scholarly journals Protein Expression Profiles in an Endosymbiotic Cyanobacterium Revealed by a Proteomic Approach

2006 ◽  
Vol 19 (11) ◽  
pp. 1251-1261 ◽  
Author(s):  
Martin Ekman ◽  
Petter Tollbäck ◽  
Johan Klint ◽  
Birgitta Bergman
Keyword(s):  
Mass Spectrometry ◽  
Protein Expression ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Calvin Cycle ◽  
Pentose Phosphate ◽  
Free Living ◽  
Two Dimensional Gel Electrophoresis ◽  
Proteomic Approach ◽  
Nostoc Strain

Molecular mechanisms behind adaptations in the cyano-bacterium (Nostoc sp.) to a life in endosymbiosis with plants are still not clarified, nor are the interactions between the partners. To get further insights, the proteome of a Nostoc strain, freshly isolated from the symbiotic gland tissue of the angiosperm Gunnera manicata Linden, was analyzed and compared with the proteome of the same strain when free-living. Extracted proteins were separated by two-dimensional gel electrophoresis and were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry combined with tandem mass spectrometry. Even when the higher percentage of differentiated cells (heterocysts) in symbiosis was compensated for, the majority of the proteins detected in the symbiotic cyanobacteria were present in the free-living counterpart, indicating that most cellular processes were common for both stages. However, differential expression profiling revealed a significant number of proteins to be down-regulated or missing in the symbiotic stage, while others were more abundant or only expressed in symbiosis. The differential protein expression was primarily connected to i) cell envelope-associated processes, including proteins involved in exopolysaccharide synthesis and surface and membrane associated proteins, ii) to changes in growth and metabolic activities (C and N), including upregulation of nitrogenase and proteins involved in the oxidative pentose phosphate pathway and downregu-lation of Calvin cycle enzymes, and iii) to the dark, micro-aerobic conditions offered inside the Gunnera gland cells, including changes in relative phycobiliprotein concentrations. This is the first comprehensive analysis of proteins in the symbiotic state.

Protein expression profiles in pediatric multiple sclerosis: potential biomarkers

2009 ◽  
Vol 15 (4) ◽  
pp. 455-464 ◽  
Author(s):  
KN Rithidech ◽  
L Honikel ◽  
M Milazzo ◽  
D Madigan ◽  
R Troxell ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Mass Spectrometry ◽  
Protein Expression ◽  
Expression Profiles ◽  
Low Frequency ◽  
Complement Factor ◽  
Protein Biomarkers ◽  
Two Dimensional Gel Electrophoresis ◽  
Pediatric Multiple Sclerosis ◽  
Proteomic Approach

The diagnosis of pediatric multiple sclerosis (MS) is challenging due to its low frequency and the overlap with other acquired childhood demyelinating disorders of the central nervous system. To identify potential protein biomarkers which could facilitate the diagnosis, we used two-dimensional gel electrophoresis (2-DE) in combination with mass spectrometry to identify proteins associated with pediatric MS. Plasma samples from nine children with MS and nine healthy subjects, matched in aggregate by age and gender, were analyzed for differences in their patterns of protein expression. We found 12 proteins that were significantly up regulated in the pediatric MS group: alpha-1-acid-glycoprotein 1, alpha-1-B-glycoprotein, transthyretin, apoliprotein-C-III, serum amyloid P component, complement factor-I, clusterin, gelsolin, hemopexin, kininogen-1, hCG1993037-isoform, and vitamin D-binding protein. These results show that 2-DE in combination with mass spectrometry is a highly sensitive technique for the identification of blood-based biomarkers. This proteomic approach could lead to a new panel of diagnostic and prognostic markers in pediatric MS.

scholarly journals New insights into Trypanosoma cruzi evolution and genotyping based on system-wide protein expression profiles (PhyloQuant)

2020 ◽  
Author(s):  
Simon Ngao Mule ◽  
Andrè Guillherme da Costa Martins ◽  
Livia Rosa-Fernandes ◽  
Gilberto Santos de Oliveira ◽  
Carla Monadeli Rodrigues ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Trypanosoma Cruzi ◽  
Protein Expression ◽  
Large Scale ◽  
Expression Profiles ◽  
Shotgun Proteomics ◽  
Close Correlation ◽  
Evolutionary Relationships ◽  
Trypanosome Species ◽  
Protein Expression Profiles

AbstractThe etiological agent of Chagas disease, Trypanosoma cruzi, is subdivided into seven genetic subdivisions termed discrete typing units (DTUs), TcI-TcVI and Tcbat. The relevance of T. cruzi genetic diversity to the variable clinical course of the disease, virulence, pathogenicity, drug resistance, transmission cycles and ecological distribution justifies the concerted efforts towards understanding the population structure of T. cruzi strains. In this study, we introduce a novel approach termed ‘phyloquant’ to infer the evolutionary relationships and assignment of T. cruzi strains to their DTUs based on differential protein expression profiles evidenced by bottom up large scale mass spectrometry-based quantitative proteomic features. Mass spectrometry features analyzed using parsimony (MS1, iBAQ and LFQ) showed a close correlation between protein expression and T. cruzi DTUs and closely related trypanosome species. Although alternative topologies with minor differences between the three MS features analyzed were demonstrated, we show congruence to well accepted evolutionary relationships of T. cruzi DTUs; in all analyses TcI and Tcbat were sister groups, and the parental nature of genotype TcII and the hybrid genotypes TcV/TcVI were corroborated. Character mapping of genetic distance matrices based on phylogenetics and phyloquant clustering showed statistically significant correlations. We propose the first quantitative shotgun proteomics approach as a complement strategy to the genetic-based assignment of T. cruzi strains to DTUs and evolutionary inferences. Moreover, this approach allows for the identification of differentially regulated and strain/DTU/species-specific proteins, with potential application in the identification of strain/DTU specific biomarkers and candidate therapeutic targets. In addition, the correlation between multi-gene protein expression and divergence of trypanosome species was evaluated, adding another level to understand the genetic subdivisions among T. cruzi DTUs.

The high-resolution mass spectrometry study of the protein composition of amyloid-like urine aggregates associated with preeclampsia

2019 ◽  
Vol 26 (2) ◽  
pp. 158-161 ◽  
Author(s):  
Victoria A Sergeeva ◽  
Natalia V Zakharova ◽  
Anna E Bugrova ◽  
Natalia L Starodubtseva ◽  
Maria I Indeykina ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Pregnant Women ◽  
Congo Red ◽  
Molecular Mechanisms ◽  
High Resolution Mass Spectrometry ◽  
Protein Composition ◽  
High Resolution Mass ◽  
Proteomic Approach ◽  
Resolution Mass

The study of protein misfolding and post-translational processing abnormalities is a promising diagnostic approach for socially significant pathologies associated with the accumulation of abnormal forms of proteins. Recently, it was shown that amyloid-like aggregates can be observed in the urine of pregnant women with preeclampsia, which is the most severe hypertensive complication that can lead to fateful outcomes. The protein composition of urine aggregates may clarify the molecular mechanisms underlying the pathology and has not yet been studied in detail. Using a proteomic approach based on high-resolution mass spectrometry, we studied the protein composition of amyloid-like structures that aggregate in the presence of Congo red azo-dye in the urine of pregnant women with preeclampsia. Fragments of β-sheets of α-1-antitrypsin, complement 3, haptoglobin, ceruloplasmin, and trypstatin were identified as most likely targets for Congo red binding.

scholarly journals Proteomic profiles of unilateral cryptorchidism in pigs at different ages using MALDI-TOF mass spectrometry and in-gel digestion coupled with mass spectrometry (GeLC-MS/MS) approaches

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Nathamon Yimpring ◽  
Sittiruk Roytrakul ◽  
Janthima Jaresitthikunchai ◽  
Narumon Phaonakrop ◽  
Sucheewin Krobthong ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Expression ◽  
Western Blot ◽  
Blot Analysis ◽  
Western Blot Analysis ◽  
Expression Profiles ◽  
Tumor Necrosis Factor Receptor ◽  
Principal Component ◽  
Peptide Mass ◽  
Different Ages

Abstract Background Cryptorchidism is a condition that occurs when one or both testes fail to descend into the scrotum. It is a common congenital disorder, causing economic loss in pig production. However, there have been only limited studies of differential protein expression profiles in undescended testes (UDTs) in the abdomen and descended testes (DTs) in cryptorchid pigs, especially at the peptidome and proteome levels. The present study aimed to analyze the peptidome of UDTs and DTs in unilateral cryptorchid pigs aged 1–2, 6, 15 and 20 weeks and in normal testes of healthy pigs aged 1–2 and 12 weeks, using peptide mass fingerprinting and three-dimensional principal component analysis (3D-PCA) with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and to identify potential protein candidates, using in-gel digestion coupled with mass spectrometry (GeLC-MS/MS). Western blot analysis was used to verify protein expression. Protein sequence was affirmed by liquid chromatography–tandem mass spectrometry. Results A PCA plot showed a discrete cluster for each sample group. Peptide mass fingerprints (PMFs) demonstrated unique peptide fragments in UDTs at different ages. A number of markedly expressed proteins from GeLC-MS/MS were identified, including the multifunctional tumor necrosis factor receptor superfamily member 18 (TNFRSF18), in DTs at 1–2 and 6 weeks and in UDTs at 15 and 20 weeks of age. Using western blot analysis, high expression of TNFRSF18 was observed in the UDTs at 15 weeks. Using the STITCH database, this protein was found to be related to apoptosis, corresponding to the previous report in the UDTs at the same age. Conclusions The present study revealed the specific PMFs and clusters for porcine cryptorchidism, and a novel protein, TNFRSF18, associated with the disease mechanism. These results could provide further insights into the pathogenesis of the disease.

scholarly journals Transcriptome profiling of peanut (Arachis hypogaea) gynophores in gravitropic response

2013 ◽  
Vol 40 (12) ◽  
pp. 1249 ◽  
Author(s):  
Hai-fen Li ◽  
Xiao-Ping Chen ◽  
Fang-he Zhu ◽  
Hai-Yan Liu ◽  
Yan-Bin Hong ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Arachis Hypogaea ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Pentose Phosphate ◽  
Differentially Expressed ◽  
Pcr Analysis

Peanut (Arachis hypogaea L.) produces flowers aerially, but the fruit develops underground. This process is mediated by the gynophore, which always grows vertically downwards. The genetic basis underlying gravitropic bending of gynophores is not well understood. To identify genes related to gynophore gravitropism, gene expression profiles of gynophores cultured in vitro with tip pointing upward (gravitropic stimulation sample) and downward (control) at both 6 and 12 h were compared through a high-density peanut microarray. After gravitropic stimulation, there were 174 differentially expressed genes, including 91 upregulated and 83 downregulated genes at 6 h, and 491 differentially expressed genes including 129 upregulated and 362 downregulated genes at 12 h. The differentially expressed genes identified were assigned to 24 functional categories. Twenty pathways including carbon fixation, aminoacyl-tRNA biosynthesis, pentose phosphate pathway, starch and sucrose metabolism were identified. The quantitative real-time PCR analysis was performed for validation of microarray results. Our study paves the way to better understand the molecular mechanisms underlying the peanut gynophore gravitropism.

A Potential Biomarker Panel of Multiple Myeloma Identified Using Label-Free Mass Spectrometry-Based Quantitative Proteomics

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2890-2890
Author(s):  
Attaya Suvannasankha ◽  
Colin D. Crean ◽  
Heather M. Sahm ◽  
Rafat Abonour ◽  
Sherif Farag ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Multiple Myeloma ◽  
Protein Expression ◽  
Plasma Cells ◽  
Expression Profiles ◽  
Peptide Identification ◽  
Clinical Samples ◽  
Normal Plasma ◽  
Potential Biomarker ◽  
Significant Difference

Abstract Abstract 2890 Background: Multiple myeloma is an incurable and fatal hematologic malignancy. Recent gene microarray studies showed distinct gene expression profiles defining MM subgroups and their association with cytogenetic abnormalities and treatment outcome. However, aside from transcriptional control, a variety of post-transcriptional/post-translational modifications likely play an important role in regulating protein expression and function, and ultimately may prove informative for predicting tumor behavior. Objectives: We hypothesize that the protein profile in MM cells is different than normal plasma cells. Methodology: Normal plasma cells and myeloma cells were isolated using CD138 immune magnetic beads from bone marrow aspirates from healthy volunteers or patients with newly diagnosed MM, respectively. CD138+ cells were frozen and subsequently analyzed in one batch. Proteins were digested by trypsin. Tryptic peptides were injected onto an HPLC system and analyzed on a Thermo-Fisher LTQ mass spectrometer. Peptide identification and quantification were carried out using proprietary algorithms. Identified proteins were categorized into priority groups based on the quality of the peptide identification by tandem mass spectrometry. Proteins with significant changes in expression level were further analyzed by bioinformatics tools for the determination of the biological significance. Results: In the discovery phase of this study, 433 proteins were identified and their expression levels were quantitatively compared. 169 of these proteins demonstrated a significant difference between normal plasma cells and MM cells. Among the significantly changed proteins, 18 were identified and quantified with high confidence, and were therefore chosen for further validation. The identified proteins are known to be involved in the glycolysis/gluconeogenesis pathway, the oxidative phosphorylation pathway, cysteine metabolism and the pentose phosphate pathway. None of these proteins are known to be of prognostic value or being currently targeted for therapy in MM. A high-throughput LC/MS-based multiple-reaction-monitoring (MRM) assay for quantitative validation of these candidates with clinical samples is ongoing. To date, using the MRM assay, we were able to detect MRM peptides for 13 of the 18 targeted proteins in clinical samples. The quantification of these peptides will be further confirmed using a separate set of clinical samples. Conclusion: Significant differences in protein expression were observed between MM and normal plasma cells. The study presents an important step toward using proteomics as a tool to develop diagnostic and/or prognostic biomarkers in the clinical setting. However, both follow-up analytical and clinical validations are required before they can serve as disease-specific biomarkers. Disclosures: Abonour: Celgene: Membership on an entity's Board of Directors or advisory committees.

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