scholarly journals Changes in the human plasma and urinary metabolome associated with acute dietary exposure to sucrose and the identification of potential biomarkers of sucrose intake

2015 ◽  
Vol 60 (2) ◽  
pp. 444-457 ◽  
Author(s):  
Manfred Beckmann ◽  
Annemiek M. Joosen ◽  
Michelle M. Clarke ◽  
Owen Mugridge ◽  
Gary Frost ◽  
...  
Keyword(s):  
Human Plasma ◽  
Dietary Exposure ◽  
Sucrose Intake ◽  
Potential Biomarkers

scholarly journals Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Jun Yao ◽  
Douglas C Wu ◽  
Ryan M Nottingham ◽  
Alan M Lambowitz
Keyword(s):  
Human Plasma ◽  
Binding Sites ◽  
Full Length ◽  
Peak Calling ◽  
Healthy Individuals ◽  
Protein Coding ◽  
Protein Binding Sites ◽  
Protein Coding Genes ◽  
Non Coding Rnas ◽  
Potential Biomarkers

Human plasma contains > 40,000 different coding and non-coding RNAs that are potential biomarkers for human diseases. Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) combined with peak calling to simultaneously profile all RNA biotypes in apheresis-prepared human plasma pooled from healthy individuals. Extending previous TGIRT-seq analysis, we found that human plasma contains largely fragmented mRNAs from > 19,000 protein-coding genes, abundant full-length, mature tRNAs and other structured small non-coding RNAs, and less abundant tRNA fragments and mature and pre-miRNAs. Many of the mRNA fragments identified by peak calling correspond to annotated protein-binding sites and/or have stable predicted secondary structures that could afford protection from plasma nucleases. Peak calling also identified novel repeat RNAs, miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and biomarker significance, including a family of full-length excised intron RNAs, subsets of which correspond to mirtron pre-miRNAs or agotrons.

scholarly journals Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma

2019 ◽  
Vol 38 (11) ◽  
Author(s):  
Maria D Giraldez ◽  
Ryan M Spengler ◽  
Alton Etheridge ◽  
Annika J Goicochea ◽  
Missy Tuck ◽  
...  
Keyword(s):  
Human Plasma ◽  
Small Rna ◽  
Rna Seq ◽  
Potential Biomarkers

scholarly journals The possibility of using PlasmaDeepDive™ MRM panel in clinical diagnostics

2015 ◽  
Vol 61 (2) ◽  
pp. 272-278
Author(s):  
Iu.V. Miroshnichenko ◽  
N.A. Petushkova ◽  
N.E. Moskaleva ◽  
N.B. Teryaeva ◽  
V.G. Zgoda ◽  
...  
Keyword(s):  
Nervous System ◽  
Blood Plasma ◽  
Human Plasma ◽  
Human Blood ◽  
Proteomic Analysis ◽  
Clinical Diagnostics ◽  
Human Blood Plasma ◽  
Plasma Samples ◽  
Human Plasma Samples ◽  
Potential Biomarkers

Concentrations of 46 proteins have been determined in human blood plasma using PlasmaDeepDive™ MRM Panel ("Biognosys AG", Switzerland). 18 of them were included into the group of proteins with higher concentrations, also identified by the shotgun proteomic analysis. Based on literature data it is concluded that the PlasmaDeepDive™ MRM Panel is applicable for studies of human plasma samples for potential biomarkers of various nervous system disorders.

Diagnosis of pancreatic cancer via1H NMR metabolomics of human plasma

The Analyst ◽  
2018 ◽  
Vol 143 (24) ◽  
pp. 5974-5978 ◽  
Author(s):  
Lenka Michálková ◽  
Štěpán Horník ◽  
Jan Sýkora ◽  
Lucie Habartová ◽  
Vladimír Setnička
Keyword(s):  
Pancreatic Cancer ◽  
Blood Plasma ◽  
Human Plasma ◽  
Nmr Metabolomics ◽  
H Nmr ◽  
Potential Biomarkers

The investigation of blood plasma via1H NMR metabolomics revealed a panel of potential biomarkers of pancreatic cancer.

UHPLC–MS/MS bioanalysis of human plasma coproporphyrins as potential biomarkers for organic anion-transporting polypeptide-mediated drug interactions

Bioanalysis ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 633-644 ◽  
Author(s):  
Hamza Kandoussi ◽  
Jianing Zeng ◽  
Kumar Shah ◽  
Patricia Paterson ◽  
Rasa Santockyte ◽  
...  
Keyword(s):  
Drug Interactions ◽  
Human Plasma ◽  
Organic Anion ◽  
Organic Anion Transporting Polypeptide ◽  
Potential Biomarkers

scholarly journals Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling

2020 ◽  
Author(s):  
Jun Yao ◽  
Douglas C. Wu ◽  
Ryan M. Nottingham ◽  
Alan M. Lambowitz
Keyword(s):  
Human Plasma ◽  
Binding Sites ◽  
Full Length ◽  
Peak Calling ◽  
Healthy Individuals ◽  
Protein Coding ◽  
Protein Binding Sites ◽  
Protein Coding Genes ◽  
Non Coding Rnas ◽  
Potential Biomarkers

SummaryHuman plasma contains >40,000 different coding and non-coding RNAs that are potential biomarkers for human diseases. Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) combined with peak calling to simultaneously profile all RNA biotypes in apheresis-prepared human plasma pooled from healthy individuals. Extending previous TGIRT-seq analysis, we found that human plasma contains largely fragmented mRNAs from >19,000 protein-coding genes, abundant full-length, mature tRNAs and other structured small non-coding RNAs, and less abundant tRNA fragments and mature and pre-miRNAs. Many of the mRNA fragments identified by peak calling correspond to annotated protein-binding sites and/or have stable predicted secondary structures that could afford protection from plasma nucleases. Peak calling also identified novel repeat RNAs, miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and biomarker significance, including a family of full-length excised introns RNAs, subsets of which correspond to mirtron pre-miRNAs or agotrons.

scholarly journals Determination of the concentration range for 267 proteins from 21 lots of commercial human plasma using highly multiplexed multiple reaction monitoring mass spectrometry

The Analyst ◽  
2020 ◽  
Vol 145 (10) ◽  
pp. 3634-3644
Author(s):  
Claudia Gaither ◽  
Robert Popp ◽  
Yassene Mohammed ◽  
Christoph H. Borchers
Keyword(s):  
Mass Spectrometry ◽  
Human Plasma ◽  
Multiple Reaction Monitoring ◽  
Reaction Monitoring ◽  
Biomarker Validation ◽  
Potential Biomarkers

Multiple reaction monitoring (MRM) is a key tool for biomarker validation and the translation of potential biomarkers into the clinic.

scholarly journals Development of the analytical method for the quantification of 3-nitrotirosin and 3-chlorothyrosin in human plasma as potential biomarkers to evaluate minimal liver encephalopathy (MHE)

2020 ◽  
Vol 19 ◽  
pp. 21
Author(s):  
A. Villaseñor Todd ◽  
J.A. Hernández-Hernández ◽  
R.C. López-Sanchez ◽  
F.J. Bosques-Padilla ◽  
C.A. Cortez-Hernandez ◽  
...  
Keyword(s):  
Human Plasma ◽  
Analytical Method ◽  
Potential Biomarkers

scholarly journals Investigation of human plasma depletome from patients with schizophrenia

2019 ◽  
Author(s):  
Licia Carla da Silva Costa ◽  
Daniel Martins de Souza ◽  
Sheila Garcia Rosa ◽  
Paulo A. Baldasso ◽  
Johann Steiner
Keyword(s):  
Mass Spectrometry ◽  
Blood Plasma ◽  
Psychiatric Disorders ◽  
Treatment Outcomes ◽  
Human Plasma ◽  
High Abundance ◽  
Improve Treatment ◽  
Dynamic Concentration ◽  
Shotgun Mass Spectrometry ◽  
Potential Biomarkers

The proteome of blood plasma is an interesting source of biomarkers and a potential way to improve treatment outcomes in psychiatric disorders. Respire that, its wide dynamic concentration range makes reducing its complexity necessary. Thus, in proteomic studies, a few of the most abundant proteins are depleted and normally discarded. This high-abundance fraction, called the depletome, however, is a source of potential biomarkers due to nonspecific bindings with low abundance proteins. In this work, we aimed to characterize the high-abundance fraction using a shotgun mass spectrometry approach. These proteins show the importance of studying depletome proteins in the quest for biomarkers.

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