scholarly journals MONTE enables serial immunopeptidome, ubiquitylome, proteome, phosphoproteome, acetylome analyses of sample-limited tissues

2021 ◽  
Author(s):  
Jennifer G. Abelin ◽  
Erik J. Bergstrom ◽  
Hannah B. Taylor ◽  
Keith D. Rivera ◽  
Susan Klaeger ◽  
...  
Keyword(s):  
Tissue Sample ◽  
Phosphorylation Sites ◽  
Label Free ◽  
Post Translational Modification ◽  
Chemical Labeling ◽  
Highly Sensitive ◽  
Full Analysis ◽  
Ct Antigens ◽  
Robust Integration

Multiomic characterization of patient tissues provides insights into the function of different biological pathways in the context of disease. Much work has been done to serialize proteome and post-translational modification (PTM) analyses to conserve precious patient samples. However, characterizing clinically relevant tissues with multi-ome workflows that have distinct sample processing requirements remains challenging. To overcome the obstacles of combining enrichment workflows that have unique input amounts and utilize both label free and chemical labeling strategies, we developed a highly-sensitive multi-omic networked tissue enrichment (MONTE) workflow for the full analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome and acetylome all from the same tissue sample. The MONTE workflow enables identification of a median of 9,000 HLA-I peptides, 6,000 HLA-II peptides, 10,000 Ub sites, 12,000 proteins, 20,000 phosphorylation sites and 15,000 acetylation sites from patient LUAD tumors. Because all omes are generated from the exact same tissue sample, there is less biological variability in the data enabling more robust integration. The information available in MONTE datasets facilitates the identification of putative immunotherapeutic targets, such as CT antigens and neoantigens presented by HLA complexes, as well as reveal insights into how disease-specific changes in protein expression, protein degradation, cell signaling, metabolic, and epigenetic pathways are involved in disease pathology and treatment.

scholarly journals Characterization of Phosphorylated Proteins Using Mass Spectrometry

2020 ◽  
Vol 21 ◽  
Author(s):  
Li-Rong Yu ◽  
Timothy D. Veenstra
Keyword(s):  
Gene Expression ◽  
Mass Spectrometry ◽  
Phosphorylation Sites ◽  
Post Translational Modification ◽  
Specific Antibodies ◽  
Phosphorylated Proteins

Abstract:: Phosphorylation is arguably the most important post-translational modification that occurs within proteins. Phosphorylation is used as a signal to control numerous physiological activities ranging from gene expression to metabo-lism. Identifying phosphorylation sites within proteins was historically a challenge as it required either radioisotope label-ing or the use of phospho-specific antibodies. The advent of mass spectrometry (MS) has had a major impact on the abil-ity to qualitatively and quantitatively characterize phosphorylated proteins. In this article we describe MS methods for characterizing phosphorylation sites within individual proteins as well as entire proteome samples. The utility of these methods is illustrated in examples that show the information that can be gained using these MS techniques.

Resonant Microcavities Coupled to a Photonic Crystal Waveguide for Multi-channel Biodetection

2009 ◽  
Vol 1191 ◽  
Author(s):  
Elisa Guillermain ◽  
Philippe M. Fauchet
Keyword(s):  
Photonic Crystal ◽  
Food Safety ◽  
Transmission Spectrum ◽  
Channel Structure ◽  
Photonic Crystal Waveguide ◽  
Label Free ◽  
Highly Sensitive ◽  
Fabrication And Characterization ◽  
Double Channel

AbstractMiniaturized and highly sensitive bio-sensors are attractive in various applications, such as medicine or food safety. Photonic crystal (PhC) microcavities present multiple advantages for rapid and accurate label-free optical detection. But their principle of operation (i.e. observation of a peak in transmission) makes their integration in serial arrays difficult. We present in this paper a multi-channel sensor consisting of several resonant PhC microcavities coupled to the same waveguide. The transmission spectrum shows as many dips as there are cavities, and each of the microcavities can act as an independent sensor. Preliminary results show the fabrication and characterization of a double-channel structure with small defects used as a solvent sensor.

scholarly journals High-performance Nanocavities-based Meta-crystals for Enhanced Plasmonic Sensing

2016 ◽  
Vol 2 (1) ◽  
Author(s):  
M. Rippa ◽  
R. Castagna ◽  
M. Pannico ◽  
P. Musto ◽  
E. Bobeico ◽  
...  
Keyword(s):  
Photonic Crystals ◽  
High Performance ◽  
Surface Enhanced Raman Spectroscopy ◽  
Label Free ◽  
Self Assembling ◽  
Plasmonic Sensing ◽  
Highly Sensitive ◽  
Surface Enhanced ◽  
Surface Enhanced Raman

AbstractWe report on a novel procedure of fabrication to easily obtain highly reproducible nanocavities-shaped photonic crystals with strong plasmonic performances. Thus, we also report on the morphological and optical characterization of the obtained structures. They are classifiable as 2-layers (organic and inorganic) photonic crystals based on iso-Y-shaped nano-cavities. Such novel designed structures are compelling candidates for the development of highly sensitive biosensors due to their unique surface plasmon resonances (SPRs) and SPR enabled surface-enhanced Raman spectroscopy (SERS). The planar photonic crystal comprises a polymeric (ZEP520A) layer (thickness ~80 nm) sandwiched between a layer of gold (~50 nm thickness) and a glass substrate. For what concerns the cavities’ shape, iso-Y units are chosen on the basis of their third order nonlinearity and are coupled in hexagonal-based configuration to produce extended meta-structures. The substrates are functionalized with a probe made by a self-assembling monolayer (SAM) of 4-mercaptobenzoic acid (4-MBA). The average SERS Enhancement Factor >106 and SPR sensitivity of ~300 nm/RIU confirm that the proposed 2-layers iso-Y meta-structure is very suitable for high sensitive label-free plasmonic sensing.

Synthesis and 31 P NMR characterization of new low toxic highly sensitive pH probes designed for in vivo acidic pH studies

2002 ◽  
Vol 10 (5) ◽  
pp. 1451-1458 ◽  
Author(s):  
Sophie Martel ◽  
Jean-Louis Clément ◽  
Agnès Muller ◽  
Marcel Culcasi ◽  
Sylvia Pietri
Keyword(s):  
Acidic Ph ◽  
Highly Sensitive ◽  
Nmr Characterization ◽  
Low Toxic ◽  
Ph Probes

scholarly journals Shiga Toxin (Stx)-Binding Glycosphingolipids of Primary Human Renal Cortical Epithelial Cells (pHRCEpiCs) and Stx-Mediated Cytotoxicity

Toxins ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 139
Author(s):  
Johanna Detzner ◽  
Elisabeth Krojnewski ◽  
Gottfried Pohlentz ◽  
Daniel Steil ◽  
Hans-Ulrich Humpf ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Epithelial Cells ◽  
Shiga Toxin ◽  
Saturated Fatty Acids ◽  
Human Kidney ◽  
Enterohemorrhagic Escherichia Coli ◽  
Highly Sensitive ◽  
Liquid Ordered ◽  
Uremic Syndrome

Human kidney epithelial cells are supposed to be directly involved in the pathogenesis of the hemolytic–uremic syndrome (HUS) caused by Shiga toxin (Stx)-producing enterohemorrhagic Escherichia coli (EHEC). The characterization of the major and minor Stx-binding glycosphingolipids (GSLs) globotriaosylceramide (Gb3Cer) and globotetraosylceramide (Gb4Cer), respectively, of primary human renal cortical epithelial cells (pHRCEpiCs) revealed GSLs with Cer (d18:1, C16:0), Cer (d18:1, C22:0), and Cer (d18:1, C24:1/C24:0) as the dominant lipoforms. Using detergent-resistant membranes (DRMs) and non-DRMs, Gb3Cer and Gb4Cer prevailed in the DRM fractions, suggesting their association with microdomains in the liquid-ordered membrane phase. A preference of Gb3Cer and Gb4Cer endowed with C24:0 fatty acid accompanied by minor monounsaturated C24:1-harboring counterparts was observed in DRMs, whereas the C24:1 fatty acid increased in relation to the saturated equivalents in non-DRMs. A shift of the dominant phospholipid phosphatidylcholine with saturated fatty acids in the DRM to unsaturated species in the non-DRM fractions correlated with the GSL distribution. Cytotoxicity assays gave a moderate susceptibility of pHRCEpiCs to the Stx1a and Stx2a subtypes when compared to highly sensitive Vero-B4 cells. The results indicate that presence of Stx-binding GSLs per se and preferred occurrence in microdomains do not necessarily lead to a high cellular susceptibility towards Stx.

scholarly journals Potential Phosphorylation of Viral Nonstructural Protein 1 in Dengue Virus Infection

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1393
Author(s):  
Thanyaporn Dechtawewat ◽  
Sittiruk Roytrakul ◽  
Yodying Yingchutrakul ◽  
Sawanya Charoenlappanit ◽  
Bunpote Siridechadilok ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Nonstructural Protein ◽  
Antiviral Drug ◽  
Denv Infection ◽  
Site Directed Mutagenesis ◽  
Phosphorylation Sites ◽  
Post Translational Modification ◽  
Multifunctional Protein ◽  
Nonstructural Protein 1 ◽  
Underlying Mechanisms

Dengue virus (DENV) infection causes a spectrum of dengue diseases that have unclear underlying mechanisms. Nonstructural protein 1 (NS1) is a multifunctional protein of DENV that is involved in DENV infection and dengue pathogenesis. This study investigated the potential post-translational modification of DENV NS1 by phosphorylation following DENV infection. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), 24 potential phosphorylation sites were identified in both cell-associated and extracellular NS1 proteins from three different cell lines infected with DENV. Cell-free kinase assays also demonstrated kinase activity in purified preparations of DENV NS1 proteins. Further studies were conducted to determine the roles of specific phosphorylation sites on NS1 proteins by site-directed mutagenesis with alanine substitution. The T27A and Y32A mutations had a deleterious effect on DENV infectivity. The T29A, T230A, and S233A mutations significantly decreased the production of infectious DENV but did not affect relative levels of intracellular DENV NS1 expression or NS1 secretion. Only the T230A mutation led to a significant reduction of detectable DENV NS1 dimers in virus-infected cells; however, none of the mutations interfered with DENV NS1 oligomeric formation. These findings highlight the importance of DENV NS1 phosphorylation that may pave the way for future target-specific antiviral drug design.

scholarly journals Optical Monitoring of the Production Quality of Si-Nanoribbon Chips Intended for the Detection of ASD-Associated Oligonucleotides

Micromachines ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 147
Author(s):  
Kristina A. Malsagova ◽  
Tatyana O. Pleshakova ◽  
Vladimir P. Popov ◽  
Igor N. Kupriyanov ◽  
Rafael A. Galiullin ◽  
...  
Keyword(s):  
Production Quality ◽  
Autism Spectrum ◽  
Covalent Immobilization ◽  
Biological Macromolecules ◽  
Label Free ◽  
Raman Scattering Spectroscopy ◽  
Dna Oligonucleotides ◽  
Highly Sensitive ◽  
Highly Sensitive Detection

Gas-phase etching and optical lithography were employed for the fabrication of a silicon nanoribbon chip (Si-NR chip). The quality of the so-fabricated silicon nanoribbons (Si-NRs) was monitored by optical Raman scattering spectroscopy. It was demonstrated that the structures of the Si-NRs were virtually defect-free, meaning they could be used for highly sensitive detection of biological macromolecules. The Si-NR chips were then used for the highly sensitive nanoelectronics detection of DNA oligonucleotides (oDNAs), which represent synthetic analogs of 106a-5p microRNA (miR-106a-5p), associated with the development of autism spectrum disorders in children. The specificity of the analysis was attained by the sensitization of the Si-NR chip sur-face by covalent immobilization of oDNA probes, whose nucleotide sequence was complementary to the known sequence of miR-106a-5p. The use of the Si-NR chip was demonstrated to al-low for the rapid label-free real-time detection of oDNA at ultra-low (~10−17 M) concentrations.

scholarly journals Terahertz characterization of two-dimensional low-conductive layers enabled by metal gratings

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Prashanth Gopalan ◽  
Yunshan Wang ◽  
Berardi Sensale-Rodriguez
Keyword(s):  
Optical Transmission ◽  
Terahertz Spectroscopy ◽  
Design Guidelines ◽  
Two Dimensional ◽  
Highly Sensitive ◽  
Transmission Measurements ◽  
Metal Gratings ◽  
Low Sensitivity ◽  
Non Destructive

AbstractWhile terahertz spectroscopy can provide valuable information regarding the charge transport properties in semiconductors, its application for the characterization of low-conductive two-dimensional layers, i.e., σs <  < 1 mS, remains elusive. This is primarily due to the low sensitivity of direct transmission measurements to such small sheet conductivity levels. In this work, we discuss harnessing the extraordinary optical transmission through gratings consisting of metallic stripes to characterize such low-conductive two-dimensional layers. We analyze the geometric tradeoffs in these structures and provide physical insights, ultimately leading to general design guidelines for experiments enabling non-contact, non-destructive, highly sensitive characterization of such layers.

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