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peptide microarrays

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https://www.readbyqxmd.com/read/28212615/molecular-pathways-underlying-inhibitory-effect-of-antimicrobial-peptide-nal-p-113-on-bacteria-biofilms-formation-of-porphyromonas-gingivalis-w83-by-dna-microarray
#1
Hong-Yan Wang, Li Lin, Li-Si Tan, Hui-Yuan Yu, Jya-Wei Cheng, Ya-Ping Pan
BACKGROUND: Wound-related infection remains a major challenge for health professionals. One disadvantage in conventional antibiotics is their inability to penetrate biofilms, the main protective strategy for bacteria to evade irradiation. Previously, we have shown that synthetic antimicrobial peptides could inhibit bacterial biofilms formation. RESULTS: In this study, we first delineated how Nal-P-113, a novel antimicrobial peptide, exerted its inhibitory effects on Porphyromonas gingivalis W83 biofilms formation at a low concentration...
February 17, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28192214/immune-recognition-surface-construction-of-mycobacterium-tuberculosis-epitope-specific-antibody-responses-in-tuberculosis-patients-identified-by-peptide-microarrays
#2
REVIEW
Davide Valentini, Martin Rao, Giovanni Ferrara, Marc Perkins, Ernest Dodoo, Alimuddin Zumla, Markus Maeurer
BACKGROUND: Understanding of humoral immune responses in tuberculosis (TB) is gaining interest, since B-cells and antibodies may be important in diagnosis as well as protective immune responses. High-content peptide microarrays (HCPM) are highly precise and reliable for gauging specific antibody responses to pathogens, as well as autoantigens. METHODS: An HCPM comprising epitopes spanning 154 proteins of Mycobacterium tuberculosis was used to gauge specific IgG antibody responses in sera of TB patients from Africa and South America...
February 10, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28191734/integrative-proteomics-genomics-and-translational-immunology-approaches-reveal-mutated-forms-of-proteolipid-protein-1-plp1-and-mutant-specific-immune-response-in-multiple-sclerosis
#3
Veneta Qendro, Grace A Bugos, Debbie H Lundgren, John Glynn, May H Han, David K Han
In order to gain mechanistic insights into multiple sclerosis (MS) pathogenesis, we utilized a multi-dimensional approach to test the hypothesis that mutations in myelin proteins lead to immune activation and central nervous system autoimmunity in MS. Mass spectrometry-based proteomic analysis of human MS brain lesions revealed seven unique mutations of PLP1; a key myelin protein that is known to be destroyed in MS. Surprisingly, in-depth genomic analysis of two MS patients at the genomic DNA and mRNA confirmed mutated PLP1 in RNA, but not in the genomic DNA...
February 12, 2017: Proteomics
https://www.readbyqxmd.com/read/28181499/involvement-of-%C3%AE-defensin-130-defb130-in-the-macrophage-microbicidal-mechanisms-for-killing-plasmodium-falciparum
#4
Mohamad Alaa Terkawi, Ryo Takano, Atsushi Furukawa, Fumi Murakoshi, Kentaro Kato
Understanding the molecular defense mechanism of macrophages and identifying their effector molecules against malarial parasites may provide important clues for the discovery of new therapies. To analyze the immunological responses of malarial parasite-induced macrophages, we used DNA microarray technology to examine the gene profile of differentiated macrophages phagocytizing Plasmodium falciparum-parasitized erythrocytes (iRBC). The transcriptional gene profile of macrophages in response to iRBCs represented 168 down-regulated genes, which were mainly involved in the cellular immune response, and 216 upregulated genes, which were involved in cellular proteolysis, growth, and adhesion...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28161459/peptide-microarray-based-characterization-of-antibody-responses-to-host-proteins-after-bacille-calmette-gu%C3%A3-rin-vaccination
#5
REVIEW
Davide Valentini, Martin Rao, Lalit Rane, Sayma Rahman, Rebecca Axelsson-Robertson, Rainer Heuchel, Matthias Löhr, Daniel Hoft, Susanna Brighenti, Alimuddin Zumla, Markus Maeurer
BACKGROUND: Bacille Calmette-Guérin (BCG) is the world's most widely distributed vaccine, used against tuberculosis (TB), in cancer immunotherapy, and in autoimmune diseases due to its immunomodulatory properties. To date, the effect of BCG vaccination on antibody responses to host proteins has not been reported. High-content peptide microarrays (HCPM) offer a unique opportunity to gauge specific humoral immune responses. METHODS: The sera of BCG-vaccinated healthy adults were tested on a human HCPM platform (4953 randomly selected epitopes of human proteins) to detect specific immunoglobulin gamma (IgG) responses...
February 2, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28159576/humoral-immune-profiling-of-mycobacterial-antigen-recognition-in-sarcoidosis-and-l%C3%A3-fgren-s-syndrome-using-high-content-peptide-microarrays
#6
REVIEW
Giovanni Ferrara, Davide Valentini, Martin Rao, Jan Wahlström, Johan Grunewald, Lars-Olof Larsson, Susanna Brighenti, Ernest Dodoo, Alimuddin Zumla, Markus Maeurer
INTRODUCTION: Sarcoidosis is considered an idiopathic granulomatous disease, although similar immunological and clinical features with tuberculosis (TB) suggest mycobacterial involvement in its pathogenesis. High-content peptide microarrays (HCPM) may help to decipher mycobacteria-specific antibody reactivity in sarcoidosis. METHODS: Serum samples from patients with sarcoidosis, Löfgren's syndrome, and TB, as well as from healthy individuals (12/group), were tested on HCPM containing 5964 individual peptides spanning 154 Mycobacterium tuberculosis proteins displayed as 15-amino acid stretches...
January 31, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28148779/adverse-left-ventricular-remodeling-by-glycoprotein-nonmetastatic-melanoma-protein-b-in-myocardial-infarction
#7
Anne Järve, Silke Mühlstedt, Fatimunnisa Qadri, Bernadette Nickl, Herbert Schulz, Norbert Hübner, Cemil Özcelik, Michael Bader
Cardiac diseases are the leading cause of death. Available treatment approaches are not sufficient to reverse persistent cardiac damage after injury; thus, the search for new therapeutic targets is essential. Our microarray-based screening in rat hearts 24 h after myocardial infarction (MI) yielded glycoprotein nonmetastatic melanoma protein B (GPNMB), which is known to be involved in inflammation and fibrosis after tissue injury. However, its role in the heart was elusive. We found increased cardiac expression levels of GPNMB in rats and mice after MI...
February 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28138675/targeting-peptide-functionalized-liposomes-towards-aminopeptidase-n-for-precise-tumor-diagnosis-and-therapy
#8
Xiangqian Jia, Qiuju Han, Zihua Wang, Yixia Qian, Yunhong Jia, Weizhi Wang, Zhiyuan Hu
Aminopeptidase N (APN/CD13) is closely related to the growth of cancers and is suggested as a suitable target for anti-cancer therapy. Based on the "one-bead-one-compound" (OBOC) approach on a microarray device, we screened out a novel affinity peptide LN (YEVGHRC). It was determined that LN could specifically recognize and bind to APN. Moreover, LN-functionalized liposomes (LN-LS) could achieve efficient nano-encapsulated drug delivery under APN-overexpressing tumor conditions in vitro and in vivo. We expect that LN-LS could provide a new strategy for APN-positive tumor diagnosis and therapy...
January 31, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28125577/identification-of-three-immunodominant-motifs-with-atypical-isotype-profile-scattered-over-the-onchocerca-volvulus-proteome
#9
Ole Lagatie, Bieke Van Dorst, Lieven J Stuyver
Understanding the immune response upon infection with the filarial nematode Onchocerca volvulus and the mechanisms that evolved in this parasite to evade immune mediated elimination is essential to expand the toolbox available for diagnostics, therapeutics and vaccines development. Using high-density peptide microarrays we scanned the proteome-wide linear epitope repertoire in Cameroonian onchocerciasis patients and healthy controls from Southern Africa which led to the identification of 249 immunodominant antigenic peptides...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28123583/association-of-leptin-visfatin-apelin-resistin-and-adiponectin-with-clear-cell-renal-cell-carcinoma
#10
Hai-Ping Zhang, Jian Zou, Zhuo-Qun Xu, Jun Ruan, Shu-Dong Yang, Ying Yin, Hui-Jun Mu
Although an association between obesity and the occurrence of renal cell carcinoma (RCC) has been identified, the mechanism by which obesity functions to increase this risk of cancer remains unclear. Leptin, visfatin, apelin, resistin and adiponectin are peptide hormones secreted by adipocytes; it is considered that these may affect RCC development by exerting effects on proliferation, cell growth and inflammation. The aim of the present study was to investigate the association between the aforementioned adipokine genes and clear cell RCC (CC-RCC)...
January 2017: Oncology Letters
https://www.readbyqxmd.com/read/28121444/whole-proteome-peptide-microarrays-for-profiling-autoantibody-repertoires-within-multiple-sclerosis-and-narcolepsy
#11
Arash Zandian, Björn Forsström, Anna Häggmark-Månberg, Jochen M Schwenk, Mathias Uhlén, Peter Nilsson, Burcu Ayoglu
The underlying molecular mechanisms of autoimmune diseases are poorly understood. To unravel the autoimmune processes across diseases, comprehensive and unbiased analyses of proteins targets recognized by the adaptive immune system are needed. Here we present an approach starting from high-density peptide arrays to characterize autoantibody repertoires and to identify new autoantigens. A set of ten plasma and serum samples from subjects with multiple sclerosis, narcolepsy, and without any disease diagnosis were profiled on a peptide array representing the whole proteome, hosting 2...
February 9, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28116121/syndecan-4-as-a-biomarker-to-predict-clinical-outcome-for-glioblastoma-multiforme-treated-with-wt1-peptide-vaccine
#12
Satoshi Takashima, Yoshihiro Oka, Fumihiro Fujiki, Soyoko Morimoto, Hiroko Nakajima, Yoshiki Nakae, Jun Nakata, Sumiyuki Nishida, Naoki Hosen, Naoya Tatsumi, Kenji Mizuguchi, Naoya Hashimoto, Yusuke Oji, Akihiro Tsuboi, Atsushi Kumanogoh, Haruo Sugiyama
AIM: In cancer immunotherapy, biomarkers are important for identification of responsive patients. This study was aimed to find biomarkers that predict clinical outcome of WT1 peptide vaccination. MATERIALS & METHODS: Candidate genes that were expressed differentially between long- and short-term survivors were identified by cDNA microarray analysis of peripheral blood mononuclear cells that were extracted from 30 glioblastoma patients (discovery set) prior to vaccination and validated by quantitative RT-PCR using discovery set and different 23 patients (validation set)...
December 2016: Future Science OA
https://www.readbyqxmd.com/read/28114888/transcriptome-profiling-of-gene-expression-during-immunisation-trial-against-fasciola-hepatica-identification-of-genes-and-pathways-involved-in-conferring-immunoprotection-in-a-murine-model
#13
Jose Rojas-Caraballo, Julio López-Abán, Darwin Andrés Moreno-Pérez, Belén Vicente, Pedro Fernández-Soto, Esther Del Olmo, Manuel Alfonso Patarroyo, Antonio Muro
BACKGROUND: Fasciolosis remains a significant food-borne trematode disease causing high morbidity around the world and affecting grazing animals and humans. A deeper understanding concerning the molecular mechanisms by which Fasciola hepatica infection occurs, as well as the molecular basis involved in acquiring protection is extremely important when designing and selecting new vaccine candidates. The present study provides a first report of microarray-based technology for describing changes in the splenic gene expression profile for mice immunised with a highly effective, protection-inducing, multi-epitope, subunit-based, chemically-synthesised vaccine candidate against F...
January 23, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28095436/arraypitope-automated-analysis-of-amino-acid-substitutions-for-peptide-microarray-based-antibody-epitope-mapping
#14
Christian Skjødt Hansen, Thomas Østerbye, Paolo Marcatili, Ole Lund, Søren Buus, Morten Nielsen
Identification of epitopes targeted by antibodies (B cell epitopes) is of critical importance for the development of many diagnostic and therapeutic tools. For clinical usage, such epitopes must be extensively characterized in order to validate specificity and to document potential cross-reactivity. B cell epitopes are typically classified as either linear epitopes, i.e. short consecutive segments from the protein sequence or conformational epitopes adapted through native protein folding. Recent advances in high-density peptide microarrays enable high-throughput, high-resolution identification and characterization of linear B cell epitopes...
2017: PloS One
https://www.readbyqxmd.com/read/28092044/high-throughput-quantification-of-sh2-domain-phosphopeptide-interactions-with-cellulose-peptide-conjugate-microarrays
#15
Brett W Engelmann
The Src Homology 2 (SH2) domain family primarily recognizes phosphorylated tyrosine (pY) containing peptide motifs. The relative affinity preferences among competing SH2 domains for phosphopeptide ligands define "specificity space," and underpins many functional pY mediated interactions within signaling networks. The degree of promiscuity exhibited and the dynamic range of affinities supported by individual domains or phosphopeptides is best resolved by a carefully executed and controlled quantitative high-throughput experiment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092031/expression-and-production-of-sh2-domain-proteins
#16
Bernard A Liu, Mari Ogiue-Ikeda, Kazuya Machida
The Src Homology 2 (SH2) domain lies at the heart of phosphotyrosine signaling, coordinating signaling events downstream of receptor tyrosine kinases (RTKs), adaptors, and scaffolds. Over a hundred SH2 domains are present in mammals, each having a unique specificity which determines its interactions with multiple binding partners. One of the essential tools necessary for studying and determining the role of SH2 domains in phosphotyrosine signaling is a set of soluble recombinant SH2 proteins. Here we describe methods, based on a broad experience with purification of all SH2 domains, for the production of SH2 domain proteins needed for proteomic and biochemical-based studies such as peptide arrays, mass-spectrometry, protein microarrays, reverse-phase microarrays, and high-throughput fluorescence polarization (HTP-FP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28091360/collagen-peptide-ingestion-alters-lipid-metabolism-related-gene-expression-and-the-unfolded-protein-response-in-mouse-liver
#17
Chisa Tometsuka, Yoh-Ichi Koyama, Tomoko Ishijima, Tsudoi Toyoda, Miki Teranishi, Kazushige Takehana, Keiko Abe, Yuji Nakai
Ingestion of collagen peptide (CP) elicits beneficial effects on the body, including improvement in blood lipid profiles, but the underlying mechanisms remain unclear. The purpose of this study was to investigate the effects of CP ingestion on the liver, which controls lipid metabolism in the body. Male BALB/cCrSlc mice were bred with the AIN-93M diet containing 14 % casein or the AIN-93M-based low-protein diet containing 10 % casein or a diet containing 6 % casein+4 % CP for 10 weeks (n 12/group). Total, free and esterified cholesterol levels in the blood decreased in the CP group...
January 16, 2017: British Journal of Nutrition
https://www.readbyqxmd.com/read/28079948/induction-of-antibodies-directed-against-branched-core-o-mannosyl-glycopeptides-selectivity-complimentary-to-the-cona-lectin
#18
Jin Yu, Oliver C Grant, Christian Pett, Sabine Strahl, Robert J Woods, Ulrika Westerlind
Mammalian protein O-mannosylation comprise a group of post-translational modifications (PTMs) involved in muscle and brain development. Despite the enormous progress made, to date the biological impact of the mammalian O-mannosyl glycoproteome remains largely unknown. Tools are still needed to investigate the structure, role and abundance of O-mannosyl glycans. While O-mannosyl branching has been shown to be of relevance in integrin-dependent cell-migration, and also plays a role in demyelinating diseases, a broader understanding of the biological roles of branched O-mannosyl glycans is lacking in part due to the paucity of detection tools...
January 12, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28070829/functional-analysis-of-kif20a-a-potential-immunotherapeutic-target-for-glioma
#19
Katsuya Saito, Shigeki Ohta, Yutaka Kawakami, Kazunari Yoshida, Masahiro Toda
Kinesin family member 20A (KIF20A), an ideal cancer-testis antigen, was reported to be a promising immunotherapeutic target for pancreatic cancers. Clinical trials of KIF20A peptide vaccine immunotherapy have been conducted against pancreatic cancers. To demonstrate the efficacy of KIF20A as a candidate molecular target for gliomas, we analyzed the expression and function of KIF20A in gliomas. Western blot and quantitative PCR analyses showed that KIF20A expression in glioma cell lines and glioma tissues was high compared with that found in a normal brain...
January 9, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28013407/proteomic-based-biomarker-discovery-for-development-of-next-generation-diagnostics
#20
REVIEW
Akbar Khalilpour, Tugba Kilic, Saba Khalilpour, Mario Moisés Álvarez, Iman K Yazdi
In the post-genome age, proteomics is receiving significant attention because they provide an invaluable source of biological structures and functions at the protein level. The search for disease-specific biomarkers for diagnostic and/or therapeutic applications is one of the areas that proteomics is having a significant impact. Thus, the identification of a "good" biomarker enables a more accurate early diagnosis and prognosis of disease. Rapid advancements in mass spectrometry (MS) instrumentation, liquid chromatography MS (LCMS), protein microarray technology, and other protein profiling methodologies have a substantial expansion of our toolbox to identify disease-specific protein and peptide biomarkers...
January 2017: Applied Microbiology and Biotechnology
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