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https://www.readbyqxmd.com/read/27920218/a-molecular-basis-for-the-presentation-of-phosphorylated-peptides-by-hla-b-antigens
#1
Adán Alpízar, Fabio Marino, Antonio Ramos-Fernández, Manuel Lombardía, Anita Jeko, Florencio Pazos, Alberto Paradela, César Santiago, Albert J R Heck, Miguel Marcilla
As aberrant protein phosphorylation is a hallmark of tumor cells, the display of tumor-specific phosphopeptides by Human Leukocyte Antigen (HLA) class I molecules can be exploited in the treatment of cancer by T-cell-based immunotherapy. Yet, the characterization and prediction of HLA-I phospholigands is challenging as the molecular determinants of the presentation of such post-translationally modified peptides are not fully understood. Here, we employed a peptidomic workflow to identify 256 unique phosphorylated ligands associated with HLA-B*40, -B*27, -B*39 or -B*07...
December 5, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27914455/mediators-and-biomarkers-of-inflammation-in-meningitis-cytokine-and-peptidome-profiling-of-cerebrospinal-fluid
#2
A A Belogurov, O M Ivanova, Y A Lomakin, R H Ziganshin, M I Vaskina, V D Knorre, E A Klimova, A G Gabibov, V T Ivanov, V M Govorun
Differential diagnosis of bacterial and viral meningitis is an urgent problem of the modern clinical medicine. Early and accurate detection of meningitis etiology largely determines the strategy of its treatment and significantly increases the likelihood of a favorable outcome for the patient. In the present work, we analyzed the peptidome and cytokine profiles of cerebrospinal fluid (CSF) of 17 patients with meningitis of bacterial and viral etiology and of 20 neurologically healthy controls. In addition to the identified peptides (potential biomarkers), we found significant differences in the cytokine status of the CSF of the patients...
November 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27895531/follicular-fluid-biomarkers-for-human-in-vitro-fertilization-outcome-proof-of-principle
#3
Fang Chen, Carl Spiessens, Thomas D'Hooghe, Karen Peeraer, Sebastien Carpentier
BACKGROUND: Human follicular fluid (FF) is a unique biological fluid in which the oocyte develops in vivo, and presents an optimal source for non-invasive biochemical predictors. Oocyte quality directly influences the embryo development and hence, may be used as a predictor of embryo quality. Peptide profiling of FF and its potential use as a biomarker for oocyte quality has never been reported. METHODS: This study screened FF for peptide biomarkers that predict the outcome of in vitro fertilization (IVF)...
2016: Proteome Science
https://www.readbyqxmd.com/read/27873209/large-scale-interaction-profiling-of-protein-domains-through-proteomic-peptide-phage-display-using-custom-peptidomes
#4
Moon-Hyeong Seo, Satra Nim, Jouhyun Jeon, Philip M Kim
Protein-protein interactions are essential to cellular functions and signaling pathways. We recently combined bioinformatics and custom oligonucleotide arrays to construct custom-made peptide-phage libraries for screening peptide-protein interactions, an approach we call proteomic peptide-phage display (ProP-PD). In this chapter, we describe protocols for phage display for the identification of natural peptide binders for a given protein. We finally describe deep sequencing for the analysis of the proteomic peptide-phage display...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27863112/label-free-quantitative-comparison-of-cerebrospinal-fluid-glycoproteins-and-endogenous-peptides-in-subjects-with-alzheimer-s-disease-mild-cognitive-impairment-and-healthy-individuals
#5
Jingxin Wang, Robert Cunningham, Henrik Zetterberg, Sanjay Asthana, Cynthia Carlsson, Ozioma Okonkwo, Lingjun Li
PURPOSE: The goal of this study is to investigate putative molecular dynamic changes in cerebrospinal fluids (CSFs) collected from individuals with mild cognitive impairment (MCI) and Alzheimer's disease (AD) as compared to healthy controls. EXPERIMENTAL DESIGN: The CSF samples from 12 subjects comprised of four cognitively normal individuals and eight patients with MCI and AD, respectively. Two aliquots of each CSF samples (total 1 mL) of each participant were used for this study...
November 9, 2016: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/27862975/purification-of-soluble-hla-class-i-complexes-from-human-serum-or-plasma-deliver-high-quality-immuno-peptidomes-required-for-biomarker-discovery
#6
Danilo Ritz, Andreas Gloger, Dario Neri, Tim Fugmann
Soluble human leukocyte antigen class I (sHLA)-peptide complexes have been suggested to play a role in the modulation of immune responses and in immune evasion of cancer cells. The set of peptides eluted from sHLA molecules could serve as biomarker for the monitoring of patients with cancer or other conditions. Here, we describe an improved sHLA peptidomics methodology resulting in the identification of 1816 to 2761 unique peptide sequences from triplicate analyses of serum or plasma taken from three healthy donors...
November 12, 2016: Proteomics
https://www.readbyqxmd.com/read/27861808/peptidomic-analysis-of-type-1-diabetes-associated-hla-dq-molecules-and-the-impact-of-hla-dm-on-peptide-repertoire-editing
#7
Zemin Zhou, Eduardo Reyes-Vargas, Hernando Escobar, Kuan Y Chang, Adam P Barker, Alan L Rockwood, Julio C Delgado, Xiao He, Peter E Jensen
HLA-DM and class II associated invariant chain (Ii) are key cofactors in the MHC class II (MHCII) antigen processing pathway. We used tandem mass spectrometry sequencing to directly interrogate the global impact of DM and Ii on the repertoire of MHCII-bound peptides in human embryonic kidney 293T cells expressing HLA-DQ molecules in the absence or presence of these cofactors. Ii and DM have a major impact on the repertoire of peptides presented by DQ1 and DQ6, with the caveat that this technology is not quantitative...
November 15, 2016: European Journal of Immunology
https://www.readbyqxmd.com/read/27860201/peptidome-characterization-of-the-antipyretic-fraction-of-bubali-cornu-aqueous-extract-by-nano-liquid-chromatography-with-orbitrap-mass-spectrum-detection
#8
Rui Liu, Qiong Huang, Jin-Ao Duan, Zhenhua Zhu, Pei Liu, Yong Bian, Jinhua Tao, Dawei Qian
In the present study, the antipyretic activity of Bubali Cornu (water buffalo horn) fraction and its metabolomics were investigated. The fraction decreased rat rectal temperature, and 13 endogenous metabolites were identified as potential biomarkers. Selected metabolites were involved in arachidonic acid metabolism and glycerophospholipid metabolism etc. Following treatment with the fraction, four metabolites, pyroglutamic acid, palmitelaidic acid, leukotriene A4, and prostaglandin A2 were reversed. In addition, the levels of interleukin-1β, tumor necrosis factor-α, prostaglandin E2 , and cyclic adenosine monophosphate in plasma were also reversed after treatment as determined by enzyme linked immunosorbent assay...
November 9, 2016: Journal of Separation Science
https://www.readbyqxmd.com/read/27847340/relevance-of-pre-analytical-blood-management-on-the-emerging-cardiovascular-protein-biomarkers-tweak-and-hmgb1-and-on-mirna-serum-and-plasma-profiling
#9
Daniela Basso, Andrea Padoan, Thomas Laufer, Vittorio Aneloni, Stefania Moz, Hannah Schroers, Michela Pelloso, Anna Saiz, Medea Krapp, Paola Fogar, Paola Cornoldi, Carlo-Federico Zambon, Elisa Rossi, Marco La Malfa, Alberto Marotti, Thomas Brefort, Tanja M Weis, Hugo A Katus, Mario Plebani
BACKGROUND: Disease-independent sources of biomarker variability include pre-analytical, analytical and biological variance. The aim of the present study was to evaluate whether the pre-analytical phase has any impact on the emerging heart disease TWEAK and HMGB1 protein markers and miRNA biomarkers, and whether peptidome profiling allows the identification of pre-analytical quality markers. METHODS: An assessment was made of sample type (serum, EDTA-Plasma, Citrate-Plasma, ACD-plasma, Heparin-plasma), temperature of sample storage (room temperature or refrigerated), time of sample storage (0...
November 12, 2016: Clinical Biochemistry
https://www.readbyqxmd.com/read/27823957/prediction-of-a-neuropeptidome-for-the-eyestalk-ganglia-of-the-lobster-homarus-americanus-using-a-tissue-specific-de-novo-assembled-transcriptome
#10
Andrew E Christie, Vittoria Roncalli, Matthew C Cieslak, Micah G Pascual, Andy Yu, Tess J Lameyer, Meredith E Stanhope, Patsy S Dickinson
In silico transcriptome mining is a powerful tool for crustacean peptidome prediction. Using homology-based BLAST searches and a simple bioinformatics workflow, large peptidomes have recently been predicted for a variety of crustaceans, including the lobster, Homarus americanus. Interestingly, no in silico studies have been conducted on the eyestalk ganglia (lamina ganglionaris, medulla externa, medulla interna and medulla terminalis) of the lobster, although the eyestalk is the location of a major neuroendocrine complex, i...
November 4, 2016: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/27789347/prediction-of-a-peptidome-for-the-western-tarnished-plant-bug-lygus-hesperus
#11
Andrew E Christie, J Joe Hull, Josh A Richer, Scott M Geib, Erica E Tassone
Many strategies for controlling insect pests require an understanding of their hormonal signaling agents, peptides being the largest and most diverse single class of these molecules. Lygus hesperus is a pest species of particular concern, as it is responsible for significant damage to a wide variety of commercially important plant crops. At present, little is known about the peptide hormones of L. hesperus. Here, transcriptomic data were used to predict a peptidome for L. hesperus. Fifty-three L. hesperus transcripts encoding peptide precursors were identified, with a subset amplified by PCR for sequence verification...
October 24, 2016: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/27782050/a-combinational-strategy-upon-rna-sequencing-and-peptidomics-unravels-a-set-of-novel-toxin-peptides-in-scorpion-mesobuthus-martensii
#12
Ning Luan, Wang Shen, Jie Liu, Bo Wen, Zhilong Lin, Shilong Yang, Ren Lai, Siqi Liu, Mingqiang Rong
Scorpion venom is deemed to contain many toxic peptides as an important source of natural compounds. Out of the two hundred proteins identified in Mesobuthus martensii (M. martensii), only a few peptide toxins have been found so far. Herein, a combinational approach based upon RNA sequencing and Liquid chromatography-mass spectrometry/mass spectrometry (LC MS/MS) was employed to explore the venom peptides in M. martensii. A total of 153 proteins were identified from the scorpion venom, 26 previously known and 127 newly identified...
October 5, 2016: Toxins
https://www.readbyqxmd.com/read/27775574/proteome-and-peptidome-of-vipera-berus-berus-venom
#13
Aleksandra Bocian, Małgorzata Urbanik, Konrad Hus, Andrzej Łyskowski, Vladimír Petrilla, Zuzana Andrejčáková, Monika Petrillová, Jaroslav Legath
Snake venom is a rich source of peptides and proteins with a wide range of actions. Many of the venom components are currently being tested for their usefulness in the treatment of many diseases ranging from neurological and cardiovascular to cancer. It is also important to constantly search for new proteins and peptides with properties not yet described. The venom of Vipera berus berus has hemolytic, proteolytic and cytotoxic properties, but its exact composition and the factors responsible for these properties are not known...
October 19, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27750368/dual-function-small-regulatory-rnas-in-bacteria
#14
Matthias Gimpel, Sabine Brantl
Dual-function sRNAs are a subgroup of small regulatory RNAs that act on the one hand as base-pairing sRNAs to inhibit or activate target gene expression and on the other hand as peptide-encoding mRNAs that function either in the same or in another metabolic pathway. Here, we review and compare the five currently known and intensively characterized dual-function sRNAs with regard to their two functions, their biological role, their evolutionary conservation and their requirements for RNA chaperones. Furthermore, we summarize the data available on five potential dual-function sRNAs, whose base-pairing function is well established whereas the role of their encoded peptides has not yet been elucidated...
October 17, 2016: Molecular Microbiology
https://www.readbyqxmd.com/read/27726374/examination-of-endogenous-peptides-in-medicago-truncatula-using-mass-spectrometry-imaging
#15
Erin Gemperline, Caitlin Keller, Dhileepkumar Jayaraman, Junko Maeda, Michael R Sussman, Jean-Michel Ané, Lingjun Li
Plant science is an important, rapidly developing area of study. Within plant science, one area of study that has grown tremendously with recent technological advances, such as mass spectrometry, is the field of plant-omics; however, plant peptidomics is relatively underdeveloped in comparison with proteomics and metabolomics. Endogenous plant peptides can act as signaling molecules and have been shown to affect cell division, development, nodulation, reproduction, symbiotic associations, and defense reactions...
October 11, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27705817/peptidomics-of-the-zebrafish-danio-rerio-in-search-for-neuropeptides
#16
Kristien A Van Camp, Geert Baggerman, Ronny Blust, Steven J Husson
: (Neuro)peptides are small messenger molecules that are derived from larger, inactive precursor proteins by the highly controlled action of processing enzymes. These biologically active peptides can be found in all metazoan species where they orchestrate a wide variety of physiological processes. Obviously, detailed knowledge on the actual peptide sequences, including the potential existence of truncated versions or presence of post-translation modifications, is of high importance when studying their function...
October 2, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27704694/analysis-of-proteins-and-peptides-by-electromigration-methods-in-microchips
#17
REVIEW
Sille Štěpánová, Václav Kašička
This review presents the developments and applications of microchip electromigration methods in the separation and analysis of peptides and proteins in the period 2011-mid-2016. The developments in sample preparation and preconcentration, microchannel material, and surface treatment are described. Separations by various microchip electromigration methods (zone electrophoresis in free and sieving media, affinity electrophoresis, isotachophoresis, isoelectric focusing, electrokinetic chromatography, and electrochromatography) are demonstrated...
October 5, 2016: Journal of Separation Science
https://www.readbyqxmd.com/read/27685651/analysis-of-the-yeast-peptidome-and-comparison-with-the-human-peptidome
#18
Sayani Dasgupta, Ciyu Yang, Leandro M Castro, Alexandre K Tashima, Emer S Ferro, Robyn D Moir, Ian M Willis, Lloyd D Fricker
Peptides function as signaling molecules in species as diverse as humans and yeast. Mass spectrometry-based peptidomics techniques provide a relatively unbiased method to assess the peptidome of biological samples. In the present study, we used a quantitative peptidomic technique to characterize the peptidome of the yeast Saccharomyces cerevisiae and compare it to the peptidomes of mammalian cell lines and tissues. Altogether, 297 yeast peptides derived from 75 proteins were identified. The yeast peptides are similar to those of the human peptidome in average size and amino acid composition...
2016: PloS One
https://www.readbyqxmd.com/read/27650042/deciphering-bioactive-peptides-and-their-action-mechanisms-through-proteomics
#19
Osmel Fleitas Martinez, Caleb Mawuli Agbale, Fernanda Nomiyama, Octávio Luiz Franco
Bioactive peptides such as antimicrobial peptides (AMPs), ribosomally synthesized and post translationally modified peptides (RiPPs) and the non-ribosomal peptides (NRPs) have emerged with promising applications in medicine, agriculture and industry. However, their development has been limited by several difficulties making it necessary to search for novel discovery methods. In this context, proteomics has been considered a reliable tool. Areas covered: This review highlights recent developments in proteomic tools that facilitate the discovery of AMPs, RiPPs and NRPs as well as the elucidation of action mechanisms of AMPs and resistance mechanisms of pathogens to them...
October 8, 2016: Expert Review of Proteomics
https://www.readbyqxmd.com/read/27645745/separation-of-peptides-by-capillary-electrophoresis
#20
Gerhard K E Scriba
Peptides are an important class of analytes in chemistry, biochemistry, food chemistry, as well as medical and pharmaceutical sciences including biomarker analysis in peptidomics and proteomics. As a high-resolution technique, capillary electrophoresis (CE) is well suited for the analysis of polar compounds such as peptides. In addition, CE is orthogonal to high-performance liquid chromatography (HPLC) as both techniques are based on different physicochemical separation principles. For the successful development of peptide separations by CE, operational parameters including puffer pH, buffer concentration and buffer type, applied voltage, capillary dimensions, as well as background electrolyte additives such as detergents, ion-pairing reagents, cyclodextrins, (poly)amines, and soluble polymers have to be considered and optimized...
2016: Methods in Molecular Biology
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