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Antibody identification

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https://www.readbyqxmd.com/read/28813459/%C3%AE-2-microglobulin-gene-duplication-in-cetartiodactyla-remains-intact-only-in-pigs-and-possibly-confers-selective-advantage-to-the-species
#1
Thong Minh Le, Quy Van Chanh Le, Dung Minh Truong, Hye-Jeong Lee, Min-Kyeung Choi, Hyesun Cho, Hak-Jae Chung, Jin-Hoi Kim, Jeong-Tae Do, Hyuk Song, Chankyu Park
Several β2-microglobulin (B2M) -bound protein complexes undertake key roles in various immune system pathways, including the neonatal Fc receptor (FcRn), cluster of differentiation 1 (CD1) protein, non-classical major histocompatibility complex (MHC), and well-known MHC class I molecules. Therefore, the duplication of B2M may lead to an increase in the biological competence of organisms to the environment. Based on the pig genome assembly SSC10.2, a segmental duplication of ~45.5 kb, encoding the entire B2M protein, was identified in pig chromosome 1...
2017: PloS One
https://www.readbyqxmd.com/read/28813434/detection-of-anti-hspx-antibodies-and-hspx-protein-in-patient-sera-for-the-identification-of-recent-latent-infection-by-mycobacterium-tuberculosis
#2
Jorge Castro-Garza, Paola García-Jacobo, Lydia G Rivera-Morales, Frederick D Quinn, James Barber, Russell Karls, Debra Haas, Shelly Helms, Tuhina Gupta, Henry Blumberg, Jane Tapia, Itza Luna-Cruz, Adrián Rendon, Javier Vargas-Villarreal, Lucio Vera-Cabrera, Cristina Rodríguez-Padilla
Mycobacterium tuberculosis is a pathogen causing tuberculosis (TB) a spectrum of disease including acute and asymptomatic latent stages. Identifying and treating latently-infected patients constitutes one of the most important impediments to TB control efforts. Those individuals can remain undiagnosed for decades serving as potential reservoirs for disease reactivation. Tests for the accurate diagnosis of latent infection currently are unavailable. HspX protein (α-crystallin), encoded by Rv2031c gene, is produced in vitro by M...
2017: PloS One
https://www.readbyqxmd.com/read/28811664/structure-based-cross-docking-analysis-of-antibody-antigen-interactions
#3
Krishna Praneeth Kilambi, Jeffrey J Gray
Antibody-antigen interactions are critical to our immune response, and understanding the structure-based biophysical determinants for their binding specificity and affinity is of fundamental importance. We present a computational structure-based cross-docking study to test the identification of native antibody-antigen interaction pairs among cognate and non-cognate complexes. We picked a dataset of 17 antibody-antigen complexes of which 11 have both bound and unbound structures available, and we generated a representative ensemble of cognate and non-cognate complexes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28810661/identification-of-lectin-counter-receptors-on-cell-membranes-by-proximity-labeling
#4
Gang Wu, Manjula Nagala, Paul R Crocker
Lectin-glycan interactions play important roles in many biological systems, but the nature of glycoprotein counter-receptors expressed on cell membranes is often poorly understood. To help overcome this problem, we developed a method based on proximity labeling technology. Using a peroxidase-coupled lectin, addition of H2O2 and tyramide-biotin substrates leads to generation of short-range biotin radicals that biotinylate proteins in the immediate vicinity of the bound lectin, which can subsequently be identified...
September 1, 2017: Glycobiology
https://www.readbyqxmd.com/read/28808999/studying-protein-protein-interactions-by-biotin-ap-tagged-pulldown-and-ltq-orbitrap-mass-spectrometry
#5
Zhongqiu Xie, Yuemeng Jia, Hui Li
The study of protein-protein interactions represents a key aspect of biological research. Identifying unknown protein binding partners using mass spectrometry (MS)-based proteomics has evolved into an indispensable strategy in drug discovery. The classic approach of immunoprecipitation with specific antibodies against the proteins of interest has limitations, such as the need for immunoprecipitation-qualified antibody. The biotin AP-tag pull-down system has the advantage of high specificity, ease of use, and no requirement for antibody...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808043/allosteric-alterations-in-the-androgen-receptor-and-activity-in-prostate-cancer
#6
REVIEW
Takuma Uo, Stephen R Plymate, Cynthia C Sprenger
Organisms have evolved to generate biological complexity in their proteome and transcriptome from a limited number of genes. This concept holds true for the androgen receptor, which displays a diversity of inclusion/exclusion events in its structural motifs as a mechanism of resistance to the most forefront anti-androgen therapies. More than 20 androgen receptor variants that lack various portions of ligand-binding domain have been identified in human prostate cancer (PCa) samples. Most of the variants are inactive on their own, with a few exceptions displaying constitutive activity...
September 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28807517/trim21-and-the-function-of-antibodies-inside-cells
#7
REVIEW
David A Rhodes, David A Isenberg
Therapeutic antibodies targeting disease-associated antigens are key tools in the treatment of cancer and autoimmunity. So far, therapeutic antibodies have targeted antigens that are, or are presumed to be, extracellular. A largely overlooked property of antibodies is their functional activity inside cells. The diverse literature dealing with intracellular antibodies emerged historically from studies of the properties of some autoantibodies. The identification of tripartite motif (TRIM) 21 as an intracellular Fc receptor linking cytosolic antibody recognition to the ubiquitin proteasome system brings this research into sharper focus...
August 11, 2017: Trends in Immunology
https://www.readbyqxmd.com/read/28807087/allergic-bronchopulmonary-mycosis-due-to-exposure-to-eurotium-herbariorum-after-the-great-east-japan-earthquake
#8
Chiyako Oshikata, Maiko Watanabe, Akemi Saito, Masatsugu Ishida, Seiichi Kobayashi, Rumi Konuma, Yoichi Kamata, Jun Terajima, Junichi Cho, Masaru Yanai, Naomi Tsurikisawa
BACKGROUND: Indoor mold levels typically increase after natural disasters, flooding, and water damage. Eurotium herbariorum is the sexual stage of Aspergillus glaucus. Case Presentation A 66-year-old, Japanese male, ex-smoker had been diagnosed with bronchial asthma when he was five years old; he achieved remission at the age of 13 years. He was displaced from his home during the Great East Japan Earthquake on March 11, 2011 and moved to temporary housing in Miyagi Prefecture in June 2011...
August 15, 2017: Prehospital and Disaster Medicine
https://www.readbyqxmd.com/read/28806188/tubulointerstitial-nephritis-and-uveitis
#9
Kaivon Pakzad-Vaezi, Kathryn L Pepple
PURPOSE OF REVIEW: Tubulointerstitial nephritis and uveitis (TINU) is an important yet underrecognized ocular inflammatory syndrome. This review summarizes key historical publications that identified and defined the syndrome, and more recent literature that reveal the importance of urinary β2-microglobulin testing and kidney biopsy in the diagnostic evaluation of patients with TINU. Additionally, research studies providing new insights into disease pathogenesis are highlighted. RECENT FINDINGS: In contrast with initial reports of TINU manifesting exclusively as an anterior uveitis in pediatric patients, more recent reports have identified TINU in patients of all ages with a wide range of ocular manifestations...
August 12, 2017: Current Opinion in Ophthalmology
https://www.readbyqxmd.com/read/28805498/gingiskhan%C3%A2-protease-cleavage-allows-a-high-throughput-antibody-to-fab-conversion-enabling-direct-functional-assessment-during-lead-identification-of-human-monoclonal-and-bispecific-igg1-antibodies
#10
Jörg Moelleken, Manuel Endesfelder, Christian Gassner, Sabine Lingke, Simone Tomaschek, Oksana Tyshchuk, Stefan Lorenz, Ulrike Reiff, Michael Mølhøj
The determination of the binding strength of immunoglobulins (IgGs) to targets can be influenced by avidity when the targets are soluble di- or multimeric proteins, or associated to cell surfaces, including surfaces introduced from heterogeneous assays. However, for the understanding of the contribution of a second drug-to-target binding site in molecular design, or for ranking of monovalent binders during lead identification, affinity-based assessment of the binding strength is required. Typically, monovalent binders like antigen-binding fragments (Fabs) are generated by proteolytic cleavage with papain, which often results in a combination of under- and over-digestion, and requires specific optimization and chromatographic purification of the desired Fabs...
August 14, 2017: MAbs
https://www.readbyqxmd.com/read/28804830/solid-phase-immunoassay-for-the-detection-of-anticardiolipin-antibodies
#11
Rohan Willis, Elizabeth Papalardo, E Nigel Harris
The anticardiolipin (aCL) test was first developed in the 1980s and proved to be a valuable addition to the lupus anticoagulant assay for identifying patients with a disorder that came to be later known as the antiphospholipid syndrome (APS). Although the test has relatively poor specificity for APS diagnosis, particularly at low positive levels, it has continued to play a major role in the identification and management of these patients because of its high sensitivity and ability to be measured in both serum and plasma, and despite concomitant presence of anticoagulants normally given to APS patients...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28803843/high-throughput-screening-of-hybridoma-supernatants-using-multiplexed-fluorescent-cell-barcoding-on-live-cells
#12
Mei Lu, Brian M Chan, Peter W Schow, Wesley S Chang, Chadwick T King
With current available assay formats using either immobilized protein (ELISA, enzyme-linked immunosorbent assay) or immunostaining of fixed cells for primary monoclonal antibody (mAb) screening, researchers often fail to identify and characterize antibodies that recognize the native conformation of cell-surface antigens. Therefore, screening using live cells has become an integral and important step contributing to the successful identification of therapeutic antibody candidates. Thus the need for developing high-throughput screening (HTS) technologies using live cells has become a major priority for therapeutic mAb discovery and development...
August 10, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28803708/anti-phospholipid-syndrome-current-opinion-on-mechanisms-involved-laboratory-characterization-and-diagnostic-aspects
#13
REVIEW
Jean Amiral, Marie Peyrafitte, Claire Dunois, Anne Marie Vissac, Jerard Seghatchian
Anti-phospholipid syndrome is a complex and severe clinical situation, associated with symptoms such as recurrent thrombosis, arterial or venous, at any site, pregnancy loss, and other related syndromes. These clinical burdens, are highly variable from patient to patient, and are associated with biological abnormalities, such as the presence of the Lupus Anticoagulant or phospholipid dependent antibodies, confirmed on two occasions at least 12 weeks apart. From the diagnosis standpoint, both, functional (clotting) or immunological assays, are difficult to standardize and to optimize, due to the absence of reference material, or a characteristic clinical group, and international reference preparations...
July 15, 2017: Transfusion and Apheresis Science
https://www.readbyqxmd.com/read/28802838/identification-of-immune-correlates-of-protection-in-shigella-infection-by-application-of-machine-learning
#14
Jorge M Arevalillo, Marcelo B Sztein, Karen L Kotloff, Myron M Levine, Jakub K Simon
BACKGROUND: Immunologic correlates of protection are important in vaccine development because they give insight into mechanisms of protection, assist in the identification of promising vaccine candidates, and serve as endpoints in bridging clinical vaccine studies. Our goal is the development of a methodology to identify immunologic correlates of protection using the Shigella challenge as a model. METHODS: The proposed methodology utilizes the Random Forests (RF) machine learning algorithm as well as Classification and Regression Trees (CART) to detect immune markers that predict protection, identify interactions between variables, and define optimal cutoffs...
August 9, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28801948/a-proteomics-method-using-immunoaffinity-fluorogenic-derivatization-liquid-chromatography-tandem-mass-spectrometry-fd-lc-ms-ms-to-identify-a-set-of-interacting-proteins
#15
Katsunori Nakata, Ryoichi Saitoh, Masaki Ishigai, Kazuhiro Imai
Biological functions in organisms are usually controlled by a set of interacting proteins, and identifying the proteins that interact is useful for understanding the mechanism of the functions. Immunoprecipitation is a method that utilizes the affinity of an antibody to isolate and identify the proteins that have interacted in a biological sample. In this study, the FD-LC-MS/MS method, which involves fluorogenic derivatization followed by separation and quantification by HPLC and finally identification of proteins by HPLC-tandem mass spectrometry, was used to identify proteins in immunoprecipitated samples, using Heat shock protein 90 (HSP90) as a model of an interacting protein in HepaRG cells...
August 12, 2017: Biomedical Chromatography: BMC
https://www.readbyqxmd.com/read/28801897/chromatin-immunoprecipitation-and-quantitative-real-time-pcr-to-assess-binding-of-a-protein-of-interest-to-identified-predicted-binding-sites-within-a-promoter
#16
Jordan E Read
Chromatin immunoprecipitation (ChIP) has become a widely used methodology for assessment of protein/DNA interactions. The technique allows the analysis of direct binding of transcription factors to gene promoters, identification of histone modifications, and localization of DNA modifying enzymes. Antibodies conjugated to agarose beads can be utilized to immunoprecipitate specific proteins, cross-linked to sheared chromatin regions to which they are bound endogenously. With downstream applications including quantitative real-time polymerase chain reaction (qRT-PCR), genome-wide sequencing (ChIP-seq), microarray analysis (ChIP-chip), and mass spectrometry (ChIP-MS), the technique enables comprehensive assessment of protein/DNA interactions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28801824/two-dimensional-capillary-zone-electrophoresis-mass-spectrometry-for-the-characterization-of-intact-monoclonal-antibody-charge-variants-including-deamidation-products
#17
Kevin Jooß, Jens Hühner, Steffen Kiessig, Bernd Moritz, Christian Neusüß
Capillary zone electrophoresis (CZE) is a powerful tool that is progressively being applied for the separation of monoclonal antibody (mAb) charge variants. Mass spectrometry (MS) is the desired detection method concerning identification of mAb variants. In biopharmaceutical applications, there exist optimized and validated electrolyte systems for mAb variant quantification. However, these electrolytes interfere greatly with the electrospray ionization (ESI) process. Here, a heart-cut CZE-CZE-MS setup with an implemented mechanical four-port valve interface was developed that used a generic ε-aminocaproic acid based background electrolyte in the first dimension and acetic acid in the second dimension...
August 12, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28800361/identification-of-a-common-ara-h-3-epitope-recognized-by-both-the-capture-and-the-detection-monoclonal-antibodies-in-an-elisa-detection-kit
#18
Lipei Zhao, Liang Zhao, Buchang Zhang, Jason M Robotham, Kenneth H Roux, Hengli Tang
Allergy to peanuts has become a common and severe problem, especially in westernized countries. In this study, we evaluated the target and epitope specificity of the capture and detection mouse monoclonal antibodies (mAbs) used in a commercial peanut allergen detection platform. We first identified the target of these antibodies as Ara h 3 and then used an overlapping peptide array of Ara h 3 to determine the antibody-binding epitopes. Further amino acids critical for the binding via alanine substitutions at individual amino acid residues within the epitope were mapped...
2017: PloS One
https://www.readbyqxmd.com/read/28796948/identification-of-polyphenol-specific-innate-epitopes-originated-from-a-resveratrol-analogue
#19
Mai Furuhashi, Yukinori Hatasa, Sae Kawamura, Takahiro Shibata, Mitsugu Akagawa, Koji Uchida
Polyphenols have received significant attention in disease prevention due to their unique chemical and biological properties. However, the underlying molecular mechanism for their beneficial effects remains unclear. We have now identified a polyphenol as a source of innate epitopes detected in natural IgM and established a unique gain-of-function mechanism in the formation of innate epitopes by polyphenol via the polymerization of proteins. Upon incubation with bovine serum albumin (BSA) under physiological conditions, several polyphenols converted the protein into the innate epitopes recognized by the IgM antibodies...
August 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28796894/subtractive-phage-display-selection-for-screening-and-identification-of-peptide-sequences-with-potential-use-in-serodiagnosis-of-paracoccidioidomycosis-caused-by-paracoccidioides-brasiliensis
#20
Leticia da Silva Portes, Erika Seki Kioshima, Zoilo Pires de Camargo, Wagner Luiz Batista, Patricia Xander
Paracoccidioidomycosis (PCM) is a systemic granulomatous disease endemic in Latin America whose aetiologic agents are the thermodimorphic fungi Paracoccidioides brasiliensis and Paracoccidioides lutzii. Despite technological advances, some problems have been reported for the fungal antigens used for serological diagnosis, and inconsistencies among laboratories have been reported. The use of synthetic peptides in the serological diagnosis of infectious diseases has proved to be a valuable strategy because in some cases, the reactions are more specific and sensitive...
August 10, 2017: Letters in Applied Microbiology
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