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[IEEE IGARSS 2018 - 2018 IEEE International Geoscience and Remote Sensing Symposium - Valencia (2018.7.22-2018.7.27)] IGARSS 2018 - 2018 IEEE International Geoscience and Remote Sensing Symposium - A Geometric Active Contour Model Using Symmetrical Kullback-Leibler Distance for SAR Image Segmentation
摘要： A previous study by our group indicated that combined treatment with taurine, epigallocatechin gallate (EGCG) and genistein protects against liver fibrosis. The aim of the present study was to elucidate the antifibrotic mechanism of this combination treatment using isobaric tag for relative and absolute quantification (iTRAQ)-based proteomics in an activated rat hepatic stellate cell (HSC) line. In the present study, HSC-T6 cells were incubated with taurine, EGCG and genistein, and cellular proteins were extracted and processed for iTRAQ labeling. Quantification and identification of proteins was performed using two-dimensional liquid chromatography coupled with tandem mass spectrometry. Proteomic analysis indicated that the expression of 166 proteins were significantly altered in response to combination treatment with taurine, EGCG and genistein. A total 76 of these proteins were upregulated and 90 were downregulated. Differentially expressed proteins were grouped according to their association with specific Kyoto Encyclopedia of Genes and Genomes pathways. The results indicated that the differentially expressed proteins hexokinase-2 and lysosome-associated membrane glycoprotein 1 were associated with glycolysis, gluconeogenesis and lysosome signaling pathways. The expression of these proteins was validated using western blot analysis; the expression of hexokinase-2 was significantly decreased and the expression of lysosome-associated membrane glycoprotein 1 was significantly increased in HSC-T6 cells treated with taurine, EGCG and genistein compared with the control, respectively (P<0.05). These results were in accordance with the changes in protein expression identified using the iTRAQ approach. Therefore, the antifibrotic effect of combined therapy with taurine, EGCG and genistein may be associated with the activation of several pathways in HSCs, including glycolysis, gluconeogenesis, and the ribosome and lysosome signaling pathways. The differentially expressed proteins identified in the current study may be useful for treatment of liver fibrosis in the future.
关键词： rat hepatic stellate cell,isobaric tags for relative and absolute quantitation,proteomics,epigallocatechin gallate,taurine,genistein
更新于2025-09-23 15:22:29
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High-throughput Proteomics Enabled by a Photocleavable Surfactant
摘要： Mass spectrometry (MS)-based proteomics provides unprecedented opportunities for understanding the structure and function of proteins in complex biological systems; however, protein solubility and sample preparation before MS analysis remain a bottleneck preventing high-throughput proteomics. Herein, we report for the first time a high-throughput bottom-up proteomics method enabled by a newly developed MS-compatible photocleavable surfactant, 4-hexylphenylazosulfonate (Azo)[1] that facilitates robust protein extraction, rapid enzymatic digestion (30 min compared to overnight), and subsequent MS-analysis following UV degradation. Moreover, we developed an Azo-aided bottom-up method for efficient analysis of integral membrane proteins, which are key drug targets and are generally underrepresented in global proteomic studies. Furthermore, we demonstrated the unique ability of Azo to serve as an “all-in-one” MS-compatible surfactant for both top-down and bottom-up proteomics, with streamlined workflows for high-throughput proteomics amenable to clinical applications.
关键词： membrane proteomics,high-throughput proteomics,photocleavable surfactant
更新于2025-09-23 15:19:57
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The invasive proteome of glioblastoma revealed by laser-capture microdissection
摘要： Background: Glioblastomas are heterogeneous tumors composed of a necrotic and tumor core and an invasive periphery. Methods: Here, we performed a proteomics analysis of laser-capture micro-dissected glioblastoma core and invasive areas of patient-derived xenografts. Results: Bioinformatics analysis identified enriched proteins in central and invasive tumor areas. Novel markers of invasion were identified, the genes proteolipid protein 1 (PLP1) and Dynamin-1 (DNM1), which were subsequently validated in tumors and by functional assays. Conclusion: In summary, our results identify new networks and molecules that may play an important role in glioblastoma development and may constitute potential novel therapeutic targets.
关键词： Proteomics analysis,patient-derived xenograft,intra-tumor heterogeneity,invasion,glioblastoma
更新于2025-09-23 15:19:57
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Ultrasensitive detection of nonlabelled bovine serum albumin using photothermal optical phase shift detection with UV excitation
摘要： Ultrasensitive detection of nonlabelled bovine serum albumin is performed in micro/nano?uidic chips using a photothermal optical phase shift (POPS) detection system. Currently, micro- and nano?uidics allow the analysis of various single cells, and their targets of interest are shifting from nucleic acids to proteins. Previously, our group developed photothermal detection techniques for the sensitive detection of non?uorescent molecules. For example, we developed a thermal lens microscope (TLM) with ultrahigh sensitivity at the single-molecule level and a POPS detector that is applicable to nanochannels smaller than the wavelength of light. The POPS detector also realized the detection of nonlabelled proteins in nanochannels, although its detection sensitivity is less than that of the TLM in microchannels due to insu?cient background light reduction. To overcome this problem, we developed a new POPS detector using relay optics for further reduction of the background light. In addition, heat transfer from the sample solution to the nanochannel wall was thoroughly investigated to achieve ultrahigh sensitivity. The limit of detection (LOD) obtained with the new POPS detector is 30 molecules in 1.0 fL. Considering this LOD, the performance of the new POPS detector is comparable with that of the TLM. Owing to the applicability of the POPS detector for sensitive detection even in nanochannels or single-μm channels, which cannot be realized with the TLM, combinations of the POPS detector and separation techniques employing unique nanochannel properties will contribute to advances in single-cell proteomics in the future.
关键词： Ultrasensitive detection,micro/nano?uidic chips,single-cell proteomics,photothermal optical phase shift,bovine serum albumin
更新于2025-09-23 15:19:57
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Proteomic Profiles in Advanced Age-Related Macular Degeneration Using an Aptamer-Based Proteomic Technology
摘要： Purpose: To explore top-ranked plasma proteins related to neovascular age-related macular degeneration (AMD) and geographic atrophy (GA), and explore pathways related to neovascular AMD and GA. Methods: We conducted a pilot study of patients with neovascular AMD (n = 10), GA (n = 10), and age-matched cataract controls (n = 10) who were recruited into an AMD registry. We measured 4001 proteins in ethylenediaminetetraacetic acid plasma samples using an aptamer-based proteomic technology. Relative concentrations of each of 4001 proteins were log (base 2) transformed and compared between cases of neovascular AMD and GA versus controls using linear regression. Pathway analysis was conducted using pathways downloaded from Reactome. Results: In this pilot study, higher levels of vinculin and lower levels of CD177 were found in patients with neovascular AMD compared with controls. Neuregulin-4 was higher and soluble intercellular adhesion molecule-1 was lower in patients with GA compared with controls. For neovascular AMD, cargo trafficking to the periciliary membrane, fibroblast growth factor receptor 3b ligand binding and activation, and vascular endothelial growth factor–related pathways were in the top ranked pathways. The top-ranked pathways for GA included several related to ErbB4 signaling. Conclusions: We found different proteins and different pathways associated with neovascular AMD and GA. Vinculin and some of the top-ranked pathways have been previously associated with AMD, whereas others have not been described.
关键词： neovascular AMD,aptamer-based technologies,geographic atrophy,proteomics
更新于2025-09-19 17:15:36
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Comparative physiological and proteomic analysis of Arabidopsis thaliana revealed differential wound stress responses following the exposure to different LED light sources
摘要： A comparative proteomic analysis was carried out to investigate the effects of various Light Emitting Diode (LED) light qualities (wavelengths), including red LED (R), blue LED (B), red (70%) + blue (30%) LED (RB), and white LED (W), on the wounding response in Arabidopsis thaliana. The majority of differentially expressed proteins were unique to each light condition. The highest (54%) and the lowest (22%) changes in total protein expression were observed in plants exposed to RB and B light, respectively. In wounded plants exposed to red + blue LED (RB) light, expression of antioxidant enzymes and a number of proteins related to dark reaction of photosynthesis decreased while the abundance of several proteins involved in the resistance to pathogen and lignin biosynthesis increased. Under blue LED (B) light, plants responded to wounding mainly through cell wall modification, biosynthesis of lignin and over expression of glutathione peroxidase. The results also indicated enhanced antioxidative capacity in response to wounding under red LED (R) light as compared to the other LED light conditions. The analyses of hormone metabolism suggested an increase in gibberellic acid (GA), abscisic acid (ABA) and salicylic acid (SA) signaling in the red + blue LED (RB), an enhancement in ethylene biosynthesis in the red LED (R), and increased jasmonic acid (JA) and brassinosteroid (BR) biosynthesis in the white LED (W) light conditions in response to wounding. Consistent with proteomic results related to JA metabolism, the highest concentration of methyl jasmonate (MeJA) was detected in white LED exposed plants. Late induction of JA biosynthesis-associated genes (AOC and AOS) in response to wounding was observed in all LED conditions, with the highest intensity in W light exposed plants. Collectively, we conclude that although white LED (W) light induces JA signaling pathway, red + blue LED (RB) light condition provides a better capability to recover from wound stress in A. thaliana. The results of H2O2 detection between different LED exposed plants showed different amounts of hydrogen peroxide production in response to wounding suggesting the possible signaling role of ROS in light-induced wound responses.
关键词： Abiotic stress,Pathogen resistance,Biotic stress,Wounding,Proteomics,LED
更新于2025-09-19 17:13:59
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[IEEE 2019 IEEE International Conference on Consumer Electronics - Asia (ICCE-Asia) - Bangkok, Thailand (2019.6.12-2019.6.14)] 2019 IEEE International Conference on Consumer Electronics - Asia (ICCE-Asia) - Development of Automated LED Light Compensation System for Lycopersicon Esculentum
摘要： The cells in an organism emit different amounts of proteins according to their clinical state (healthy/pathological, for instance). The resulting proteomic pro?le can be used for early detection, diagnosis, and therapy planning. In this paper, we study the classi?cation of a proteomic sample from the point of view of an inverse problem with a joint Bayesian solution, called inversion-classi?cation. We propose a hierarchical physical forward model and present encouraging results from both simulation and clinical data.
关键词： proteins,classi?cation algorithms,proteomics,Statistical signal processing,probability,liquid chromatography,mass spectrometry,selective reaction monitoring,inverse problems,mathematical modelling
更新于2025-09-19 17:13:59
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Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue
摘要： Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. We first optimized the protocol for efficient LCM analysis of FFPE tissue specimens. The use of SDS containing extraction buffer in combination with the single-pot solid-phase-enhanced sample preparation (SP3) digest method gave the best results regarding protein yield and protein/peptide identifications. Microdissected FFPE human substantia nigra tissue samples (~3,000 cells) were then analysed, using tandem mass tag (TMT) labelling and LC-MS/MS, resulting in the quantification of >5,600 protein groups. Nigral proteins were classified and analysed by abundance, showing an enrichment of extracellular exosome and neuron-specific gene ontology (GO) terms among the higher abundance proteins. Comparison of microdissected samples with intact tissue sections, using a label-free shotgun approach, revealed an enrichment of neuronal cell type markers, such as tyrosine hydroxylase and alpha-synuclein, as well as proteins annotated with neuron-specific GO terms. Overall, this study provides a detailed protocol for laser-capture proteomics using FFPE tissue and demonstrates the efficiency of LCM analysis of distinct cell subpopulations for proteomic analysis using low sample amounts.
关键词： TMT labelling,LC-MS/MS,proteomics,substantia nigra,FFPE tissue,Laser-capture microdissection
更新于2025-09-19 17:13:59
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A Simple Way to Simultaneously Release the Interface Stress and Realize the Inner Encapsulation for Highly Efficient and Stable Perovskite Solar Cells
摘要： Protein post-translational modification by the small ubiquitin-like modifier (SUMO) is a mechanism that allows a diverse response of cells to stress. Five SUMO family members, SUMO1?5, are expressed in mammals. We hypothesized that because kidney epithelial cells are often subject to stresses arising from various physiological conditions, multiple proteins in the kidney will be SUMOylated. Here, we profiled SUMO1- and SUMO2-modified proteins in a polarized epithelial cell model of the renal cortical collecting duct (mpkCCD14 cells). Modified forms of SUMO1 or SUMO2, with a histidine tag and a Thr to Lys mutation preceding the carboxyl-terminal di-gly motif, were expressed in mpkCCD14 cells, allowing SUMO-conjugated proteins to be purified and identified. Protein mass spectrometry identified 1428 SUMO1 and 1957 SUMO2 sites, corresponding to 741 SUMO1 and 971 SUMO2 proteins. Gene ontology indicated that the function of the majority of SUMOylated proteins in mpkCCD14 cells was related to gene transcription. After treatment of the mpkCCD14 cells for 24 h with aldosterone, the levels of SUMOylation at a specific site on the proton and oligopeptide/antibiotic cotransporter protein Pept2 were greatly increased. In conclusion, the SUMOylation landscape of mpkCCD14 cells suggests that protein modification by SUMOylation is a mechanism within renal epithelial cells to modulate gene transcription under various physiological conditions.
关键词： ion transport,post-translational modification,proteomics,kidney,epithelia
更新于2025-09-19 17:13:59
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The impact of ultraviolet- and infrared-based laser microdissection technology on phosphoprotein detection in the laser microdissection-reverse phase protein array workflow
摘要： Reversible protein phosphorylation represents a key mechanism by which signals are transduced in eukaryotic cells. Dysregulated phosphorylation is also a hallmark of carcinogenesis and represents key drug targets in the precision medicine space. Thus, methods that preserve phosphoprotein integrity in the context of clinical tissue analyses are crucially important in cancer research. Here we investigated the impact of UV laser microdissection (UV LMD) and IR laser capture microdissection (IR LCM) on phosphoprotein abundance of key cancer signaling protein targets assessed by reverse-phase protein microarray (RPPA). Tumor epithelial cells from consecutive thin sections obtained from four high-grade serous ovarian cancers were harvested using either UV LMD or IR LCM methods. Phosphoprotein abundances for ten phosphoproteins that represent important drug targets were assessed by RPPA and revealed no significant differences in phosphoprotein integrity from those obtained using higher-energy UV versus the lower-energy IR laser methods.
关键词： Reverse phase protein array,Phosphoprotein,Proteomics,Laser capture microdissection,Laser microdissection
更新于2025-09-19 17:13:59