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https://www.readbyqxmd.com/read/28514659/the-intergenic-recombinant-hla-b%C3%A2-46-01-has-a-distinctive-peptidome-that-includes-kir2dl3-ligands
#1
Hugo G Hilton, Curtis P McMurtrey, Alex S Han, Zakia Djaoud, Lisbeth A Guethlein, Jeroen H Blokhuis, Jason L Pugh, Ana Goyos, Amir Horowitz, Rico Buchli, Ken W Jackson, Wilfred Bardet, David A Bushnell, Philip J Robinson, Juan L Mendoza, Michael E Birnbaum, Morten Nielsen, K Christopher Garcia, William H Hildebrand, Peter Parham
HLA-B(∗)46:01 was formed by an intergenic mini-conversion, between HLA-B(∗)15:01 and HLA-C(∗)01:02, in Southeast Asia during the last 50,000 years, and it has since become the most common HLA-B allele in the region. A functional effect of the mini-conversion was introduction of the C1 epitope into HLA-B(∗)46:01, making it an exceptional HLA-B allotype that is recognized by the C1-specific natural killer (NK) cell receptor KIR2DL3. High-resolution mass spectrometry showed that HLA-B(∗)46:01 has a low-diversity peptidome that is distinct from those of its parents...
May 16, 2017: Cell Reports
https://www.readbyqxmd.com/read/28490095/a-cold-induced-phytosulfokine-peptide-is-related-to-the-improvement-of-loquat-fruit-chilling-tolerance
#2
Huwei Song, Xinfeng Wang, Weicheng Hu, Xianghui Yang, Enjie Diao, Ting Shen, Qian Qiang
A novel peptidomics approach was used to discover cold-induced peptides in loquat fruit. Twenty unique peptides derived from 18 proproteins were identified, and they were involved in sugar signalling, protein metabolism and stress response. The quantitative analysis revealed 7 peptides with more than 2-fold upregulation, especially a 4.96-fold increase detected in the phytosulfokine (PSK) peptide. To further evaluate effects of PSK1 on fruit chilling tolerance, weight loss, firmness and internal browning were investigated in PSK1-treated loquat fruit at 0°C...
October 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28482090/p4p-a-peptidome-based-strain-level-genome-comparison-web-tool
#3
Aitor Blanco-Míguez, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez
Peptidome similarity analysis enables researchers to gain insights into differential peptide profiles, providing a robust tool to discriminate strain-specific peptides, true intra-species differences among biological replicates or even microorganism-phenotype variations. However, no in silico peptide fingerprinting software existed to facilitate such phylogeny inference. Hence, we developed the Peptidomes for Phylogenies (P4P) web tool, which enables the survey of similarities between microbial proteomes and simplifies the process of obtaining new biological insights into their phylogeny...
May 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28474961/urine-peptidomic-biomarkers-for-diagnosis-of-patients-with-systematic-lupus-erythematosus
#4
M Pejchinovski, J Siwy, W Mullen, H Mischak, M A Petri, L C Burkly, R Wei
Background Systematic lupus erythematosus (SLE) is characterized with various complications which can cause serious organ damage in the human body. Despite the significant improvements in disease management of SLE patients, the non-invasive diagnosis is entirely missing. In this study, we used urinary peptidomic biomarkers for early diagnosis of disease onset to improve patient risk stratification, vital for effective drug treatment. Methods Urine samples from patients with SLE, lupus nephritis (LN) and healthy controls (HCs) were analyzed using capillary electrophoresis coupled to mass spectrometry (CE-MS) for state-of-the-art biomarker discovery...
January 1, 2017: Lupus
https://www.readbyqxmd.com/read/28473704/cancerpdf-a-repository-of-cancer-associated-peptidome-found-in-human-biofluids
#5
Sherry Bhalla, Ruchi Verma, Harpreet Kaur, Rajesh Kumar, Salman Sadullah Usmani, Suresh Sharma, Gajendra P S Raghava
CancerPDF (Cancer Peptidome Database of bioFluids) is a comprehensive database of endogenous peptides detected in the human biofluids. The peptidome patterns reflect the synthesis, processing and degradation of proteins in the tissue environment and therefore can act as a gold mine to probe the peptide-based cancer biomarkers. Although an extensive data on cancer peptidome has been generated in the recent years, lack of a comprehensive resource restrains the facility to query the growing community knowledge...
May 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28460924/a-peptidomic-approach-for-the-identification-of-antioxidant-and-ace-inhibitory-peptides-in-sardinelle-protein-hydrolysates-fermented-by-bacillus-subtilis-a26-and-bacillus-amyloliquefaciens-an6
#6
Ines Jemil, Leticia Mora, Rim Nasri, Ola Abdelhedi, Maria-Concepción Aristoy, Mohamed Hajji, Moncef Nasri, Fidel Toldrá
Antioxidant and angiotensin I-converting enzyme (ACE)-inhibitory activities of sardinelle (Sardinella aurita) protein hydrolysates (SPHs) obtained by fermentation with Bacillus subtilis A26 (SPH-A26) and Bacillus amyloliquefaciens An6 (SPH-An6) were investigated. Both hydrolysates showed dose-dependent antioxidant activities evaluated using various in vitro antioxidant assays. Further, they were found to exhibit ACE-inhibitory activity. Peptides from SPH-A26 and SPH-An6 were analyzed by nESI-LC-MS/MS and approximately 800 peptides were identified...
November 2016: Food Research International
https://www.readbyqxmd.com/read/28456018/unique-features-in-the-presentation-of-insulin-epitopes-in-autoimmune-diabetes-an-update
#7
REVIEW
Xiaoxiao Wan, Emil R Unanue
Although an autoimmune disease involves diverse self-antigens, the initiation stage may require recognition of a limited number. This concept is verified in the non-obese diabetic (NOD) mouse model of autoimmune diabetes, in which strong evidence points to insulin as the prime antigen. The NOD mouse bears the I-A(g7) class II-MHC molecules (MHCII) that share common biochemical features and peptidome selection with the human diabetes-susceptible HLA-DQ8. Furthermore, both NOD mice and patients with type 1 diabetes (T1D) display an early appearance of insulin autoantibodies (IAAs) and subsequent insulin-reactive T cell infiltration into the islets...
April 26, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28453489/changes-of-cerebrospinal-fluid-peptides-due-to-tauopathy
#8
Petra Majerova, Peter Barath, Alena Michalicova, Stanislav Katina, Michal Novak, Andrej Kovac
Alzheimer's disease (AD) and progressive supranuclear palsy are two common neurodegenerative tauopathies, and the most common cause of progressive brain dementia in elderly affecting more than 35 million people. The tauopathies are characterized by abnormal deposition of microtubule associated protein tau into intracellular neurofibrillary tangles composed mainly of the hyperphosphorylated form of the protein. The diagnosis of tauopathies is based on the presence of clinical features and pathological changes...
2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28446606/the-beh%C3%A3-et-s-disease-associated-variant-of-the-aminopeptidase-erap1-shapes-a-low-affinity-hla-b-51-peptidome-by-differential-subpeptidome-processing
#9
Pablo Guasp, Eilon Barnea, M Francisca González-Escribano, Anaïs Jiménez-Reinoso, José R Regueiro, Arie Admon, José A López de Castro
A low activity variant of endoplasmic reticulum aminopeptidase 1 (ERAP1), Hap10, is associated with the autoinflammatory Behcet s disease (BD) in epistasis with HLA-B*51, which is the main risk factor for this disorder. The role of Hap10 in BD pathogenesis is unknown. We sought to define the effects of Hap10 on the HLA-B*51 peptidome and to distinguish these effects from those due to HLA-B*51 polymorphisms unrelated to disease. The peptidome of the BD-associated HLA-B*51:08 subtype expressed in a Hap10-positive cell line was isolated, characterized by mass spectrometry, and compared with the HLA-B*51:01 peptidome from cells expressing more active ERAP1 allotypes...
April 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28438560/longitudinal-investigation-of-salivary-proteomic-profiles-in-the-development-of-early-childhood-caries
#10
Shuang Ao, Xiangyu Sun, Xiangru Shi, Xin Huang, Feng Chen, Shuguo Zheng
OBJECTIVES: To investigate differentially expressed salivary peptides in the development of early childhood caries (ECC) in 3-4 year-old children. MATERIALS AND METHODS: Eighty-two caries-free children at baseline were followed-up for 1year, during which period 15 of them had developed ECC (Group C), whilst another 15 cases out of the 31 individuals who remained healthy were marked as Group H. Stimulated whole saliva samples were collected at 0, 6 and 12 months, and analyzed using weak cation exchange magnetic beads combined with matrix assisted laser desorption/ionization time-of-flight mass spectrometry...
April 22, 2017: Journal of Dentistry
https://www.readbyqxmd.com/read/28435107/wasp-venomic-unravelling-the-toxins-arsenal-of-polybia-paulista-venom-and-its-potential-pharmaceutical-applications
#11
REVIEW
Amilcar Perez-Riverol, José Roberto Aparecido Dos Santos-Pinto, Alexis Musacchio Lasa, Mario Sergio Palma, Márcia Regina Brochetto-Braga
Polybia paulista (Hymenoptera: Vespidae) is a neotropical social wasp from southeast Brazil. As most social Hymenoptera, venom from P. paulista comprises a complex mixture of bioactive toxins ranging from low molecular weight compounds to peptides and proteins. Several efforts have been made to elucidate the molecular composition of the P. paulista venom. Data derived from proteomic, peptidomic and allergomic analyses has enhanced our understanding of the whole envenoming process caused by the insect sting...
April 19, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28430386/peptidome-analysis-of-human-serum-from-normal-and-preeclamptic-pregnancies
#12
Xiaonan Dai, Xuejing Song, Can Rui, Li Meng, Xuan Xue, Hongjuan Ding, Rong Shen, Jun Li, Jingyun Li, Yuanqing Lu, Wei Long
Preeclampsia is a kind of disease that severely harms the health of pregnant women and infants. To better understand the molecular mechanisms involved in preeclampsia, we used liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) to construct a comparative peptidomic profiling of human serum between normal and preeclamptic pregnancies. A total of 201 peptides were confidently identified, with 21 up-regulated and 3 down-regulated. Further analysis indicated that these differentially expressed peptides correlate with enzyme regulator activity, biological regulation, and coagulation cascades occurring during pathological changes of preeclampsia...
April 21, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28424255/analysis-of-milk-from-mothers-who-delivered-prematurely-reveals-few-changes-in-proteases-and-protease-inhibitors-across-gestational-age-at-birth-and-infant-postnatal-age
#13
Veronique Demers-Mathieu, Søren Drud Nielsen, Mark A Underwood, Robyn Borghese, David C Dallas
Background: Peptidomics research has demonstrated that protease activity is higher in breast milk from preterm-delivering mothers than from term-delivering mothers. However, to our knowledge, the effect of the degree of prematurity and postnatal age on proteases and protease inhibitors in human milk remains unknown.Objective: We aimed to determine the change of proteases and protease inhibitors in milk from mothers who delivered prematurely across gestational age (GA) and postnatal age.Methods: Milk samples were collected from 18 mothers aged 26-40 y who delivered preterm infants and who lacked mastitis...
April 19, 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28407976/peptidomics-as-a-tool-for-characterizing-bioactive-milk-peptides
#14
Jasminka Giacometti, Alena Buretić-Tomljanović
Food peptidomics is a sub-field of proteomics that focuses on the composition, interactions, and properties of bioactive peptides present in different food matrices. The milk peptidome is considered a valuable source of a number of biologically active peptides. Increasing use of peptidomic techniques-including the application of high-resolution techniques, such as mass spectrometry-has led to enhancements of our knowledge regarding the health benefits of dairy products, as well as improved monitoring for food control and food safety...
September 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28407089/gibbscluster-unsupervised-clustering-and-alignment-of-peptide-sequences
#15
Massimo Andreatta, Bruno Alvarez, Morten Nielsen
Receptor interactions with short linear peptide fragments (ligands) are at the base of many biological signaling processes. Conserved and information-rich amino acid patterns, commonly called sequence motifs, shape and regulate these interactions. Because of the properties of a receptor-ligand system or of the assay used to interrogate it, experimental data often contain multiple sequence motifs. GibbsCluster is a powerful tool for unsupervised motif discovery because it can simultaneously cluster and align peptide data...
April 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28396735/clinical-proteomics-in-kidney-disease-as-an-exponential-technology-heading-towards-the-disruptive-phase
#16
Maria Dolores Sanchez-Niño, Ana B Sanz, Adrian M Ramos, Beatriz Fernandez-Fernandez, Alberto Ortiz
Exponential technologies double in power or processing speed every year, whereas their cost halves. Deception and disruption are two key stages in the development of exponential technologies. Deception occurs when, after initial introduction, technologies are dismissed as irrelevant, while they continue to progress, perhaps not as fast or with so many immediate practical applications as initially thought. Twenty years after the first publications, clinical proteomics is still not available in most hospitals and some clinicians have felt deception at unfulfilled promises...
April 2017: Clinical Kidney Journal
https://www.readbyqxmd.com/read/28368494/multi-omics-based-identification-of-specific-biochemical-changes-associated-with-pfkelch13-mutant-artemisinin-resistant-plasmodium-falciparum
#17
Ghizal Siddiqui, Anubhav Srivastava, Adrian S Russell, Darren J Creek
Background.: The emergence of artemisinin resistance in the malaria parasite, Plasmodium falciparum, poses a major threat to the control and elimination of malaria. Certain point mutations in the propeller domain of PfKelch13 are associated with resistance, but PfKelch13 mutations do not always result in clinical resistance. The underlying mechanisms associated with artemisinin resistance are poorly understood and the impact of PfKelch13 mutations on cellular biochemistry is not defined...
March 27, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28367149/major-histocompatibility-complex-mhc-class-i-and-mhc-class-ii-proteins-conformational-plasticity-in-antigen-presentation
#18
REVIEW
Marek Wieczorek, Esam T Abualrous, Jana Sticht, Miguel Álvaro-Benito, Sebastian Stolzenberg, Frank Noé, Christian Freund
Antigen presentation by major histocompatibility complex (MHC) proteins is essential for adaptive immunity. Prior to presentation, peptides need to be generated from proteins that are either produced by the cell's own translational machinery or that are funneled into the endo-lysosomal vesicular system. The prolonged interaction between a T cell receptor and specific pMHC complexes, after an extensive search process in secondary lymphatic organs, eventually triggers T cells to proliferate and to mount a specific cellular immune response...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28362475/the-genetic-basis-of-obesity-complications
#19
Katarzyna Skrypnik, Joanna Suliburska, Damian Skrypnik, Łukasz Pilarski, Julita Reguła, Paweł Bogdański
Intensive research is currently being performed into the genetic background of excess body mass compli- cations such as diabetes, cardiovascular disorders, especially atherosclerosis and coronary heart disease. Chronic inflammation is an important process in the pathogenesis of obesity, wherein there is an aberrant ex- pression of genes encoding adipokines. Visceral tissue is characterized by a higher expression and secretion of interleukin-8, interleukin-1ß and plasminogen activator inhibitor 1 in the subcutaneous tissue secretion of leptin prevails...
January 2017: Acta Scientiarum Polonorum. Technologia Alimentaria
https://www.readbyqxmd.com/read/28356487/a-structural-and-functional-analogue-of-a-bowman-birk-type-protease-inhibitor-from-odorrana-schmackeri
#20
Yuxin Wu, Qilin Long, Ying Xu, Shaodong Guo, Tianbao Chen, Lei Wang, Mei Zhou, Yingqi Zhang, Chris Shaw, Brian Walker
Frog skin secretions contain complex peptidomes and peptidic protease inhibitors that are one of the biologically and structurally described groups of components. In the present study, by use of molecular 'shotgun' cloning and LC MS/MS fractionation sequencing, a novel Bowman-Birk-type heptadecapeptide (AALKGCWTKSIPPKPCF-amide), named Odorrana schmackeriTrypsin Inhibitor (OSTI), with a canonical Cys(6)-Cys(16) disulfide bridge, was isolated and identified in piebald odorous frog (O. schmackeri) skin secretion...
April 30, 2017: Bioscience Reports
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