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peptide microarrays

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https://www.readbyqxmd.com/read/27929733/antibody-repertoire-profiling-with-mimotope-arrays
#1
Shina Pashova, Christoph Schneider, Stephan von Gunten, Anastas Pashov
Large-scale profiling and monitoring of antibody repertoires is possible through next generation sequencing (NGS), phage display libraries and microarrays. These methods can be combined in a pipeline, which ultimately maps the antibody reactivities onto defined arrays of structures - peptides or carbohydrates. The arrays can help analyze the individual specificities or can be used as complex patterns. In any case, the targets recognized should formally be considered mimotopes unless they are proven to be epitopes driving the antibody synthesis...
December 8, 2016: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/27919444/mechanistic-genomic-and-proteomic-study-on-the-effects-of-bisgma-derived-biodegradation-product-on-cariogenic-bacteria
#2
Lida Sadeghinejad, Dennis G Cvitkovitch, Walter L Siqueira, Justin Merritt, J Paul Santerre, Yoav Finer
OBJECTIVES: Investigate the effects of a Bis-phenyl-glycidyl-dimethacrylate (BisGMA) biodegradation product, bishydroxypropoxyphenyl-propane (BisHPPP), on gene expression and protein synthesis of cariogenic bacteria. METHODS: Quantitative real-time polymerase chain reaction was used to investigate the effects of BisHPPP on the expression of specific virulence-associated genes, i.e. gtfB, gtfC, gbpB, comC, comD, comE and atpH in Streptococcus mutans UA159. Possible mechanisms for bacterial response to BisHPPP were explored using gene knock-out and associated complemented strains of the signal peptide encoding gene, comC...
December 2, 2016: Dental Materials: Official Publication of the Academy of Dental Materials
https://www.readbyqxmd.com/read/27908274/a-novel-approach-to-probe-host-pathogen-interactions-of-bovine-digital-dermatitis-a-model-of-a-complex-polymicrobial-infection
#3
Paolo Marcatili, Martin W Nielsen, Thomas Sicheritz-Pontén, Tim K Jensen, Claus Schafer-Nielsen, Mette Boye, Morten Nielsen, Kirstine Klitgaard
BACKGROUND: Polymicrobial infections represent a great challenge for the clarification of disease etiology and the development of comprehensive diagnostic or therapeutic tools, particularly for fastidious and difficult-to-cultivate bacteria. Using bovine digital dermatitis (DD) as a disease model, we introduce a novel strategy to study the pathogenesis of complex infections. RESULTS: The strategy combines meta-transcriptomics with high-density peptide-microarray technology to screen for in vivo-expressed microbial genes and the host antibody response at the site of infection...
December 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27906504/combination-of-two-epitope-identification-techniques-enables-the-rational-design-of-soy-allergen-gly-m-4-mutants
#4
Heide Havenith, Karolin Kern, Paul Rautenberger, Holger Spiegel, Michael Szardenings, Elke Ueberham, Jörg Lehmann, Matthias Buntru, Simon Vogel, Regina Treudler, Rainer Fischer, Stefan Schillberg
BACKGROUND: Detailed IgE-binding epitope analysis is a key requirement for the understanding and development of diagnostic and therapeutic agents to address food allergies. METHODS: We combined an IgE-specific linear peptide microarray with random phage peptide display for the high-resolution mapping of IgE-binding epitopes of the major soybean allergen Gly m 4, which is a homologue to the birch pollen allergen Bet v1. RESULTS: Three epitopes were identified and mapped to a resolution of four key amino acids, allowing the rational design and the production of three Gly m 4 mutants with the aim to abolish or reduce the binding of epitope-specific IgE...
December 1, 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/27890856/sirna-cell-penetrating-peptides-complexes-as-a-combinatorial-therapy-against-chronic-myeloid-leukemia-using-bv173-cell-line-as-model
#5
João Miguel Freire, Inês Rego de Figueiredo, Javier Valle, Ana Salomé Veiga, David Andreu, Francisco J Enguita, Miguel A R B Castanho
Chronic myeloid leukemia (CML) is a myeloproliferative disorder caused by a single gene mutation, a reciprocal translocation that originates the Bcr-Abl gene with constitutive tyrosine kinase activity. As a monogenic disease, it is an optimum target for RNA silencing therapy. We developed a siRNA-based therapeutic approach in which the siRNA is delivered by pepM or pepR, two cell-penetrating peptides (CPPs) derived from the dengue virus capsid protein. These peptides have a dual role: siRNA delivery into cells and direct action as bioportides, i...
November 24, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/27873207/profiling-phosphopeptide-binding-domain-recognition-specificity-using-peptide-microarrays
#6
Michele Tinti, Simona Panni, Gianni Cesareni
Cellular organization and response to internal and external stimuli are mediated by an intricate web of protein interactions. Some of these interactions are regulated by covalent posttranslational modifications such as phosphorylation and acetylation. These modifications can change the chemical nature of the interaction interfaces and modulate the binding affinity of the interacting partners. In signal transduction, the most frequent modification is reversible phosphorylation of tyrosine, serine or threonine residues...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27873205/protein-protein-interaction-inhibitors-of-brca1-discovered-using-small-molecule-microarrays
#7
Zhenkun Na, Sijun Pan, Mahesh Uttamchandani, Shao Q Yao
Microarray screening technology has transformed the life sciences arena over the last decade. The platform is widely used in the area of mapping interaction networks, to molecular fingerprinting and small molecular inhibitor discovery. The technique has significantly impacted both basic and applied research. The microarray platform can likewise enable high-throughput screening and discovery of protein-protein interaction (PPI) inhibitors. Herein we demonstrate the application of microarray-guided PPI inhibitor discovery, using human BRCA1 as an example...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27867751/t7-phage-display-library-a-promising-strategy-to-detect-tuberculosis-specific-biomarkers
#8
Harvinder Talwar, Jaya Talreja, Lobelia Samavati
One-third of the world's population is infected with tuberculosis, only 10% will develop active disease and the remaining 90% is considered to have latent TB (LTB). While active TB is contagious and can be lethal, the LTB can evolve to active TB. The diagnosis of TB can be challenging, especially in the early stages, due to the variability in presentation and nonspecific signs and symptoms. Currently, we have limited tools available to diagnose active TB, predict treatment efficacy and cure of active tuberculosis, the reactivation of latent tuberculosis infection, and the induction of protective immune responses through vaccination...
June 2016: Mycobacterial Diseases: Tuberculosis & Leprosy
https://www.readbyqxmd.com/read/27865268/epitope-mapping-of-campylobacter-jejuni-flagellar-capping-protein-flid-by-chicken-gallus-gallus-domesticus-sera
#9
Hung-Yueh Yeh, Arife Ezgi Telli, Jarra F Jagne, Christopher L Benson, Kelli L Hiett, John E Line
Campylobacter jejuni, a Gram-negative rod, is a zoonotic pathogen associated with human acute bacterial gastroenteritis worldwide. The flagellum, composed of more than 35 proteins, is responsible for colonization of C. jejuni in the host gastrointestinal tract as well as inducing protective antibodies against the homologous serotype. In our previous study, we demonstrated that the flagellar capping protein (FliD) is an immunodominant protein that reacted strongly to sera from field chickens. In this communication, we mapped linear immunoreactive epitopes on FliD using a set of 158 synthetic peptides of 15-mer overlapping with 11 amino acid residues on peptide microarrays with sera from field chickens...
December 2016: Comparative Immunology, Microbiology and Infectious Diseases
https://www.readbyqxmd.com/read/27864322/e-coli-proteome-microarrays-identified-the-substrates-of-clpyq-protease
#10
Chih-Hsuan Tsai, Yu-Hsuan Ho, Tzu-Cheng Sung, Whei-Fen Wu, Chien-Sheng Chen
Proteolysis is a vital mechanism to regulate the cellular proteome in all kingdoms of life, and ATP-dependent proteases play a crucial role within this process. In Escherichia coli, ClpYQ is one of the primary ATP-dependent proteases. In addition to function with removals of abnormal peptides in the cells, ClpYQ degrades regulatory proteins if necessary and thus let cells adjust to various environmental conditions. In E. coli, SulA, RcsA, RpoH and TraJ as well as RNase R, have been identified as natural protein substrates of ClpYQ...
November 18, 2016: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/27858316/clinical-outcomes-linked-to%C3%A2-expression%C3%A2-of-gene-subsets-for-protein-hormones-and-their-cognate-receptors-from-lcm-procured-breast%C3%A2-carcinoma-cells
#11
Michael W Daniels, Guy N Brock, James L Wittliff
PURPOSE: Certain peptide hormones and/or their cognate receptors influencing normal cellular pathways also have been detected in breast cancers. The hypothesis is that gene subsets of these regulatory molecules predict risk of breast carcinoma recurrence in patients with primary disease. METHODS: Gene expression levels of 61 hormones and 81 receptors were determined by microarray with LCM-procured carcinoma cells of 247 de-identified biopsies. Univariable and multivariable Cox regressions were determined using expression levels of each hormone/receptor gene, individually or as a pair...
November 17, 2016: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/27836618/a-new-classification-method-for-maldi-imaging-mass-spectrometry-data-acquired-on-formalin-fixed-paraffin-embedded-tissue-samples
#12
Tobias Boskamp, Delf Lachmund, Janina Oetjen, Yovany Cordero Hernandez, Dennis Trede, Peter Maass, Rita Casadonte, Jörg Kriegsmann, Arne Warth, Hendrik Dienemann, Wilko Weichert, Mark Kriegsmann
Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) shows a high potential for applications in histopathological diagnosis, and in particular for supporting tumor typing and subtyping. The development of such applications requires the extraction of spectral fingerprints that are relevant for the given tissue and the identification of biomarkers associated with these spectral patterns. We propose a novel data analysis method based on the extraction of characteristic spectral patterns (CSPs) that allow automated generation of classification models for spectral data...
November 9, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27824137/highly-sensitive-dual-mode-electrochemical-platform-for-microrna-detection
#13
Pawan Jolly, Marina R Batistuti, Anna Miodek, Pavel Zhurauski, Marcelo Mulato, Mark A Lindsay, Pedro Estrela
MicroRNAs (miRNAs) play crucial regulatory roles in various human diseases including cancer, making them promising biomarkers. However, given the low levels of miRNAs present in blood, their use as cancer biomarkers requires the development of simple and effective analytical methods. Herein, we report the development of a highly sensitive dual mode electrochemical platform for the detection of microRNAs. The platform was developed using peptide nucleic acids as probes on gold electrode surfaces to capture target miRNAs...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27824133/high-throughput-immuno-profiling-of-mamba-dendroaspis-venom-toxin-epitopes-using-high-density-peptide-microarrays
#14
Mikael Engmark, Mikael R Andersen, Andreas H Laustsen, Jigar Patel, Eric Sullivan, Federico de Masi, Christian S Hansen, Jens V Kringelum, Bruno Lomonte, José María Gutiérrez, Ole Lund
Snakebite envenoming is a serious condition requiring medical attention and administration of antivenom. Current antivenoms are antibody preparations obtained from the plasma of animals immunised with whole venom(s) and contain antibodies against snake venom toxins, but also against other antigens. In order to better understand the molecular interactions between antivenom antibodies and epitopes on snake venom toxins, a high-throughput immuno-profiling study on all manually curated toxins from Dendroaspis species and selected African Naja species was performed based on custom-made high-density peptide microarrays displaying linear toxin fragments...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27805868/ovariectomy-alters-gene-expression-of-the-hippocampal-formation-in-middle-aged-rats
#15
Miklós Sárvári, Imre Kalló, Erik Hrabovszky, Norbert Solymosi, Zsolt Liposits
Ovarian hormones regulate the transcriptome of the hippocampus and modulate its functions. During menopause this complex signaling declines, leading to impaired learning and memory. This study was undertaken to clarify the effects of long-term, surgical ovariectomy (OVX) on the rat hippocampal transcriptome. At age of 13 months, intact control and ovariectomized groups were formed. All animals were sacrificed 5 weeks after gonadectomy, hippocampal formations were dissected and processed for transcriptome analysis...
November 2, 2016: Endocrinology
https://www.readbyqxmd.com/read/27784647/annexin-a2-and-alpha-actinin-4-expression-correlates-with-metastatic-potential-of-primary-endometrial-cancer
#16
Parul Mittal, Manuela Klingler-Hoffmann, Georgia Arentz, Lyron Winderbaum, Gurjeet Kaur, Lyndal Anderson, James Scurry, Yee Leung, Colin Jr Stewart, Jonathan Carter, Peter Hoffmann, Martin K Oehler
The prediction of lymph node metastasis using clinic-pathological data and molecular information from endometrial cancers lacks accuracy and is therefore currently not routinely used in patient management. Consequently, although only a small percentage of patients with endometrial cancers suffer from metastasis, the majority undergo radical surgery including removal of pelvic lymph nodes. Upon analysis of publically available data and published research, we compiled a list of 60 proteins having the potential to display differential abundance between primary endometrial cancers with versus those without lymph node metastasis...
October 23, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27782803/co-activator-candidate-interactions-for-orphan-nuclear-receptor-nr2e1
#17
Ximena Corso-Díaz, Charles N de Leeuw, Vivian Alonso, Diana Melchers, Bibiana K Y Wong, René Houtman, Elizabeth M Simpson
BACKGROUND: NR2E1 (Tlx) is an orphan nuclear receptor that regulates the maintenance and self-renewal of neural stem cells, and promotes tumourigenesis. Nr2e1-null mice exhibit reduced cortical and limbic structures and pronounced retinal dystrophy. NR2E1 functions mainly as a repressor of gene transcription in association with the co-repressors atrophin-1, LSD1, HDAC and BCL11A. Recent evidence suggests that NR2E1 also acts as an activator of gene transcription. However, co-activator complexes that interact with NR2E1 have not yet been identified...
October 26, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27767002/experience-with-rapid-microarray-based-diagnostic-technology-and-antimicrobial-stewardship-for-patients-with-gram-positive-bacteremia
#18
Elizabeth A Neuner, Andrea M Pallotta, Simon W Lam, David Stowe, Steven M Gordon, Gary W Procop, Sandra S Richter
OBJECTIVE To describe the impact of rapid diagnostic microarray technology and antimicrobial stewardship for patients with Gram-positive blood cultures. DESIGN Retrospective pre-intervention/post-intervention study. SETTING A 1,200-bed academic medical center. PATIENTS Inpatients with blood cultures positive for Staphylococcus aureus, Enterococcus faecalis, E. faecium, Streptococcus pneumoniae, S. pyogenes, S. agalactiae, S. anginosus, Streptococcus spp., and Listeria monocytogenes during the 6 months before and after implementation of Verigene Gram-positive blood culture microarray (BC-GP) with an antimicrobial stewardship intervention...
November 2016: Infection Control and Hospital Epidemiology
https://www.readbyqxmd.com/read/27764126/upregulation-of-hla-expression-in-primary-uveal-melanoma-by-infiltrating-leukocytes
#19
T Huibertus van Essen, Sake I van Pelt, Inge H G Bronkhorst, Mieke Versluis, Fariba Némati, Cécile Laurent, Gregorius P M Luyten, Thorbald van Hall, Peter J van den Elsen, Pieter A van der Velden, Didier Decaudin, Martine J Jager
INTRODUCTION: Uveal melanoma (UM) with an inflammatory phenotype, characterized by infiltrating leukocytes and increased human leukocyte antigen (HLA) expression, carry an increased risk of death due to metastases. These tumors should be ideal for T-cell based therapies, yet it is not clear why prognostically-infaust tumors have a high HLA expression. We set out to determine whether the level of HLA molecules in UM is associated with other genetic factors, HLA transcriptional regulators, or microenvironmental factors...
2016: PloS One
https://www.readbyqxmd.com/read/27754384/metabolomic-profiling-of-the-effects-of-melittin-on-cisplatin-resistant-and-cisplatin-sensitive-ovarian-cancer-cells-using-mass-spectrometry-and-biolog-microarray-technology
#20
Sanad Alonezi, Jonans Tusiimire, Jennifer Wallace, Mark J Dufton, John A Parkinson, Louise C Young, Carol J Clements, Jin Kyu Park, Jong Woon Jeon, Valerie A Ferro, David G Watson
In the present study, liquid chromatography-mass spectrometry (LC-MS) was employed to characterise the metabolic profiles of two human ovarian cancer cell lines A2780 (cisplatin-sensitive) and A2780CR (cisplatin-resistant) in response to their exposure to melittin, a cytotoxic peptide from bee venom. In addition, the metabolomics data were supported by application of Biolog microarray technology to examine the utilisation of carbon sources by the two cell lines. Data extraction with MZmine 2.14 and database searching were applied to provide metabolite lists...
October 13, 2016: Metabolites
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