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peptide array

Purnandhu Bose, Pradip K Sukul, Omar M Yaghi, Kentaro Tashiro
We demonstrate a method for the synthesis of a water-soluble multimetallic peptidic array containing a predetermined sequence of metal centers such as Ru(II), Pt(II), and Rh(III). The compound, named as a water-soluble metal-organic complex array (WSMOCA), is obtained through 1) the conventional solution-chemistry-based preparation of the corresponding metal complex monomers having a 9-fluorenylmethyloxycarbonyl (Fmoc)-protected amino acid moiety and 2) their sequential coupling together with other water-soluble organic building units on the surface-functionalized polymeric resin by following the procedures originally developed for the solid-phase synthesis of polypeptides, with proper modifications...
October 8, 2016: Journal of Visualized Experiments: JoVE
Wei Zhang, M Can Gulersonmez, Thomas Hankemeier, Rawi Ramautar
In metabolomics, a wide range of analytical techniques is used for the global profiling of (endogenous) metabolites in complex samples. In this paper, a protocol is presented for the analysis of anionic and cationic metabolites in biological samples by capillary electrophoresis-mass spectrometry (CE-MS). CE is well-suited for the analysis of highly polar and charged metabolites as compounds are separated on the basis of their charge-to-size ratio. A recently developed sheathless interfacing design, i.e., a porous tip interface, is used for coupling CE to electrospray ionization (ESI) MS...
October 1, 2016: Journal of Visualized Experiments: JoVE
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
Alessandro Gori, Laura Sola, Paola Gagni, Giulia Bruni, Marta Liprino, Claudio Peri, Giorgio Colombo, Marina Cretich, Marcella Chiari
The generation of robust analytical data using microarray platforms strictly relies on optimal ligand-target interaction at the sensor surface which, in turn, is inherently bound to the correct immobilization scheme of the interrogated bioprobes. In the present work, we performed a rigorous comparative analysis of the impact of peptide ligands immobilization strategy in the screening of Burkholderia cepacia complex (BCC) infections in patients affected by cystic fibrosis (CF). We generated arrays of previously validated Burkholderia-derived peptide probes, that were selectively oriented on polymeric coatings by means of different click-type reactions including thiol-maleimide, copper-catalyzed-azide-alkyne-cycloaddition (CuAAC) and strain-promoted-azide-alkyne-cycloaddition (SPAAC)...
October 12, 2016: Bioconjugate Chemistry
Walter J Lukiw
The human microbiome consists of ~3.8 × 10(13) symbiotic microorganisms that form a highly complex and dynamic ecosystem: the gastrointestinal (GI) tract constitutes the largest repository of the human microbiome by far, and its impact on human neurological health and disease is becoming increasingly appreciated. Bacteroidetes, the largest phylum of Gram-negative bacteria in the GI tract microbiome, while generally beneficial to the host when confined to the GI tract, have potential to secrete a remarkably complex array of pro-inflammatory neurotoxins that include surface lipopolysaccharides (LPSs) and toxic proteolytic peptides...
2016: Frontiers in Microbiology
Sibaprasad Maity, Ekaterina Viazovkina, Alexander Gall, Yuri Lyubchenko
Probing of biomolecular complexes by single-molecule force spectroscopy (SMFS) methods including AFM requires proper and suitable coupling methods for immobilization of biomolecules onto the AFM tip and the surface. The use of flexible tethers for the coupling process has dual advantages. First, they allow the specific immobilization of interacting molecules, and second, their flexibility facilitates the proper orientation of the interacting partners. Recently, we developed an approach termed Flexible Nano Array (FNA) in which interacting partners are located on the same polymeric FNA molecule separated by a flexible segment with a defined length...
2016: Journal of Nature and Science
Hafiz Mamoon Rehman, Muhammad Amjad Nawaz, Le Bao, Zahid Hussain Shah, Jae-Min Lee, Muhammad Qadir Ahmad, Gyuhwa Chung, Seung Hwan Yang
Family-1 UDP-glycosyltransferases (EC 2.4.1.x; UGTs) are enzymes that glycosylate aglycones into glycoside-associated compounds with improved transport and water solubility. This glycosylation mechanism is vital to plant functions, such as regulation of hormonal homeostasis, growth and development, xenobiotic detoxification, stress response, and biosynthesis of secondary metabolites. Here, we report a genome-wide analysis of soybean that identified 149 putative UGTs based on 44 conserved plant secondary product glycosyl-transferase (PSPG) motif amino acid sequences...
September 22, 2016: Journal of Plant Physiology
Maria Pannell, Dominika Labuz, Melih Ö Celik, Jacqueline Keye, Arvind Batra, Britta Siegmund, Halina Machelska
BACKGROUND: During the inflammation which occurs following nerve damage, macrophages are recruited to the site of injury. Phenotypic diversity is a hallmark of the macrophage lineage and includes pro-inflammatory M1 and anti-inflammatory M2 populations. Our aim in this study was to investigate the ability of polarized M0, M1, and M2 macrophages to secrete opioid peptides and to examine their relative contribution to the modulation of neuropathic pain. METHODS: Mouse bone marrow-derived cells were cultured as unstimulated M0 macrophages or were stimulated into an M1 phenotype using lipopolysaccharide and interferon-γ or into an M2 phenotype using interleukin-4...
October 7, 2016: Journal of Neuroinflammation
Parvin Abraham, Tessy Thomas Maliekal
Research of the past two decades has proved the relevance of single cell biology in basic research and translational medicine. Successful detection and isolation of specific subsets is the key to understand their functional heterogeneity. Antibodies are conventionally used for this purpose, but their relevance in certain contexts is limited. In this review, we discuss some of these contexts, posing bottle neck for different fields of biology including biomedical research. With the advancement of chemistry, several methods have been introduced to overcome these problems...
October 6, 2016: Cellular and Molecular Life Sciences: CMLS
Marc A Schneider, Thomas Muley, Nicolas C Kahn, Arne Warth, Michael Thomas, Felix J F Herth, Hendrik Dienemann, Michael Meister
Malignant pleural mesothelioma (MPM) is a rare and aggressive tumor with a short survival time arising from the mesothelial cells of the pleura. Soluble mesothelin-related peptide (SMRP), osteopontin or EFEMP1 (Fibulin-3) are well described biomarkers for malignant mesothelioma with moderate sensitivity and specificity. In this study, we characterized the expression of glycodelin, a marker for risk pregnancy, in MPM by RNA and protein analyses and investigated its potential as a MPM biomarker. We were able to detect glycodelin in the serum of MPM patients...
October 4, 2016: Oncotarget
Marie de Bourayne, Yann Gallais, Zeina El Ali, Philippe Rousseau, Marie-Hélène Damiens, Claude Cochet, Odile Filhol, Sylvie Chollet-Martin, Marc Pallardy, Saadia Kerdine-Römer
Allergic contact dermatitis (ACD) represents a severe health problem with increasing worldwide prevalence. It is a T-cell-mediated inflammatory skin disease caused by chemicals present in the daily or professional environment. NiSO4 and 2,4-dinitrochlorobenzene (DNCB) are 2 chemicals involved in ACD. These contact sensitizers are known to induce an up-regulation of phenotypic markers and cytokine secretion in dendritic cells (DCs; professional APCs), leading to the generation of CD8(+) Tc1/Tc17 and CD4(+) Th1/Th17 effector T cells...
October 5, 2016: Journal of Leukocyte Biology
Elisa Pin, Frauke Henjes, Mun-Gwan Hong, Fredrik Wiklund, Patrik Magnusson, Anders Bjartell, Mathias Uhlén, Peter Nilsson, Jochen M Schwenk
There is a demand for novel targets and approaches to diagnose and treat prostate cancer (PCA). In this context, serum and plasma samples from a total of 609 individuals from two independent patient cohorts were screened for IgG reactivity against a sum of 3,833 human protein fragments. Starting from planar protein arrays with 3,786 protein fragments to screen 80 patients with and without PCA diagnosis, 161 fragments (4%) were chosen for further analysis based on their reactivity profiles. Adding 71 antigens from literature, the selection of antigens were corroborated for their reactivity in a set of 550 samples using suspension bead arrays...
October 4, 2016: Journal of Proteome Research
James P Tauber, Volker Schroeckh, Ekaterina Shelest, Axel A Brakhage, Dirk Hoffmeister
Basidiomycete fungi are characterized ecologically for their vital functional role in ecosystem carbon recycling and chemically for their capacity to produce a diverse array of small molecules. Chromophoric natural products derived from the quinone precursor atromentin, such as variegatic acid and involutin, have been shown to function in redox cycling. Yet, in the context of an inter-kingdom natural system these pigments are still elusive. Here, we co-cultured the model saprotrophic basidiomycete Serpula lacrymans with an ubiquitous terrestrial bacterium, either Bacillus subtilis, Pseudomonas putida, or Streptomyces iranensis...
October 4, 2016: Environmental Microbiology
William A Carlezon, Andrew D Krystal
Kappa-opioid receptor (KOR) antagonists are currently being considered for the treatment of a variety of neuropsychiatric conditions, including depressive, anxiety, and substance abuse disorders. A general ability to mitigate the effects of stress, which can trigger or exacerbate these conditions, may explain their putative efficacy across such a broad array of conditions. The discovery of their potentially therapeutic effects evolved from preclinical research designed to characterize the molecular mechanisms by which experience causes neuroadaptations in the nucleus accumbens (NAc), a key element of brain reward circuitry...
October 2016: Depression and Anxiety
Marcello Mascini, Daniel Pizzoni, German Perez, Emilio Chiarappa, Corrado Di Natale, Paola Pittia, Dario Compagnone
A semi-combinatorial virtual approach was used to prepare peptide-based gas sensors with binding properties towards five different chemical classes (alcohols, aldehydes, esters, hydrocarbons and ketones). Molecular docking simulations were conducted for a complete tripeptide library (8000 elements) versus 58 volatile compounds belonging to those five chemical classes. By maximizing the differences between chemical classes, a subset of 120 tripeptides was extracted and used as scaffolds for generating a combinatorial library of 7912 tetrapeptides...
September 14, 2016: Biosensors & Bioelectronics
Botros B Shenoda, Seena K Ajit
Exosome-mediated signaling is important in mediating the inflammatory response. To exert their biological or pathophysiological functions in the recipient cells, exosomes deliver a diverse array of biomacromolecules including long and short coding and non-coding RNAs, proteins, and lipids. Exosomes secreted by antigen-presenting cells can confer therapeutic benefits by attenuating or stimulating the immune response. Exosomes play a crucial role in carrying and presenting functional major histocompatibility peptide complexes to modulate antigen-specific T cell responses...
2016: Clinical Medicine Insights. Pathology
Seong-Kyun Lee, Bo Wang, Jin-Hee Han, Myat Htut Nyunt, Fauzi Muh, Patchanee Chootong, Kwon-Soo Ha, Won Sun Park, Seok-Ho Hong, Jeong-Hyun Park, Eun-Taek Han
The discovery and understanding of antigenic proteins are essential for development of a vaccine against malaria. In Plasmodium falciparum, Pf92 have been characterized as a merozoite surface protein, and this protein is expressed at the late schizont stage, but no study of Pv92, the orthologue of Pf92 in P. vivax, has been reported. Thus, the protein structure of Pv92 was analyzed, and the gene sequence was aligned with that of other Plasmodium spp. using bioinformatics tools. The recombinant Pv92 protein was expressed and purified using bacterial expression system and used for immunization of mice to gain the polyclonal antibody and for evaluation of antigenicity by protein array...
August 2016: Korean Journal of Parasitology
Fengli Qu, Minghui Yang, Avraham Rasooly
The protease BACE1 (the β-site amyloid precursor protein cleaving enzyme 1) catalyzes the first step in the synthesis of β-amyloids (Aβ), peptides that accumulate in the brain in Alzheimer's disease (AD). Measurement of BACE1 activity is important for the development of BACE1 inhibitors to slow or stop AD. To measure BACE1 cleavage of the electrode-immobilized substrate peptide, we developed a redox-generating hydroxyapatite (HAP) probe which generates electrochemical current by reaction of the nanoparticle with molybdate (MoO4(2-))...
October 17, 2016: Analytical Chemistry
Marty A Fernandez, Kelly M Biette, Georgia Dolios, Divya Seth, Rong Wang, Michael S Wolfe
The amyloid β-peptide (Aβ) of Alzheimer's disease (AD) is generated by proteolysis within the transmembrane domain (TMD) of a C-terminal fragment of the amyloid β protein-precursor (APP CTFβ) by the γ-secretase complex. This processing produces Aβ ranging from 38 to 49 residues in length. Evidence suggests that this spectrum of Aβ peptides is the result of successive γ-secretase cleavages, with endoproteolysis first occurring at the ε sites to generate Aβ48 or Aβ49, followed by C-terminal trimming mostly every three residues along two product lines to generate shorter, secreted forms of Aβ: the primary Aβ49-46-43-40 line and a minor Aβ48-45-42-38 line...
October 11, 2016: Biochemistry
Pravin C Patil, Jinlian Tan, Donald R Demuth, Frederick A Luzzio
The development and use of small-molecule inhibitors of the adherence of Porphyromonas gingivalis to oral streptococci represents a potential therapy for the treatment of periodontal disease as these organisms work in tandem to colonize the oral cavity. Earlier work from these laboratories demonstrated that a small synthetic peptide was an effective inhibitor of the interaction between P. gingivalis and Streptococcus gordonii and that a small-molecule peptidomimetic would provide a more stable, less expensive and more effective inhibitor...
November 1, 2016: Bioorganic & Medicinal Chemistry
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