Proteomics Sample Clauses

Proteomics. Center for Applied Proteomics and Molecular Medicine Laboratory The Protein Microarray and Molecular Characterization Laboratory houses Aushon 2470 Automated, High-Throughput Protein Arrayers and Dako robotic autostainers utilized to generate protein arrays for analysis of tissue and cellular samples for biomarker discovery. The Molecular Characterization Laboratory is equipped with an lllumina Bead Array Reader for high density DNA single nucleotide polymorphism (SNP) analysis. The SNP analysis is used to assess genomic copy number variation and can be used to create a molecular karyotype. The Tissue Processing and Imaging Laboratory is equipped with histology equipment to embed and cut paraffin and frozen tissue sections with a Tissue Tek VIP Tissue Processor, Thermo microtome MH325, Harvard Apparatus vibratome, and Leica CM1850UV cryostat. Five laser capture microdissection systems in the laboratory are used to isolate enriched cell populations under direct microscopic visualization (2 Arcturus XT Automated Laser Capture Microdissection Systems, and 3 Arcturus PixCell II/Ile Laser Capture Microdissection Systems). A cytospin centrifuge and RoboSep magnetic cell sorting instrument are also available for processing biological fluids. Imaging capabilities include an Olympus BX51 microscope outfitted with a digital camera, phase contrast and fluorescence, as well as an Olympus BX51 dual head, light microscope with a digital camera. The Mass Spectrometry Laboratory uses specialized chromatography, electrophoresis, and cell fractionation systems, combined with high-performance mass spectrometers (Orbitrap Fusion, LTQ-Orbitrap, Triple Quadrupole, and MALDI- TOF-TOF), to separate and analyze components of tissue, serum and other physiological samples, resulting in protein characterization, identification and biomarker discovery. The laboratory is equipped with 4 mass spectrometers that are capable of identifying and quantitating femtomole levels of biomolecules such as peptides and proteins. The Nanofabrication Laboratory is equipped to manufacture hydrogel nanoparticles used for biomarker discovery and the development of diagnostic tests. A novel protein painting technology developed in the lab identifies hot spots of protein-protein interaction. The CAP/CLIA Clinical Proteomics Laboratory, the first in the United States to be dedicated solely to proteomics translational research, operates under the College of American Pathologists (CAP) and Clinical Laborator...
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Proteomics. ELISA validation for proteomic targets Ser208 phosphorylated troponin T was tested. Initially Western blot screening identified antibodies specific for phosphorylated troponin T but these antibodies failed to bind native phosphorylated epitope conformation in ELISA. Consequently additional strategies were employed to resolve this issue by: 1) generating of monoclonal antibodies by genetic immunization; 2) screening hybridoma by ELISA to identify specific clones that detect phosphomimetic troponin T using Ser208(TnT-Glu208).positive control and mutated troponin T (TnT- Ala208), negative control; 3) selecting hybridoma secreting IgG. Furthermore, 600 hybridoma for binding to the target epitope TnT Ser208 were tested and 4 hybridoma secreting IgG-specific cell lines have been selected and confirmed following amplification. 4 hybridoma are being cultured to produce 10 mg of monoclonal antibodies ; this enabled the development of an ELISA. The biomarker CD146 was validated as a biomarker of congestion. CD146 was identified through a proteomic assay and was included in HOMAGE as a potential biomarker of interest. From February 2015, the consortium started to adapt the work plan of WP5 aiming at an optimal strategy for proteomic analysis of serum/plasma samples that maximizes the number of proteomic biomarkers measured within a minimum bio-sample volume. After the primordial TC in February 2015, P01a-Inserm was in charge to check out the existing multiplexing platforms and to study the feasibility according to the list of selected candidate biomarkers within HOMAGE. P01a-Inserm thus has worked on bibliographic research to list multiplexing companies. The following companies were contacted: OLINK, MERCK-MILLIPORE, SPARTACUS BIOMED, FIRALIS, BIO-RAD, R&D SYTEMS, MYCARTIS, SYRIUS, MESOSCALE, CBL, PARATOPES, PLUSMORE, ISOGENIA, XXXXXXX XXXXXXX P01a-Inserm asked companies to fill a “Term of reference” document including: ‐ the adequacy between HOMAGE biomarker list and the biomarkers effectively measurable ‐ the volume required to do so and ‐ a quote for either consumables alone or consumable, biomarker measurement and analysis together. Rapidly, some companies declined the possibility of developing a customized HOMAGE multiplex assay in the restricted volume available and timeline. Eventually, a few companies engaged in depth discussion and negotiation (company’s name written in bold) with P01a-Inserm and Olink technology was chosen and the SME TATAA was added as a p...
Sample 1
Proteomics. A total of 103 proteins (p < 0.05, uncorrected) were run in IPA analyses from proteomics results from contralateral amygdala samples from the same animals as from RNA sequencing. At P21, proteomics also revealed predicted reductions in pathways involved in nervous system and cellular development; Supplementary Table 2.3, 2.6; Fig. 2.3). Across proteomic and transcriptomic samples from the same animals, three genes displayed alterations of p < 0.05 in both samples (Ryr2, Slc7a14, Cacn2d1). These genes also displayed the same direction of change in both assays (reductions in Ryr2 and Cacna2d1, increase in Slc7a14). A number of pathways displayed predicted alterations across both transcriptomic and proteomic analyses at P21 (Fig. 2.4). Notably, PKA signaling, and signaling by Rho Family GTPases are the only pathways altered between saline and VPA animals at all time points (P10, 21) and in both proteomic and transcriptomic samples.
Sample 1
Proteomics. The analysis of the entire protein complement of a cell, tissue, or organism under a specific, defined set of conditions. Proto-oncogene: One of a group of normal genes that are concerned with the control of cellular proliferation and differentiation. They can be activated in various ways to forms (oncogenes) which are closely associated with one or more steps in carcinogenesis. Activating agents include chemicals and viruses. The process of proto-oncogene activation is thought to play an important part at several stages in the development of tumours.
Sample 1

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