Snippet: The analytical platform used for proteomic analysis was from Dashuo Biotech Co. Ltd (Dalian, China), the spatially resolved metabolomics platform was from MetWare Co. Ltd (Wuhan, China), and the transcriptomics platform was from Kangxiang Biotechnology Co. Ltd (Shanghai, China).

Techniques: Expressing

Journal: iScience

Article Title: Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results

doi: 10.1016/j.isci.2023.108473

Figure Lengend Snippet:

Article Snippet: Metabolomics profiling was performed at the Broad Institute, and appropriate statistical modelling was used to account for residual batch effects.

Techniques: Software

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Dormancy in Embryos: Insight from Hydrated Encysted Embryos of an Aquatic Invertebrate *

doi: 10.1074/mcp.RA117.000109

Figure Lengend Snippet: An overview of the experimental procedure, including proteomics and data analyses in dormant resting eggs (RE, EO) and nondormant amictic eggs (AM), metabolome profiling and desiccation experiments.

Article Snippet: Numerous proteins were not detected in AM (ND AM) Metabolome Profiling Samples All steps were carried out in metaSysX GmbH, Potsdam Germany.

Techniques:

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Dormancy in Embryos: Insight from Hydrated Encysted Embryos of an Aquatic Invertebrate *

doi: 10.1074/mcp.RA117.000109

Figure Lengend Snippet: The Citrate (TCA) Cycle. A, A KEGG map showing the proteins in association with the Citrate cycle (TCA) pathway. Boxes in gray show the proteins that were identified in rotifer eggs. Boxes in red show proteins that were significantly more abundant in AM versus RE. Yellow boxes show the proteins that were detected only in AM eggs. Statistically significant differences were indicated by 1-Way ANOVA test (FDR p value 0.05, FC>3), B, A comparison of the log2 relative intensities of compounds between AM and RE, as determined by metabolome analyses. Blue columns - AM eggs, Red columns- RE. A star indicates statistical significant differences (t test; p < 0.05).

Article Snippet: Numerous proteins were not detected in AM (ND AM) Metabolome Profiling Samples All steps were carried out in metaSysX GmbH, Potsdam Germany.

Techniques: Comparison

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Dormancy in Embryos: Insight from Hydrated Encysted Embryos of an Aquatic Invertebrate *

doi: 10.1074/mcp.RA117.000109

Figure Lengend Snippet: A comparison of the log2 relative intensities of adenosine compounds between AM and RE, as determined by metabolome analyses. Blue columns, AM eggs; Red columns, RE. All differences between AM and RE were statistically significant (t test; p < 0.05).

Article Snippet: Numerous proteins were not detected in AM (ND AM) Metabolome Profiling Samples All steps were carried out in metaSysX GmbH, Potsdam Germany.

Techniques: Comparison

Journal: Molecular & Cellular Proteomics : MCP

Article Title: Dormancy in Embryos: Insight from Hydrated Encysted Embryos of an Aquatic Invertebrate *

doi: 10.1074/mcp.RA117.000109

Figure Lengend Snippet: A comparison of the log2 relative intensities of amino acids between AM and RE, as determined by metabolome analyses. Blue columns, AM eggs; Red columns, RE. All differences between AM and RE were statistically significant (t test; p < 0.05).

Article Snippet: Numerous proteins were not detected in AM (ND AM) Metabolome Profiling Samples All steps were carried out in metaSysX GmbH, Potsdam Germany.

Techniques: Comparison

Journal: Scientific Reports

Article Title: Integrative proteome and metabolome unveil the central role of IAA alteration in axillary bud development following topping in tobacco

doi: 10.1038/s41598-024-66136-4

Figure Lengend Snippet: Expression patterns of the DEPs involved in flavonols and flavones biosynthesis. ( A ) Flavonols and flavones biosynthesis pathway in tobacco. The proteins identified in the proteome are shown in red, and the main flavonoid products in the metabolome are shown in bold. ( B , C ) Heat map of DEPs expression patterns during flavonols and flavones biosynthesis. ( D ) Heat map of UGTs differential expression patterns after topping.

Article Snippet: The sample preparation and metabolome profiling were performed by Metware Biotechnology Co., Ltd. (Wuhan, China) following their standard procedures.

Techniques: Expressing, Quantitative Proteomics

Journal: Scientific Reports

Article Title: Integrative proteome and metabolome unveil the central role of IAA alteration in axillary bud development following topping in tobacco

doi: 10.1038/s41598-024-66136-4

Figure Lengend Snippet: Joint metabolome and proteome analysis. ( A ) The top 10 influential metabolites and proteins based on O2PLS analysis. ( B ) The top 20 enriched KEGG terms of 435 DEPs. ( C , D ) Correlation network analysis between DEPs and metabolites. Metabolites and proteins are indicated as rhombus and circles, respectively.

Article Snippet: The sample preparation and metabolome profiling were performed by Metware Biotechnology Co., Ltd. (Wuhan, China) following their standard procedures.

Techniques: