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https://www.readbyqxmd.com/read/28306751/peptidomic-and-transcriptomic-profiling-of-four-distinct-spider-venoms
#1
Vera Oldrati, Dominique Koua, Pierre-Marie Allard, Nicolas Hulo, Miriam Arrell, Wolfgang Nentwig, Frédérique Lisacek, Jean-Luc Wolfender, Lucia Kuhn-Nentwig, Reto Stöcklin
Venom based research is exploited to find novel candidates for the development of innovative pharmacological tools, drug candidates and new ingredients for cosmetic and agrochemical industries. Moreover, venomics, as a well-established approach in systems biology, helps to elucidate the genetic mechanisms of the production of such a great molecular biodiversity. Today the advances made in the proteomics, transcriptomics and bioinformatics fields, favor venomics, allowing the in depth study of complex matrices and the elucidation even of minor compounds present in minute biological samples...
2017: PloS One
https://www.readbyqxmd.com/read/28304193/peptidomic-analysis-of-fetal-heart-tissue-for-identification-of-endogenous-peptides-involved-in-tetralogy-of-fallot
#2
Jingjing Zhang, Dong Liang, Qing Cheng, Li Cao, Yun Wu, Yan Wang, Shuping Han, Zhangbin Yu, Xianwei Cui, Tianhui Xu, Dingyuan Ma, Ping Hu, Zhengfeng Xu
Tetralogy of fallot (TOF) is one of the most prevalent types of congenital heart diseases. As a category of bioactive molecules, peptides have been proved to participate in various biological processes. However, the role of endogenous peptides in the pathogenesis of TOF has not been studied. In this study, we performed a comparative peptidomic profile in the fetal heart of TOF and the control group for the first time by liquid chromatography-tandem mass spectrometry. Our data demonstrated that a total of 201 peptides derived from 176 precursor proteins were differentially expressed in the heart tissues of TOF fetuses compared with normal controls, including 41 upregulated peptides and 160 downregulated peptides...
March 17, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28289514/modern-trends-in-animal-venom-research-omics-and-nanomaterials
#3
EDITORIAL
Yuri N Utkin
Animal venom research is a specialized investigation field, in which a number of different methods are used and this array is constantly expanding. Thus, recently emerged omics and nanotechnologies have already been successfully applied to venom research. Animal venoms have been studied for quite a long time. The traditional reductionist approach has been to isolate individual toxins and then study their structure and function. Unfortunately, the characterization of the venom as a whole system and its multiple effects on an entire organism were not possible until recent times...
February 26, 2017: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28254676/unveiling-antimicrobial-peptide-generating-human-proteases-using-proteasix
#4
Paulo Bastos, Fábio Trindade, Rita Ferreira, Mercedes Arguello Casteleiro, Robert Stevens, Julie Klein, Rui Vitorino
Extracting information from peptidomics data is a major current challenge, as endogenous peptides can result from the activity of multiple enzymes. Proteolytic enzymes can display overlapping or complementary specificity. The activity spectrum of human endogenous peptide-generating proteases is not fully known. Hence, the indirect study of proteolytic enzymes through the analysis of its substrates is largely hampered. Antimicrobial peptides (AMPs) represent a primordial set of immune defense molecules generated by proteolytic cleavage of precursor proteins...
February 27, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28228285/mass-spectrometry-profiling-of-hla-associated-peptidomes-in-mono-allelic-cells-enables-more-accurate-epitope-prediction
#5
Jennifer G Abelin, Derin B Keskin, Siranush Sarkizova, Christina R Hartigan, Wandi Zhang, John Sidney, Jonathan Stevens, William Lane, Guang Lan Zhang, Thomas M Eisenhaure, Karl R Clauser, Nir Hacohen, Michael S Rooney, Steven A Carr, Catherine J Wu
Identification of human leukocyte antigen (HLA)-bound peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS) is poised to provide a deep understanding of rules underlying antigen presentation. However, a key obstacle is the ambiguity that arises from the co-expression of multiple HLA alleles. Here, we have implemented a scalable mono-allelic strategy for profiling the HLA peptidome. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing an application-specific spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles...
February 21, 2017: Immunity
https://www.readbyqxmd.com/read/28198139/peptidomics-analysis-of-transient-regeneration-in-the-neonatal-mouse-heart
#6
Yi Fan, Qijun Zhang, Hua Li, Zijie Cheng, Xing Li, Yumei Chen, Yahui Shen, Guixian Song, Lingmei Qian
Neonatal mouse hearts have completely regenerative capability after birth, but the ability to regenerate rapidly lost after 7 days, the mechanism has not been clarified. Previous studies have shown that mRNA profile of adult mouse changed greatly compared to neonatal mouse. So far, there is no research of peptidomics related to heart regeneration. In order to explore the changes of proteins, enzymes and peptides related to the transient regeneration, we used comparative petidomics technique to compare the endogenous peptides in the mouse heart of postnatal 1 and 7 days...
February 15, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28188862/the-ascites-n-glycome-of-epithelial-ovarian-cancer-patients
#7
Karina Biskup, Elena I Braicu, Jalid Sehouli, Rudolf Tauber, Véronique Blanchard
Epithelial ovarian cancer (EOC) is worldwide the sixth most lethal form of cancer occurring in women. More than one third of ovarian patients have ascites at the time of diagnosis and almost all of them have it when recurrence occurs. Although its effect on tumor cell microenvironment remains poorly understood, its presence is correlated with bad diagnosis. In previous studies, we proposed a novel glycan-based biomarker for the diagnosis of EOC, which showed an improved sensitivity and specificity at any stage of the disease and an improved discrimination between malignant and benign ovarian tumors...
March 22, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28188227/the-hla-b27-peptidome-in-vivo-in-spondyloarthritis-susceptible-hla-b27-transgenic-rats-and-the-effect-of-erap1-deletion
#8
Eilon Barnea, Dganit Melamed Kadosh, Yael Haimovich, Nimman Satumtira, Martha L Dorris, Mylinh T Nguyen, Robert E Hammer, Tri M Tran, Robert A Colbert, Joel D Taurog, Arie Admon
HLA-B27 is a class I major histocompatibility (MHC-I) allele that confers susceptibility to the rheumatic disease ankylosing spondylitis (AS) by an unknown mechanism. ERAP1 is an aminopeptidase that trims peptides in the endoplasmic reticulum for binding to MHC-I molecules. ERAP1 shows genetic epistasis with HLA-B27 in conferring susceptibility to AS. Male HLA-B27 transgenic rats develop arthritis and serve as an animal model of AS, whereas female B27 transgenic rats remain healthy. We used large-scale quantitative mass-spectrometry to identify over 15,000 unique HLA-B27 peptide ligands, isolated after immunoaffinity purification of the B27 molecules from the spleens of HLA-B27 transgenic rats...
February 10, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28178587/top-down-hplc-esi-ms-proteomic-analysis-of-saliva-of-edentulous-subjects-evidenced-high-levels-of-cystatin-a-cystatin-b-and-sprr3
#9
Barbara Manconi, Barbara Liori, Tiziana Cabras, Federica Iavarone, Armando Manni, Irene Messana, Massimo Castagnola, Alessandra Olianas
OBJECTIVE: This study aims to analyze the salivary peptidome/proteome of edentulous subject with respect to dentate control subjects. DESIGN: Unstimulated whole saliva, collected from 11 edentulous subjects (age 60-76 years) and 11 dentate age-matched control subjects, was immediately treated with 0.2% aqueous trifluoroacetic acid and the acidic soluble fraction analyzed by High Performace Liquid Chromatography-Mass Spectrometry. The relative abundance of the salivary peptides/proteins was determined by measuring the area of the High Performace Liquid Chromatography-Mass Spectrometry eXtracted Ion Current peaks which is linearly proportional to peptide/protein concentration under identical experimental conditions...
January 31, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28159928/a-meta-analysis-of-hla-peptidome-composition-in-different-hematological-entities-entity-specific-dividing-lines-and-pan-leukemia-antigens
#10
Linus Backert, Daniel Johannes Kowalewski, Simon Walz, Heiko Schuster, Claudia Berlin, Marian Christoph Neidert, Mirle Schemionek, Tim H Brümmendorf, Vladan Vucinic, Dietger Niederwieser, Lothar Kanz, Helmut Rainer Salih, Oliver Kohlbacher, Katja Weisel, Hans-Georg Rammensee, Stefan StevanoviÄ, Juliane Sarah Walz
Hematological malignancies (HM) are highly amenable targets for immunotherapeutic intervention and may be effectively treated by antigen-specific T-cell based treatment. Recent studies demonstrate that physiologically occurring anti-cancer T-cell responses in certain HM entities target broadly presented non-mutated epitopes. HLA ligands are thus implied as prime targets for broadly applicable and antigen-specific off-the-shelf compounds. With the aim of assessing the presence of common targets shared among different HM which may enable addressing a larger patient collective we conducted a meta-analysis of 83 mass spectrometry-based HLA peptidome datasets (comprising 40,361 unique peptide identifications) across four major HM (19 AML, 16 CML, 35 CLL, and 13 MM/MCL samples) and investigated similarities and differences within the HLA presented antigenic landscape...
January 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28159781/insights-into-diabetic-kidney-disease-using-urinary-proteomics-and-bioinformatics
#11
Julie A D Van, James W Scholey, Ana Konvalinka
A number of proteomic and peptidomic analyses of urine from diabetic subjects have been published in the quest for a biomarker that predicts progression of nephropathy. Less attention has been paid to the relationships between urinary proteins and the underlying biological processes revealed by the analyses. In this review, we focus on the biological processes identified by studying urinary proteins and protein-protein interactions at each stage of diabetic nephropathy to provide an overview of the events underlying progression of kidney disease reflected in the urine...
February 3, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28135715/peptidomic-analysis-of-cultured-cardiomyocytes-exposed-to-acute-ischemic-hypoxia
#12
Lijie Wu, Hua Li, Xing Li, Yumei Chen, Qijun Zhang, Zijie Cheng, Yi Fan, Guixian Song, Lingmei Qian
BACKGROUND: Acute Myocardial Infarction (AMI) is a life-threatening cardiovascular disease involving disruption of blood flow to the heart, consequent tissue damage, and sometimes death. Peptidomics, an emerging branch of proteomics, has attracted wide attention. METHODS: A comparative peptidomic profiling was used to explore changes induced by acute ischemic-hypoxia in primary cultured neonatal rat myocardial cells. Analysis of six-plex tandem mass tag (TMT) labelled peptides was performed using nanoflow liquid chromatography coupled online with an LTQ-Orbitrap Velos mass spectrometer...
January 26, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28119961/palladium-modified-porous-silicon-as-multi-functional-maldi-chip-for-serum-peptide-detection
#13
Xiao Li, Xiaoming Chen, Jie Tan, Xiao Liang, Jianmin Wu
Interest in using mesoporous materials for peptidomic research has increased recently. The present study reports a new type of matrix assisted laser desorption/ionization (MALDI) plate derived from electrochemically etched porous silicon (PSi) whose surface was modified with palladium nanoparticles (PdNPs). Owing to the well-tailored pore size and the molecular filtration effect of the PSi, peptides in serum samples can be selectively captured and enriched in the pore channel, thereby eliminating the interference from large proteins in subsequent MALDI-MS detection...
January 25, 2017: Analyst
https://www.readbyqxmd.com/read/28118015/combined-peptidomic-and-proteomic-analysis-of-electrically-stimulated-and-manually-dissected-venom-from-the-south-american-bullet-ant-paraponera-clavata
#14
Samira R Aili, Axel Touchard, Frédéric Petitclerc, Alain Dejean, Jérôme Orivel, Matthew P Padula, Pierre Escoubas, Graham M Nicholson
Ants have evolved venoms rich in peptides and proteins used for predation, defense, and communication. However, they remain extremely understudied due to the minimal amount of venom secreted by each ant. The present study investigated the differences in the proteome and peptidome of the venom from the bullet ant, Paraponera clavata. Venom samples were collected from a single colony either by manual venom gland dissection or by electrical stimulation and were compared using proteomic methods. Venom proteins were separated by 2D-PAGE and identified by nanoLC-ESI-QTOF MS/MS...
January 31, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28117676/characterization-of-collagen-peptides-in-elaphuri-davidiani-cornu-aqueous-extract-with-proliferative-activity-on-osteoblasts-using-nano-liquid-chromatography-in-tandem-with-orbitrap-mass-spectrometry
#15
Yanjuan Zhai, Zhenhua Zhu, Yue Zhu, Dawei Qian, Rui Liu, Yunru Peng, Yuhua Ding, Zhen Ouyang, Jin-Ao Duan
First documented in Shennong Bencao Jing (about 200 B.C.-200 A.D.), Elaphuri Davidiani Cornu (EDC) has been recorded for its effects in strengthening bones and balancing other aspects of overall health for approximately 2000 years. In the present study, our aim was to investigate which are the components of the active EDC fraction by a peptidomic strategy. We explored the extent to which EDC increases the proliferation of osteoblasts by measuring the elevations in osteonectin and type I collagen mRNA levels and characterized it using nano-flow liquid chromatography in tandem with orbitrap mass spectrometry...
January 20, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28105928/computer-aided-identification-of-a-hevein-like-antimicrobial-peptide-of-bell-pepper-leaves-for-biotechnological-use
#16
Patrícia Dias Games, Elói Quintas Gonçalves daSilva, Meire de Oliveira Barbosa, Hebréia Oliveira Almeida-Souza, Patrícia Pereira Fontes, Marcos Jorge deMagalhães-Jr, Paulo Roberto Gomes Pereira, Maura Vianna Prates, Gloria Regina Franco, Alessandra Faria-Campos, Sérgio Vale Aguiar Campos, Maria Cristina Baracat-Pereira
BACKGROUND: Antimicrobial peptides from plants present mechanisms of action that are different from those of conventional defense agents. They are under-explored but have a potential as commercial antimicrobials. Bell pepper leaves ('Magali R') are discarded after harvesting the fruit and are sources of bioactive peptides. This work reports the isolation by peptidomics tools, and the identification and partially characterization by computational tools of an antimicrobial peptide from bell pepper leaves, and evidences the usefulness of records and the in silico analysis for the study of plant peptides aiming biotechnological uses...
December 15, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28095327/proteomic-and-peptidomic-analysis-of-human-sweat-with-emphasis-on-proteolysis
#17
Yijing Yu, Ioannis Prassas, Carla M J Muytjens, Eleftherios P Diamandis
Sweat is produced by eccrine and apocrine glands and represents a biological fluid with established roles in thermo-regulation and host infection defense. The composition of sweat is highly dynamic and alters significantly in various skin and other disorders. Therefore, in-depth profiling of sweat protein composition is expected to augment our understanding of the pathobiology of several skin diseases and may lead to the identification of useful sweat-based disease biomarkers. We here reported an in-depth analysis of the human sweat proteome and peptidome...
January 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28079125/establishment-of-a-integrative-multi-omics-expression-database-ckddb-in-the-context-of-chronic-kidney-disease-ckd
#18
Marco Fernandes, Holger Husi
Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28063628/separate-effects-of-the-ankylosing-spondylitis-associated-erap1-and-erap2-aminopeptidases-determine-the-influence-of-their-combined-phenotype-on-the-hla-b-27-peptidome
#19
Adrian Martín-Esteban, Alejandro Sanz-Bravo, Pablo Guasp, Eilon Barnea, Arie Admon, José A López de Castro
Ankylosing spondylitis (AS) is an inflammatory disease strongly associated with the Major Histocompatibility Complex class I (MHC-I) allotype HLA-B*27. The endoplasmic reticulum aminopeptidases (ERAP)1 and 2, which trim peptides to their optimal length for MHC-I binding, are also susceptibility factors for this disease. Both highly active ERAP1 variants and ERAP2 expression favor AS, whereas loss-of-function ERAP1 and loss-of-expression ERAP2 variants are protective. Yet, only ERAP1 is in epistasis with HLA-B*27...
January 4, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28060824/chronological-profiling-of-plasma-native-peptides-after-hepatectomy-in-pigs-toward-the-discovery-of-human-biomarkers-for-liver-regeneration
#20
Kohta Iguchi, Etsuro Hatano, Takashi Nirasawa, Noriyuki Iwasaki, Motohiko Sato, Gen Yamamoto, Kenya Yamanaka, Tatsuya Okamoto, Yosuke Kasai, Naohiko Nakamura, Hiroaki Fuji, Tomohito Sakai, Nobuto Kakuda, Satoru Seo, Kojiro Taura, Kei Tashiro, Shinji Uemoto, Masaya Ikegawa
Liver regeneration after partial hepatectomy (PHx) is a time-dependent process, which is tightly regulated by multiple signaling cascades. Failure of this complex process leads to posthepatectomy liver failure (PHLF), which is associated with a high rate of mortality. Thus, it is extremely important to establish a useful biomarker of liver regeneration to help prevent PHLF. Here, we hypothesized that alterations in the plasma peptide profile may predict liver regeneration following PHx and hence we set up a diagnostic platform for monitoring posthepatectomy outcome...
2017: PloS One
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