10 results on '"de Oliveira, Felipe Marques Souza"'
Search Results
2. A targeted proteomics approach reveals a serum protein signature as diagnostic biomarker for resectable gastric cancer
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Shen, Qiujin, Polom, Karol, Williams, Coralie, de Oliveira, Felipe Marques Souza, Guergova-Kuras, Mariana, Lisacek, Frederique, Karlsson, Niclas G., Roviello, Franco, and Kamali-Moghaddam, Masood
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- 2019
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3. Accurate detection of Newcastle disease virus using proximity-dependent DNA aptamer ligation assays
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Marnissi, Boutheina, Khalfaoui, Khouloud, Ebai, Tonge, de Oliveira, Felipe Marques Souza, Ghram, Abdeljelil, Kamali-Moghaddam, Masood, Hmila, Issam, Marnissi, Boutheina, Khalfaoui, Khouloud, Ebai, Tonge, de Oliveira, Felipe Marques Souza, Ghram, Abdeljelil, Kamali-Moghaddam, Masood, and Hmila, Issam
- Abstract
Detecting viral antigens at low concentrations in field samples can be crucial for early veterinary diagnostics. Proximity ligation assays (PLAs) in both solution and solid-phase formats are widely used for high-performance protein detection in medical research. However, the affinity reagents used, which are mainly poly- and monoclonal antibodies, play an important role in the performance of PLAs. Here, we have established the first homogeneous and solid-phase proximity-dependent DNA aptamer ligation assays for rapid and accurate detection of Newcastle disease virus (NDV). NDV is detected by a pair of extended DNA aptamers that, upon binding in proximity to proteins on the envelope of the virus, are joined by enzymatic ligation to form a unique amplicon that can be sensitively detected using real-time PCR. The sensitivity, specificity, and reproducibility of the assays were validated using 40 farm samples. The results demonstrated that the developed homogeneous and solid-phase PLAs, which use NDV-selective DNA aptamers, are more sensitive than the sandwich enzymatic-linked aptamer assay (ELAA), and have a comparable sensitivity to real-time reverse transcription PCR (rRT-PCR) as the gold standard detection method. In addition, the solid-phase PLA was shown to have a greater dynamic range with improved lower limit of detection, upper- and lower limit of quantification, and minimal detectable dose as compared with those of ELAA and rRT-PCR. The specificity of PLA is shown to be concordant with rRT-PCR.
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- 2021
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4. Protein measurements in venous plasma, earlobe capillary plasma and in plasma stored on filter paper
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Siart, Benjamin, de Oliveira, Felipe Marques Souza, Shen, Qiujin, Björkesten, Johan, Pekar, Thomas, Steinborn, Ralf, Nimmerichter, Alfred, Kamali-Moghaddam, Masood, Wallner, Bernard, Siart, Benjamin, de Oliveira, Felipe Marques Souza, Shen, Qiujin, Björkesten, Johan, Pekar, Thomas, Steinborn, Ralf, Nimmerichter, Alfred, Kamali-Moghaddam, Masood, and Wallner, Bernard
- Abstract
In this study, levels of inflammatory protein biomarkers in venous plasma, plasma derived from capillary blood from the earlobe, and capillary plasma stored as dried plasma spots (DPS) were compared. Samples from 12 male individuals were assessed with a panel of 92 inflammation-related proteins using multiplex proximity extension assay. Correlations between sample types varied greatly between analytes. A high correlation of rho > 0.8 was observed between capillary plasma and DPS for 32 analytes. At this level of correlation, 13 analytes correlated between venous and capillary plasma and 5 analytes in the comparison of venous blood with DPS.
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- 2019
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5. Development and Application of Proximity Assays for Proteome Analysis in Medicine
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de Oliveira, Felipe Marques Souza
- Subjects
glycosylation ,Enzyme-linked immunosorbent assay ,phosphorylation ,post-translational modifications ,Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) ,Solid-phase proximity ligation assay ,immunoassay and rolling circle amplification ,autoantibodies ,autoimmune disease ,Medicinsk bioteknologi (med inriktning mot cellbiologi (inklusive stamcellsbiologi), molekylärbiologi, mikrobiologi, biokemi eller biofarmaci) ,Proximity Extension Assay ,inflammation protein biomarkers - Abstract
Along with proteins, a myriad of different molecular biomarkers, such as post-translational modifications and autoantibodies, could be used in an attempt to improve disease detection and progression. In this thesis, I build on several iterations of the proximity ligation assay to develop and apply new adaptable methods to facilitate detection of proteins, autoantibodies and post-translational modifications. In paper I, we present an adaptation of the solid-phase proximity ligation assay (SP-PLA) for the detection of post-translational modification of proteins (PTMs). The assay was adapted for the detection of two of the most commons PTMs present in proteins, glycosylation and phosphorylation, offering the encouraging prospect of using detection of PTMs in a diagnostic or prognostic capacity. In paper II, we developed a variant of the proximity ligation assay using micro titer plate for detection and quantification of protein using optical density as readout in the fluorometer, termed PLARCA. With a detection limit considerably lower than ELISA, PLARCA detected femtomolar levels of these proteins in patient samples. In paper III, we aim to compare detection values of samples collected from earlobe capillary, venous plasma, as well as capillary plasma stored in dried plasma spots (DPS) assessed with a 92-plex inflammation panel using multiplex proximity extension assay (PEA). Despite the high variability in protein measurements between the three sample sources, we were able to conclude that earlobe capillary sampling is a suitable less invasive alternative, to venipuncture. In paper IV, we describe the application of PLARCA and proximity extension assay (PEA) for the detection of GAD65 autoantibodies (GADA). Thus, offering highly sensitive and specific autoimmunity detection.
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- 2018
6. Protein measurements in venous plasma, earlobe capillary plasma and in plasma stored on filter paper
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Siart, Benjamin, primary, de Oliveira, Felipe Marques Souza, additional, Shen, Qiujin, additional, Björkesten, Johan, additional, Pekar, Thomas, additional, Steinborn, Ralf, additional, Nimmerichter, Alfred, additional, Kamali-Moghaddam, Masood, additional, and Wallner, Bernard, additional
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- 2019
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7. Detection of post-translational modifications using solid-phase proximity ligation assay
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de Oliveira, Felipe Marques Souza, Mereiter, Stefan, Lönn, Peter, Siart, Benjamin, Shen, Qiujin, Heldin, Johan, Raykova, Doroteya, Karlsson, Niclas G., Polom, Karol, Roviello, Franco, Reis, Celso A., Kamali-Moghaddam, Masood, de Oliveira, Felipe Marques Souza, Mereiter, Stefan, Lönn, Peter, Siart, Benjamin, Shen, Qiujin, Heldin, Johan, Raykova, Doroteya, Karlsson, Niclas G., Polom, Karol, Roviello, Franco, Reis, Celso A., and Kamali-Moghaddam, Masood
- Abstract
Post-translational modifications (PTMs) regulate protein activities to help orchestrate and fine-tune cellular processes. Dysregulation of PTMs is often related with disorders and malignancies, and may serve as a precise biomarker of disease. Developing sensitive tools to measure and monitor low-abundant PTMs in tissue lysates or serum will be instrumental for opening up new PTM-based diagnostic avenues. Here, we investigate the use of solid-phase proximity ligation assay (SP-PLA) for detection of different PTMs. The assay depends on the recognition of the target protein molecule and its modification by three affinity binders. Using antibodies and lectins, we applied the method for detection of glycosylated CD44 and E-Cadherin, and phosphorylated p53 and EGFR. The assay was found to have superior dynamic range and limit of detection compared to standard ELISAs. In summary, we have established the use of SP-PLA as an appropriate method for sensitive detection of PTMs in lysates and sera, which may provide a basis for future PTM-based diagnostic and prognostic biomarkers
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- 2018
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8. Analytically Sensitive Protein Detection in Microtiter Plates by Proximity Ligation with Rolling Circle Amplification
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Ebai, Tonge, de Oliveira, Felipe Marques Souza, Löf, Liza, Wik, Lotta, Schweiger, Caroline, Larsson, Anders, Keilholtz, Ulrich, Haybaeck, Johannes, Landegren, Ulf, Kamali-Moghaddam, Masood, Ebai, Tonge, de Oliveira, Felipe Marques Souza, Löf, Liza, Wik, Lotta, Schweiger, Caroline, Larsson, Anders, Keilholtz, Ulrich, Haybaeck, Johannes, Landegren, Ulf, and Kamali-Moghaddam, Masood
- Abstract
BACKGROUND: Detecting proteins at low concentrations in plasma is crucial for early diagnosis. Current techniques in clinical routine, such as sandwich ELISA, provide sensitive protein detection because of a dependence on target recognition by pairs of antibodies, but detection of still lower protein concentrations is often called for. Proximity ligation assay with rolling circle amplification (PLARCA) is a modified proximity ligation assay (PLA) for analytically specific and sensitive protein detection via binding of target proteins by 3 antibodies, and signal amplification via rolling circle amplification (RCA) in microtiter wells, easily adapted to instrumentation in use in hospitals. METHODS: Proteins captured by immobilized antibodies were detected using a pair of oligonucleotide-conjugated antibodies. Upon target recognition, these PLA probes guided oligonucleotide ligation, followed by amplification via RCA of circular DNA strands that formed in the reaction. The RCA products were detected by horseradish peroxidase-labeled oligonucleotides to generate colorimetric reaction products with readout in an absorbance microplate reader. RESULTS: We compared detection of interleukin (IL)-4, IL-6, IL-8, p53, and growth differentiation factor-15 by PLARCA and conventional sandwich ELISA or immuno RCA. PLARCA detected lower concentrations of proteins and exhibited a broader dynamic range compared ELISA and iRCA using the same antibodies. IL-4 and IL-6 were detected in clinical samples at femtomolar concentrations, considerably lower than for ELISA. CONCLUSIONS: PLARCA offers detection of lower protein levels and increased dynamic ranges compared to ELISA. The PLARCA procedure may be adapted to routine instrumentation available in hospitals and research laboratories.
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- 2017
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9. Detection of post-translational modification of cancer biomarkers via proximity ligation assay
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de Oliveira, Felipe Marques Souza, Mereiter, Stefan, Persson, Nina, Blixt, Ola, Reis, Celso A., Kamali-Moghaddam, Masood, de Oliveira, Felipe Marques Souza, Mereiter, Stefan, Persson, Nina, Blixt, Ola, Reis, Celso A., and Kamali-Moghaddam, Masood
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- 2016
10. Proximity-dependent initiation of hybridization chain reaction
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Koos, Björn, Cane, Gaëlle, Grannas, Karin, Löf, Liza, Arngården, Linda, Heldin, Johan, Clausson, Carl-Magnus, Klaesson, Axel, Hirvonen, M Karoliina, de Oliveira, Felipe Marques Souza, Talibov, Vladimir O, Pham, Nhan T, Auer, Manfred, Danielson, U Helena, Haybaeck, Johannes, Kamali-Moghaddam, Masood, Söderberg, Ola, Koos, Björn, Cane, Gaëlle, Grannas, Karin, Löf, Liza, Arngården, Linda, Heldin, Johan, Clausson, Carl-Magnus, Klaesson, Axel, Hirvonen, M Karoliina, de Oliveira, Felipe Marques Souza, Talibov, Vladimir O, Pham, Nhan T, Auer, Manfred, Danielson, U Helena, Haybaeck, Johannes, Kamali-Moghaddam, Masood, and Söderberg, Ola
- Abstract
Sensitive detection of protein interactions and post-translational modifications of native proteins is a challenge for research and diagnostic purposes. A method for this, which could be used in point-of-care devices and high-throughput screening, should be reliable, cost effective and robust. To achieve this, here we design a method (proxHCR) that combines the need for proximal binding with hybridization chain reaction (HCR) for signal amplification. When two oligonucleotide hairpins conjugated to antibodies bind in close proximity, they can be activated to reveal an initiator sequence. This starts a chain reaction of hybridization events between a pair of fluorophore-labelled oligonucleotide hairpins, generating a fluorescent product. In conclusion, we show the applicability of the proxHCR method for the detection of protein interactions and posttranslational modifications in microscopy and flow cytometry. As no enzymes are needed, proxHCR may be an inexpensive and robust alternative to proximity ligation assays.
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- 2015
- Full Text
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