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Affinity maturation

Duncan K Ralph, Frederick A Matsen
The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian process of lineage diversification and selection called "affinity maturation." The resulting receptors can be sequenced in high throughput for research and diagnostics. Such a collection of sequences contains a mixture of various lineages, each of which may be quite numerous, or may consist of only a single member...
October 2016: PLoS Computational Biology
Maurizio Cirilli, Oxana Bereshchenko, Olga Ermakova, Claus Nerlov
BACKGROUND: C/EBPa and C/EBPb are transcription factors with tissue specific expression regulating several important cellular processes. They work by recruiting protein complexes to a common DNA recognition motif and both are able to compensate each other's absence in many cell types, thus showing functional redundancy. They also play distinct roles in specific cellular pathways and their abnormal functioning gives raise to different human pathologies. METHODS: To investigate the molecular basis of C/EBPa and C/EBPb specificity and redundancy we characterized their in vivo protein-protein interaction networks by Tandem Affinity Purification and Mass Spectrometry...
October 13, 2016: Biochimica et Biophysica Acta
Kazunobu Asano, Zhiliang Wu, Piyarat Srinontong, Takahide Ikeda, Isao Nagano, Hirokuyi Morita, Yoichi Maekawa
Infectious microorganisms often modify host immunity to escape from immune elimination. Trichinella is a unique nematode of the helminth family, which parasitize the inside of host muscle cells without robust eliminative reactions. There are two main species in genus Trichinella, encapsulated (T. spiralis(Ts), T. britovi) and non-encapsulated (T. pseudospiralis(Tp)). It has already been established that Trichinella infection affects host immune responses in several experimental immune diseases in animal models; however, most of those studies were done using Ts infection...
October 10, 2016: Infection and Immunity
Casandra Hoffman, Joshua Eby, Mary Gray, F Heath Damron, Jeffrey Melvin, Peggy Cotter, Erik Hewlett
Bordetella pertussis, the causative agent of whooping cough, secretes and releases adenylate cyclase toxin (ACT), which is a protein bacterial toxin that targets host cells and disarms immune defenses. ACT binds filamentous hemagglutinin (FHA), a surface-displayed adhesin, and until now, the consequences of this interaction were unknown. A B. bronchiseptica mutant lacking ACT produced more biofilm than the parental strain; leading Irie et al. to propose the ACT-FHA interaction could be responsible for biofilm inhibition...
October 12, 2016: Molecular Microbiology
Gene Kurosawa, Mariko Kondo, Yoshikazu Kurosawa
When the technology for constructing human antibody (Ab) libraries using a phage-display system was developed, many researchers in Ab-related fields anticipated that it would be widely applied to the development of pharmaceutical drugs against various diseases, including cancers. However, successful examples of such applications are very limited. Moreover, researchers who utilize phage-display technology now show divergent ways of thinking about phage Ab libraries. For example, there is debate about what should be the source of VH and VL genes for the construction of libraries to cover the whole repertoire of Abs present in the human body...
October 5, 2016: Biochemical and Biophysical Research Communications
Steven R Wiley, Vanitha S Raman
Adjuvants in vaccine formulations are designed to enhance immune responses against a target antigen or pathogen. The ability of these vaccines to induce activation and differentiation of mature naïve B cells to produce pathogen-specific antibodies (immunoglobulins; Ig) helps guarantee long-lived humoral immunity. This process involves clonal expansion of antigen-specific B cells, genomic rearrangement of Ig heavy (IgH) and light (IgL) loci, somatic hypermutation (SHM), and clonal selection for affinity-matured antibody, resulting in a vast but directed repertoire of B cells expressing highly specific antibody proteins...
2017: Methods in Molecular Biology
Tando Maduna, Vincent Lelievre
Pituitary adenylate cyclase-activating polypeptide (PACAP) and vasoactive intestinal peptide (VIP) are neuropeptides with wide, complementary, and overlapping distributions in the central and peripheral nervous systems, where they exert important regulatory roles in many physiological processes. VIP and PACAP display a large range of biological cellular targets and functions in the adult nervous system including regulation of neurotransmission and neuroendocrine secretion and neuroprotective and neuroimmune responses...
December 2016: Journal of Neuroscience Research
Masahiro Kimura, Satoshi Wakita, Kotarou Ishikawa, Kazutaka Sekine, Satoshi Yoshikawa, Akira Sato, Kazuaki Okawa, Akinori Kashimura, Masayoshi Sakaguchi, Yasusato Sugahara, Daisuke Yamanaka, Naohito Ohno, Peter O Bauer, Fumitaka Oyama
Chitotriosidase (Chit1) is an enzyme associated with various diseases, including Gaucher disease, chronic obstructive pulmonary disease, Alzheimer disease and cystic fibrosis. In this study, we first expressed mouse mature Chit1 fused with V5 and (His)6 tags at the C-terminus (Chit1-V5-His) in the cytoplasm of Escherichia coli and found that most of the expressed protein was insoluble. In contrast, Chit1 tagged with Protein A at the N-terminus and V5-His at the C-terminus, was expressed in the periplasmic space of E...
2016: PloS One
Cristian Gustavo Aguilera Rossi, Paulino Gómez-Puertas, Juan Alfonso Ayala Serrano
BACKGROUND: Community and nosocomial infections by Pseudomonas aeruginosa still create a major therapeutic challenge. The resistance of this opportunist pathogen to β-lactam antibiotics is determined mainly by production of the inactivating enzyme AmpC, a class C cephalosporinase with a regulation system more complex than those found in members of the Enterobacteriaceae family. This regulatory system also participates directly in peptidoglycan turnover and recycling. One of the regulatory mechanisms for AmpC expression, recently identified in clinical isolates, is the inactivation of LMM-PBP4 (Low-Molecular-Mass Penicillin-Binding Protein 4), a protein whose catalytic activity on natural substrates has remained uncharacterized until now...
October 6, 2016: BMC Microbiology
C Zhao, M J Fu, L H Qiu
Reduced reproductive performance of the black tiger shrimp (Penaeus monodon) has caused economic losses and hampered the fishing industry. Detailed investigation of the molecular mechanism by which the cell cycle is regulated in this organism is needed to understand the development and maturation of ovaries and oocytes, with a view to improving reproductive capacity. Cell cycle progression is mainly determined by cyclin-dependent kinase (CDK) and cyclin complexes, the cyclin E/CDK2 complex playing a key role in G1/S transition...
September 16, 2016: Genetics and Molecular Research: GMR
Michael T Ringel, Gerald Draeger, Thomas Brueser
Pyoverdines are high-affinity siderophores produced by a broad range of pseudomonads to enhance growth under iron-deficiency. They are especially relevant for pathogenic and mutualistic strains that inhabit iron-limited environments. Pyoverdines are generated from non-ribosomally synthesized highly modified peptides. They all contain an aromatic chromophore that is formed in the periplasm by intramolecular cyclization steps. While the cytoplasmic peptide synthesis and side-chain modifications are well-characterized, the periplasmic maturation steps are far from understood...
October 4, 2016: Journal of Biological Chemistry
Ebru Kocadag Kocazorbaz, Figen Zihnioglu
Prolyl oligopeptidase (POP, EC is a cytosolic serine protease that hydrolyses proline containing small peptides. The members of prolyl oligopeptidase family play important roles in many physiological processes such as neurodegenerative diseases, maturation and degradation of peptide hormones. Thus the enzyme has been purified and characterized from various sources to elucidate the potential use as therapeutics. In this study recombinant Myxococcus xanthus prolyl oligopeptidase expressed in E. coli was purified 60...
January 2017: Protein Expression and Purification
L Fialová
Autoantibodies directed against various self-antigens comprise a heterogeneous group of immunoglobulins, which differ in their qualitative and quantitative features. An important qualitative characteristic of antibodies is affinity/avidity, which changes in the process of its maturation during the immune response.This study is aimed to summarize the knowledge about avidity of selected autoantibodies in certain autoimmune diseases. The avidity of various autoantibodies differs under distinct clinical situations...
2016: Epidemiologie, Mikrobiologie, Imunologie
Zhu Li, Julie L Frey, G William Wong, Marie-Claude Faugere, Michael J Wolfgang, Jason K Kim, Ryan C Riddle, Thomas L Clemens
Recent studies have identified the osteoblast as an insulin responsive cell that participates in global energy homeostasis. Here we show that Glut4 is required for insulin-dependent uptake and oxidation of glucose in mature osteoblasts. In primary cultures of mouse osteoblasts, insulin increased uptake and oxidation of (14)C-glucose in a dose-dependent fashion, but did not significantly affect uptake or oxidation of (14)C-oleate. In vitro, undifferentiated osteoblasts expressed three high affinity glucose transporters: Glut1, Glut4, and Glut3...
September 30, 2016: Endocrinology
Daniel T Harris, Ningyan Wang, Timothy P Riley, Scott D Anderson, Nishant K Singh, Erik Procko, Brian M Baker, David M Kranz
Proteins are often engineered to have higher affinity for their ligands in order to achieve therapeutic benefit. For example, many studies have used phage- or yeast-display libraries of mutants within complementarity determining regions (CDRs) to affinity mature antibodies and T cell receptors (TCRs). However, these approaches do not allow rapid assessment or evolution across the entire interface. By combining directed evolution with deep sequencing it is now possible to generate sequence fitness landscapes that survey the impact of every amino acid substitution across the entire protein-protein interface...
September 28, 2016: Journal of Biological Chemistry
Mayumi Okamoto, Kyosuke Naka, Kiichi Ishiwata, Isao Shimizu, Jun Toyohara
OBJECTIVE: 7α-Substituted androgen derivatives may have the potential to visualize androgen receptors with positron emission tomography. In the present study, we synthesized fluoropropyl derivatives of 7α-(3-[(18)F]fluoropropyl)-testosterone ([(18)F]7) and 7α-(3-[(18)F]fluoropropyl)-dihydrotestosterone ([(18)F]15), and characterized their in vitro binding, in vivo biodistribution, and performed blocking studies in mature androgen deprived male rats. METHODS: We synthesized [(18)F]7 and [(18)F]15...
September 28, 2016: Annals of Nuclear Medicine
Sheng Lin, Lihua Lu, Tian-Shu Kang, Jean-Louis Mergny, Chung-Hang Leung, Dik-Lung Ma
Sialic acid (Sia) binding immunoglobulin (Ig)-like lectin-5 (Siglec-5) is a type-I transmembrane protein, and it has been demonstrated as a biomarker of granulocytic maturation and acute myeloid leukemia phenotype. Herein we aimed to construct a method that could sensitively detect Siglec-5 by taking advantage of the high affinity and selectivity of the K19 aptamer for its cognate target, and the selective interaction of luminescent iridium(III) transition metal complexes with G-quadruplex DNA. The iridium(III) complex 1 [Ir(tpyd)2(2,9-dmphen)]PF6 (where tpyd =2-(m-tolyl)pyridine; 2,9-dmphen =2,9-dimethyl-1,10-phenanthroline) was synthesized, and it displayed high luminescence for G-quadruplex DNA compared to dsDNA and ssDNA...
October 6, 2016: Analytical Chemistry
Ema Romão, Francisco Morales-Yánez, Yaozhong Hu, Maxine Crauwels, Pieter De Pauw, Gholamreza Ghassanzadeh Hassanzadeh, Nick Devoogdt, Chloé Ackaert, Cécile Vincke, Serge Muyldermans
BACKGROUND: The discovery of functional heavy chain-only antibodies devoid of light chains in sera of camelids and sharks in the early nineties provided access to the generation of minimal-sized, single-domain, in vivo affinity-matured, recombinant antigen-binding fragments, also known as Nanobodies. METHODS: Recombinant DNA technology and adaptation of phage display vectors form the basis to construct large naïve, synthetic or medium sized immune libraries from where multiple Nanobodies have been retrieved...
September 23, 2016: Current Pharmaceutical Design
Markéta Svobodová, Vasso Skouridou, Mary Luz Botero, Miriam Jauset-Rubio, Thomas Schubert, Abdulaziz S Bashammakh, Mohammad S El-Shahawi, Abdulrahman O Alyoubi, Ciara K O'Sullivan
The rapid and sensitive detection of small molecules is garnering increasing importance, and aptamers show great promise in replacing expensive, elaborate detection platforms exploiting chromatographic separation or antibody-based assays. The characterization of aptamer interaction with small molecule targets is not facile, and there is a mature need for a rapid, high-throughput technique for the analysis of aptamer-small molecule kinetics and affinity. In this work we present methodologies for the evaluation of aptamer-small molecule interactions, using the aptamers reported against the steroid 17β-estradiol as a model system...
September 23, 2016: Journal of Steroid Biochemistry and Molecular Biology
Myriam Lawand, Anastasia Abramova, Valérie Manceau, Sebastian Springer, Peter van Endert
Cross-presentation of phagocytosed Ags by MHC class I (MHC-I) molecules is thought to involve transport of cytosolic peptides into dendritic cell phagosomes, mediated by TAP transporters recruited from the endoplasmic reticulum. However, because pure and tightly sealed phagosomes are difficult to obtain, direct evidence for peptide transport into phagosomes has remained limited. Moreover, the parameters determining peptide uptake by, and survival in, phagosomes remain little characterized. In this study, we monitored peptide import into phagosomes by flow cytometry using two types of fluorescent reporter peptides, one of which directly bound to intraphagosomal beads...
September 23, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
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