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peptidomics

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https://www.readbyqxmd.com/read/28938643/serum-peptidome-profiling-for-the-diagnosis-of-colorectal-cancer-discovery-and-validation-in-two-independent-cohorts
#1
Hao Wang, Chenghua Luo, Shengtao Zhu, Honghong Fang, Qing Gao, Siqi Ge, Haixia Qu, Qingwei Ma, Hongwei Ren, Youxin Wang, Wei Wang
Colorectal cancer (CRC) is one of the most common malignant neoplasms worldwide. Except for the existing fecal occult blood test, colonoscopy and sigmoidoscopy, no widely accepted in vitro diagnostic methods have been available. To identify potential peptide biomarkers for CRC, serum samples from a discovery cohort (100 CRC patients and 100 healthy controls) and an independent validation cohort (91 CRC patients and 91 healthy controls) were collected. Peptides were fractionated by weak cation exchange magnetic beads (MB-WCX) and analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28918200/profiling-the-short-linear-non-disulfide-bond-containing-peptidome-from-the-venom-of-the-scorpion-tityus-obscurus
#2
Nathalia Baptista Dias, Bibiana Monson de Souza, Fernando Kamimura Cocchi, Hipócrates M Chalkidis, Valquíria Abrão Coronado Dorce, Mario Sergio Palma
Many scorpion accidents occur in the Brazilian Amazonian region and are frequently caused by Tityus obscurus. Approximately 5% of the crude venom of this species is composed of short linear, non-disulfide-bridged peptides, which have not been intensively investigated. As a consequence, only a few of these peptides have been structurally and functionally characterized to date. In the present paper, the peptide fraction of the venom was subjected to peptide profiling using an LCMS-IT-TOF/MS and MS(n) system. The analysis detected 320 non-disulfide bond-containing peptides (NDBPs), of which twenty-seven had their sequences assigned; among them, thirteen peptides were characterized, constituting novel toxins in T...
September 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28916823/digging-into-the-low-molecular-weight-peptidome-with-the-oligonet-web-server
#3
Youzhong Liu, Sara Forcisi, Marianna Lucio, Mourad Harir, Florian Bahut, Magali Deleris-Bou, Sibylle Krieger-Weber, Régis D Gougeon, Hervé Alexandre, Philippe Schmitt-Kopplin
Bioactive peptides play critical roles in regulating many biological processes. Recently, natural short peptides biomarkers are drawing significant attention and are considered as "hidden treasure" of drug candidates. High resolution and high mass accuracy provided by mass spectrometry (MS)-based untargeted metabolomics would enable the rapid detection and wide coverage of the low-molecular-weight peptidome. However, translating unknown masses (<1 500 Da) into putative peptides is often limited due to the lack of automatic data processing tools and to the limit of peptide databases...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28906320/changes-in-proteases-antiproteases-and-bioactive-proteins-from-mother-s-breast-milk-to-the-premature-infant-stomach
#4
Veronique Demers-Mathieu, Søren Drud Nielsen, Mark A Underwood, Robyn Borghese, David C Dallas
OBJECTIVES: Our previous studies suggested that human milk proteases begin to hydrolyze proteins in the mammary gland and continue within the term infant stomach. No research has measured milk protease and pepsin activity in the gastric aspirates of preterm infants after human milk feeding. This study investigated how the concentrations of human milk proteases and protease inhibitors changed in the premature infant stomach. METHODS: Human milk and infant gastric samples were collected from 18 preterm-delivering mother-infant pairs (24-32 wk gestational age)...
September 12, 2017: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/28898393/is-beh%C3%A3-et-s-disease-a-class-1-opathy-the-role-of-hla-b-51-in-the-pathogenesis-of-beh%C3%A3-et-s-disease
#5
REVIEW
Mark Giza, Danai Koftori, Liye Chen, Paul Bowness
The association between carriage of the HLA-B*51 allele and development of Behçet's Disease (BD) has been known since the early 1970s, but the exact mechanisms responsible for its role in pathogenesis remain much-debated. In an effort to explain the disease process, it has been suggested that BD constitutes one of a newly-termed group of diseases, the 'MHC-I-opathies'. Other MHC-I-opathies' include Ankylosing Spondylitis and other HLA-B*27-associated spondyloarthropathies, and HLA-C*0602-associated skin psoriasis...
September 12, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/28893643/neuropeptide-discovery-in-proasellus-cavaticus-prediction-of-the-first-large-scale-peptidome-for-a-member-of-the-isopoda-using-a-publicly-accessible-transcriptome
#6
Andrew E Christie
In silico transcriptome mining is one of the most effective methods for neuropeptide discovery in crustaceans, particularly for species that are small, rare or from geographically inaccessible habitats that make obtaining the large pools of tissue needed for other peptide discovery platforms impractical. Via this approach, large peptidomes have recently been described for members of many of the higher crustacean taxa, one notable exception being the Isopoda; no peptidome has been predicted for any member of this malacostracan order...
September 8, 2017: Peptides
https://www.readbyqxmd.com/read/28885022/effect-of-storage-on-lactase-treated-%C3%AE-casein-and-%C3%AE-lactoglobulin-with-respect-to-bitter-peptide-formation-and-subsequent-in-vitro-digestibility
#7
Di Zhao, Thao T Le, Søren Drud Nielsen, Lotte Bach Larsen
Using active lactose to hydrolyze lactose during storage is a common process to produce lactose-hydrolyzed (LH) milk. Proteolysis induced by residual proteases in commercial lactase was studied in a system using purified β-casein or β-lactoglobulin during a 60-day storage period at 22 or 38 °C. The proteolysis of β-casein by residual proteases occurred more extensively than that of β-lactoglobulin. Peptidomic analysis by LC-ESI-MS/MS revealed that Ile, Leu, Tyr, and Phe residues near the C-terminus of β-casein were the main sites of cleavage by the residual proteases, generating assumed bitter peptides...
September 18, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28884018/pp2a-b-holoenzyme-substrate-recognition-regulation-and-role-in-cytokinesis
#8
Cheng-Guo Wu, Hui Chen, Feng Guo, Vikash K Yadav, Sean J Mcilwain, Michael Rowse, Alka Choudhary, Ziqing Lin, Yitong Li, Tingjia Gu, Aiping Zheng, Qingge Xu, Woojong Lee, Eduard Resch, Benjamin Johnson, Jenny Day, Ying Ge, Irene M Ong, Mark E Burkard, Ylva Ivarsson, Yongna Xing
Protein phosphatase 2A (PP2A) is a major Ser/Thr phosphatase; it forms diverse heterotrimeric holoenzymes that counteract kinase actions. Using a peptidome that tiles the disordered regions of the human proteome, we identified proteins containing [LMFI]xx[ILV]xEx motifs that serve as interaction sites for B'-family PP2A regulatory subunits and holoenzymes. The B'-binding motifs have important roles in substrate recognition and in competitive inhibition of substrate binding. With more than 100 novel ligands identified, we confirmed that the recently identified LxxIxEx B'α-binding motifs serve as common binding sites for B' subunits with minor variations, and that S/T phosphorylation or D/E residues at positions 2, 7, 8 and 9 of the motifs reinforce interactions...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28881029/prosaas-derived-peptides-are-regulated-by-cocaine-and-are-required-for-sensitization-to-the-locomotor-effects-of-cocaine
#9
Iryna Berezniuk, Ramona M Rodriguiz, Michael L Zee, David J Marcus, John Pintar, Daniel J Morgan, William C Wetsel, Lloyd D Fricker
To identify neuropeptides that are regulated by cocaine, we used a quantitative peptidomic technique to examine the relative levels of neuropeptides in several regions of mouse brain following daily intraperitoneal administration of 10 mg/kg cocaine or saline for seven days. A total of 102 distinct peptides were identified in one or more of the following brain regions: nucleus accumbens, caudate putamen, frontal cortex, and ventral tegmental area. None of the peptides detected in the caudate putamen or frontal cortex were altered by cocaine administration...
September 7, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28873640/evolution-of-oxidised-peptides-during-the-processing-of-9months-spanish-dry-cured-ham
#10
Marta Gallego, Leticia Mora, Fidel Toldrá
Sensory and nutritional properties of dry-cured ham can be negatively affected due to oxidative modifications of muscle proteins during its processing. In this study, a peptidomic approach has been used in order to study the evolution of oxidised peptides generated throughout the dry-curing process (0, 2, 3.5, 5, 6.5 and 9months), focusing on those derived from major myofibrillar proteins. A total of 67 peptides showing methionine, proline, and tryptophan oxidations were identified in common in all samples by nano liquid chromatography coupled to tandem mass spectrometry for their relative quantification using a label-free methodology, showing the hydrolysis of some of the peptides during the process...
January 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/28873590/in-silico-analysis-and-molecular-docking-study-of-angiotensin-i-converting-enzyme-inhibitory-peptides-from-smooth-hound-viscera-protein-hydrolysates-fractionated-by-ultrafiltration
#11
Ola Abdelhedi, Rim Nasri, Letica Mora, Mourad Jridi, Fidel Toldrá, Moncef Nasri
Smooth-hound viscera hydrolysates (SHVHs) were prepared by treatment with Neutrase (SHVH-N) and Purafect (SHVH-P). Hydrolysates were then separated according to their molecular weight, using the ultra-filtration membrane system, into 5 fractions (≥50, 50-5, 5-3, 3-1 and ≤1kDa). Fractions showed different amino acid compositions and angiotensin I-converting enzyme (ACE) inhibitory potentials. The SHVH-P-FV (≤1kDa) and SHVH-N-FIV (3-1kDa) fractions showed the best ACE-inhibitory activities with IC50 values of 53...
January 15, 2018: Food Chemistry
https://www.readbyqxmd.com/read/28871256/human-leukocyte-antigen-hla-drb1-15-01-and-hla-drb5-01-01-present-complementary-peptide-repertoires
#12
Erika Margaret Scholz, Miguel Marcilla, Xavier Daura, David Arribas-Layton, Eddie A James, Iñaki Alvarez
Human leukocyte antigen (HLA)-DR15 is a haplotype associated with multiple sclerosis. It contains the two DRB* genes DRB1*1501 (DR2b) and DRB5*0101 (DR2a). The reported anchor motif of the corresponding HLA-DR molecules was determined in 1994 based on a small number of peptide ligands and binding assays. DR2a could display a set of peptides complementary to that presented by DR2b or, alternatively, a similar peptide repertoire but recognized in a different manner by T cells. It is known that DR2a and DR2b share some peptide ligands, although the degree of similarity of their associated peptidomes remains unclear...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28867173/different-processing-of-capa-and-pyrokinin-precursors-in-the-giant-mealworm-beetle-zophobas-atratus-tenebrionidae-and-the-boll-weevil-anthonomus-grandis-grandis-curculionidae
#13
Susanne Neupert, Pawel Marciniak, Rene Köhler, Ronald J Nachman, Charles P-C Suh, Reinhard Predel
Capa and pyrokinin (pk) genes in hexapods share a common evolutionary origin. Using transcriptomics and peptidomics, we analyzed products of these genes in two beetles, the giant mealworm beetle (Zophobas atratus; Tenebrionidae) and the boll weevil (Anthonomus grandis grandis; Curculionidae). Our data revealed that even within Coleoptera, which represents a very well-defined group of insects, highly different evolutionary developments occurred in the neuropeptidergic system. These differences, however, primarily affect the general structure of the precursors and differential processing of mature peptides and, to a lesser degree, the sequences of the active core motifs...
August 31, 2017: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/28855917/peptidomic-analysis-of-the-venom-of-the-solitary-bee-xylocopa-appendiculata-circumvolans
#14
Kohei Kazuma, Kenji Ando, Ken-Ichi Nihei, Xiaoyu Wang, Marisa Rangel, Marcia Regina Franzolin, Kanami Mori-Yasumoto, Setsuko Sekita, Makoto Kadowaki, Motoyoshi Satake, Katsuhiro Konno
BACKGROUND: Among the hymenopteran insect venoms, those from social wasps and bees - such as honeybee, hornets and paper wasps - have been well documented. Their venoms are composed of a number of peptides and proteins and used for defending their nests and themselves from predators. In contrast, the venoms of solitary wasps and bees have not been the object of further research. In case of solitary bees, only major peptide components in a few venoms have been addressed. Therefore, the aim of the present study was to explore the peptide component profile of the venom from the solitary bee Xylocopa appendiculata circumvolans by peptidomic analysis with using LC-MS...
2017: Journal of Venomous Animals and Toxins Including Tropical Diseases
https://www.readbyqxmd.com/read/28834231/data-independent-acquisition-of-hla-class-i-peptidomes-on-the-q-exactive-mass-spectrometer-platform
#15
Danilo Ritz, Jonny Kinzi, Dario Neri, Tim Fugmann
The characterization of peptides presented by human leukocyte antigen (HLA) class I molecules is crucial for understanding immune processes, biomarker discovery and the development of novel immunotherapies or vaccines. Mass spectrometry allows the direct identification of thousands of HLA-bound peptides from cell lines, blood or tissue. In recent years, data-independent acquisition (DIA) mass spectrometry methods have evolved, promising to increase reproducibility and sensitivity over classical data-dependent acquisition (DDA) workflows...
August 18, 2017: Proteomics
https://www.readbyqxmd.com/read/28832583/deciphering-hla-i-motifs-across-hla-peptidomes-improves-neo-antigen-predictions-and-identifies-allostery-regulating-hla-specificity
#16
Michal Bassani-Sternberg, Chloé Chong, Philippe Guillaume, Marthe Solleder, HuiSong Pak, Philippe O Gannon, Lana E Kandalaft, George Coukos, David Gfeller
The precise identification of Human Leukocyte Antigen class I (HLA-I) binding motifs plays a central role in our ability to understand and predict (neo-)antigen presentation in infectious diseases and cancer. Here, by exploiting co-occurrence of HLA-I alleles across ten newly generated as well as forty public HLA peptidomics datasets comprising more than 115,000 unique peptides, we show that we can rapidly and accurately identify many HLA-I binding motifs and map them to their corresponding alleles without any a priori knowledge of HLA-I binding specificity...
August 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28814066/mice-expressing-human-erap1-variants-associated-with-ankylosing-spondylitis-have-altered-t-cell-repertoires-and-nk-cell-functions-as-well-as-increased-in-utero-and-perinatal-mortality
#17
David P W Rastall, Fadel S Alyaquob, Patrick O'Connell, Yuliya Pepelyayeva, Douglas Peters, Sarah Godbehere-Roosa, Cristiane Pereira-Hicks, Yasser A Aldhamen, Andrea Amalfitano
Specific variants of endoplasmic reticulum-associated aminopeptidase 1 (ERAP1) identified by genome-wide association study modify the risk for developing ankylosing spondylitis. We previously confirmed that disease-associated ERAP1 variants have altered enzymatic abilities that can impact upon the production of pro-inflammatory cytokines from cells expressing the same ERAP1 variants. To determine if these ERAP1 variants also impacted immune responses in vivo, we generated two strains of transgenic mice expressing human ERAP1 genes containing non-synonymous single-nucleotide polymorphisms associated with an increased (ERAP1-High) or decreased (ERAP1-Low) risk for developing autoimmune disease...
June 1, 2017: International Immunology
https://www.readbyqxmd.com/read/28813649/a-case-for-a-human-immuno-peptidome-project-consortium
#18
Etienne Caron, Ruedi Aebersold, Amir Banaei-Esfahani, Chloe Chong, Michal Bassani-Sternberg
A multidisciplinary group of researchers gathered at the Hönggerberg Campus at ETH Zurich, Switzerland, for the first meeting on the Human Immuno-Peptidome Project (https://hupo.org/human-immuno-peptidome-project/). The long-term goal of this project is to map the entire repertoire of peptides presented by human leukocyte antigen molecules using mass spectrometry technologies, and make its robust analysis accessible to any immunologist. Here we outline the specific challenges identified toward this goal, and within this framework, describe the structure of a multipronged program aimed at addressing these challenges and implementing solutions at a community-wide level...
August 15, 2017: Immunity
https://www.readbyqxmd.com/read/28809925/salivary-peptidome-profiling-analysis-for-occurrence-of-new-carious-lesions-in-patients-with-severe-early-childhood-caries
#19
Chang Tian, Xiangyu Sun, Xiaochen Liu, Xin Huang, Feng Chen, Shuguo Zheng
This study aimed to identify differences of peptide profiles in stimulated whole saliva among children with and without occurrence of new carious lesions, and to provide a simple way for early diagnosis and prevention of the relapse of severe early childhood caries (s-ECC). Overall, 26 children aged 3-4 years were selected out from all the children in the kindergarten to be involved in the present study, among them 13 were diagnosed as s-ECC and underwent dental treatment, whilst the other 13 were matched by age and sex as control...
2017: PloS One
https://www.readbyqxmd.com/read/28802015/identification-and-characterization-of-metformin-on-peptidomic-profiling-in-human-visceral-adipocytes
#20
Yao Gao, XingYun Wang, FangYan Huang, XianWei Cui, Yun Li, Xing Wang, Yan Cao, PengFei Xu, KaiPeng Xie, RanRan Tang, Le Zhang, ChenBo Ji, LiangHui You, XiRong Guo
To gain insight into the effect of metformin on losing weight from peptidomic perspective and to screen potential active peptides for reducing fat lipid deposition. After determining the proper concentration of metformin on human primary visceral adipocytes, we constructed a comparative peptidomic profiling between control and metformin treatment group (n = 3) using a stable isobaric labeling strategy involving tandem mass tag reagents, followed by liquid chromatography tandem mass spectrometry. We identified and quantified 3065 non-redundant peptides, 304 of which were differentially expressed after metformin treatment, 206 peptides were up regulated and 98 peptides were down regulated significantly...
August 12, 2017: Journal of Cellular Biochemistry
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