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https://www.readbyqxmd.com/read/29775619/proteomic-approach-to-profiling-immune-complex-antigens-in-cerebrospinal-fluid-samples-from-patients-with-central-nervous-system-autoimmune-diseases
#1
Nozomi Aibara, Kunihiro Ichinose, Miyako Baba, Hideki Nakajima, Katsuya Satoh, Ryuichiro Atarashi, Naoya Kishikawa, Noriyuki Nishida, Atsushi Kawakami, Naotaka Kuroda, Kaname Ohyama
BACKGROUND: Immune complexes (ICs) may clearly reflect immunological abnormalities caused by disease, especially for autoimmune diseases. Although ICs have been detected in cerebrospinal fluid (CSF) from patients with CNS autoimmune diseases, identities of antigens in such ICs have not been comprehensively determined. METHODS: We used immune complexome analysis, in which nano-liquid chromatography-tandem mass spectrometry is employed to comprehensively identify antigens incorporated into ICs in biological fluids, to characterize ICs in CSF samples from patients with CNS autoimmune diseases, and to find disease-specific IC antigen to a certain CNS autoimmune disease...
May 15, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29774984/comments-on-recent-reports-on-infrared-spectral-detection-of-disease-markers-in-blood-components
#2
Max Diem
The search for disease markers in whole blood, or easily accessible blood components by spectral methods is a highly important aspect in the field of biophotonic research for disease diagnostics and screening, since it promises a minimally invasive approach to assess an individual's state of health. Fourier transform infrared spectroscopy, in particular, promises to be a fast, inexpensive method to search for markers of disease, since it detects variation in the proteome, lipidome and metabolome of biofluids, or activation of immune cells...
May 18, 2018: Journal of Biophotonics
https://www.readbyqxmd.com/read/29774870/radiomics-in-gliomas-a-promising-assistance-for-glioma-clinical-research
#3
Yueshuang Leng, Xiaoyi Wang, Weihua Liao, Ya Cao
Gliomas are the most common brain primary tumors worldwide, which is the earliest sequenced cancer gene in the Cancer Genome Atlas (TCGA) project. The World Health Organization Classification Update of Central Nervous System (CNS) Tumors 2016 highlights that glioma is the first tumor classified based on both of the molecular markers and histology. Radiomics is an extraction approach for high-throughput data which collects the quantitative image information appearing. Combined imaging data with genomics and proteomics, radiomics show promising prediction for cancer diagnosis, treatment, and prognosis...
April 28, 2018: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/29774075/plectin-targeted-liposomes-enhance-the-therapeutic-efficacy-of-a-parp-inhibitor-in-the-treatment-of-ovarian-cancer
#4
Siva Sai Krishna Dasa, Galina Diakova, Ryo Suzuki, Anne M Mills, Michael F Gutknecht, Alexander L Klibanov, Jill K Slack-Davis, Kimberly A Kelly
Advances in genomics and proteomics drive precision medicine by providing actionable genetic alterations and molecularly targeted therapies, respectively. While genomic analysis and medicinal chemistry have advanced patient stratification with treatments tailored to the genetic profile of a patient's tumor, proteomic targeting has the potential to enhance the therapeutic index of drugs like poly(ADP-ribose) polymerase (PARP) inhibitors. PARP inhibitors in breast and ovarian cancer patients with BRCA1/2 mutations have shown promise...
2018: Theranostics
https://www.readbyqxmd.com/read/29773825/consistent-prediction-of-go-protein-localization
#5
Flavio E Spetale, Debora Arce, Flavia Krsticevic, Pilar Bulacio, Elizabeth Tapia
The GO-Cellular Component (GO-CC) ontology provides a controlled vocabulary for the consistent description of the subcellular compartments or macromolecular complexes where proteins may act. Current machine learning-based methods used for the automated GO-CC annotation of proteins suffer from the inconsistency of individual GO-CC term predictions. Here, we present FGGA-CC+ , a class of hierarchical graph-based classifiers for the consistent GO-CC annotation of protein coding genes at the subcellular compartment or macromolecular complex levels...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773674/deep-sequencing-of-complex-proteoglycans-a-novel-strategy-for-high-coverage-and-site-specific-identification-of-glycosaminoglycan-linked-peptides
#6
Joshua A Klein, Le Meng, Joseph Zaia
Proteoglycans are distributed in all animal tissues and play critical, multifaceted, physiological roles.  Expressed in a spatially- and temporally-regulated manner, these molecules regulate interactions among growth factors and cell surface receptors and play key roles in basement membranes and other extracellular matrices.  Due to the high degree of glycosylation by glycosaminoglycan (GAG), N-glycan and mucin-type O-glycan classes, the peptide sequence coverage of complex proteoglycans is revealed poorly by standard mass spectrometry-based proteomics methods...
May 17, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29772700/inhibition-of-arachidonate-12-15-lipoxygenase-improves-%C3%AE-galactosidase-efficacy-in-ipsc-derived-cardiomyocytes-from-fabry-patients
#7
Yueh Chien, Shih-Jie Chou, Yuh-Lih Chang, Hsin-Bang Leu, Yi-Ping Yang, Ping-Hsing Tsai, Ying-Hsiu Lai, Kuan-Hsuan Chen, Wei-Chao Chang, Shih-Hsien Sung, Wen-Chung Yu
(1) Background: A high incidence of intervening sequence (IVS)4+919 G>A mutation with later-onset cardiac phenotype have been reported in a majority of Taiwan Fabry cohorts. Some evidence indicated that conventional biomarkers failed to predict the long-term progression and therapeutic outcome; (2) Methods: In this study, we constructed an induced pluripotent stem cell (iPSC)-based platform from Fabry cardiomyopathy (FC) patients carrying IVS4+919 G>A mutation to screen for potential targets that may help the conventional treatment; (3) Results: The FC-patient-derived iPSC-differentiated cardiomyocytes (FC-iPSC-CMs) carried an expected IVS4+919 G>A genetic mutation and recapitulated several FC characteristics, including low α-galactosidase A enzyme activity and cellular hypertrophy...
May 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29770330/the-prediction-of-drug-disease-correlation-based-on-gene-expression-data
#8
Hui Cui, Menghuan Zhang, Qingmin Yang, Xiangyi Li, Michael Liebman, Ying Yu, Lu Xie
The explosive growth of high-throughput experimental methods and resulting data yields both opportunity and challenge for selecting the correct drug to treat both a specific patient and their individual disease. Ideally, it would be useful and efficient if computational approaches could be applied to help achieve optimal drug-patient-disease matching but current efforts have met with limited success. Current approaches have primarily utilized the measureable effect of a specific drug on target tissue or cell lines to identify the potential biological effect of such treatment...
2018: BioMed Research International
https://www.readbyqxmd.com/read/29765119/elucidation-of-inhibitory-effects-on-metastatic-sentinel-lymph-nodes-of-breast-cancer-during-one-step-nucleic-acid-amplification
#9
Yoshiya Horimoto, Masahiko Tanabe, Saiko Kazuno, Yoshiki Miura, Kaoru Mogushi, Hiroshi Sonoue, Atsushi Arakawa, Kazunori Kajino, Toshiyuki Kobayashi, Mitsue Saito
One-step nucleic acid amplification (OSNA) is an established method for intraoperative diagnosis of breast cancer metastasis in sentinel lymph nodes, based on quantification of CK19 mRNA, specific to breast epithelial cells. Inhibitors interfere with the PCR amplification process of PCR. Thus, OSNA, based on gene amplification without RNA purification, might be impacted by numerous factors persisting in a sample, and thereby potentially acting as PCR inhibitors. However, neither the characteristics of breast cancers showing inhibitory effects during OSNA, nor any of the possible inhibitors, have as yet been identified...
May 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29763921/peptidomic-analysis-of-endometrial-tissue-from-patients-with-ovarian-endometriosis
#10
Yunping Xue, Pengfei Xu, Sujuan Xu, Kai Xue, Lingling Xu, Jie Chen, Juan Xu, Xiaoyan Shi, Qian Li, Lin Gu
BACKGROUND/AIMS: Ovarian endometriosis (OvE) is ovarian cyst that is lined with endometrial tissue. They are found in 17-44% of women with endometriosis. Their clinical manifestations include pelvic pain, dysmenorrhea, dyspareunia, and infertility. Although the incidence of OvE has increased yearly, the exact pathogenesis of OvE is still unclear. We used peptidomics, an emerging branch of proteomics, to identify differentially expressed peptides in order to determine the possible roles of these peptides in the pathogenesis of OvE...
May 9, 2018: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29763592/coomassie-does-it-better-a-robin-hood-approach-to-total-protein-quantification
#11
Nour Noaman, Jens R Coorssen
Quantitative comparative proteomics require accurate and reproducible assessments of total protein concentration. We report a straightforward, cost-effective adaptation of an established commercial method for total protein quantification, utilising non-proprietary materials and colloidal Coomassie Brilliant Blue (cCBB) staining to achieve greater reproducibility, equal sensitivity, and optimal linearity of signal within a practical concentration range for proteins in common solubilisation buffers (i.e. for isoelectric focussing and/or SDS-PAGE)...
May 12, 2018: Analytical Biochemistry
https://www.readbyqxmd.com/read/29762646/correcting-mistakes-in-predicting-distributions
#12
Valérie Marot-Lassauzaie, Michael Bernhofer, Burkhard Rost
Motivation: Many applications monitor predictions of a whole range of features for biological datasets, e.g. the fraction of secreted human proteins in the human proteome. Results and error estimates are typically derived from publications. Results: Here, we present a simple, alternative approximation that uses performance estimates of methods to error-correct the predicted distributions. This approximation uses the confusion matrix (TP true positives, TN true negatives, FP false positives, and FN false negatives) describing the performance of the prediction tool for correction...
May 14, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29761697/identification-of-proteins-using-itraq-and-vigs-reveals-three-bread-wheat-proteins-involved-in-the-response-to-combined-osmotic-cold-stress
#13
Ning Zhang, Lingran Zhang, Chaonan Shi, Lei Zhao, Dangqun Cui, Feng Chen
Crops are often subjected to a combination of stresses in the field. To date, studies on the physiological and molecular responses of common wheat to a combination of osmotic and cold stresses, however, remain unknown. In this study, wheat seedlings exposed to osmotic-cold stress for 24 h showed inhibited growth, as well as increased lipid peroxidation, relative electrolyte leakage, and soluble sugar contents. iTRAQ-based quantitative proteomics and liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods were employed to determine the proteomic profiles of the roots and leaves of wheat seedlings exposed to osmotic-cold stress conditions...
May 15, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29761447/integration-of-plant-metabolomics-data-with-metabolic-networks-progresses-and-challenges
#14
Nadine Töpfer, Samuel M D Seaver, Asaph Aharoni
In the last decade, plant genome-scale modeling has developed rapidly and modeling efforts have advanced from representing metabolic behavior of plant heterotrophic cell suspensions to studying the complex interplay of cell types, tissues, and organs. A crucial driving force for such developments is the availability and integration of "omics" data (e.g., transcriptomics, proteomics, and metabolomics) which enable the reconstruction, extraction, and application of context-specific metabolic networks...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29760479/immunoprofiling-of-chlamydia-trachomatis-using-whole-proteome-microarrays-generated-by-on-chip-in-situ-expression
#15
Katrin Hufnagel, Smiths Lueong, Martina Willhauck-Fleckenstein, Agnes Hotz-Wagenblatt, Beiping Miao, Andrea Bauer, Angelika Michel, Julia Butt, Michael Pawlita, Jörg D Hoheisel, Tim Waterboer
Using Chlamydia trachomatis (Ct) as a complex model organism, we describe a method to generate bacterial whole-proteome microarrays using cell-free, on-chip protein expression. Expression constructs were generated by two successive PCRs directly from bacterial genomic DNA. Bacterial proteins expressed on microarrays display antigenic epitopes, thereby providing an efficient method for immunoprofiling of patients and allowing de novo identification of disease-related serum antibodies. Through comparison of antibody reactivity patterns, we newly identified antigens recognized by known Ct-seropositive samples, and antigens reacting only with samples from cervical cancer (CxCa) patients...
May 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29759191/comparative-evaluation-of-seven-commercial-products-for-human-serum-enrichment-depletion-by-shotgun-proteomics
#16
Salvatore Pisanu, Grazia Biosa, Laura Carcangiu, Sergio Uzzau, Daniela Pagnozzi
Seven commercial products for human serum depletion/enrichment were tested and compared by shotgun proteomics. Methods were based on four different capturing agents: antibodies (Qproteome Albumin/IgG Depletion kit, ProteoPrep Immunoaffinity Albumin and IgG Depletion Kit, Top 2 Abundant Protein Depletion Spin Columns, and Top 12 Abundant Protein Depletion Spin Columns), specific ligands (Albumin/IgG Removal), mixture of antibodies and ligands (Albumin and IgG Depletion SpinTrap), and combinatorial peptide ligand libraries (ProteoMiner beads), respectively...
August 1, 2018: Talanta
https://www.readbyqxmd.com/read/29759138/impact-of-imipramine-on-proteome-of-rat-primary-glial-cells
#17
Sylwia Kedracka-Krok, Bianka Swiderska, Anna M Bielecka-Wajdman, Gabriela Prus, Bozena Skupien-Rabian, Urszula Jankowska, Ewa Obuchowicz
Microglia and astrocytes, two types of glial cells are known to be important targets for antidepressant drugs. Here we used a comprehensive proteomic analysis to examine the effect of imipramine on rat primary mixed glial culture. The two-dimensional differential gel electrophoresis method allowed us to identify 62 proteins that were altered by imipramine. Functional analysis revealed that imipramine influenced the level of proteins involved in oxidative stress; in particular, it elevated the level of glutathione transferases...
July 15, 2018: Journal of Neuroimmunology
https://www.readbyqxmd.com/read/29758408/abundant-plasma-protein-depletion-using-ammonium-sulfate-precipitation-and-protein-a-affinity-chromatography
#18
Lentel Pringels, Valérie Broeckx, Kurt Boonen, Bart Landuyt, Liliane Schoofs
Plasma is a highly valuable resource for biomarker research since it is easy obtainable and contains a high amount of information on patient health status. Although advancements in the field of proteomics enabled analysis of the plasma proteome, identification of low abundant proteins remains challenging due to high complexity and large dynamic range. In order to reduce the dynamic range of protein concentrations, a tandem depletion technique consisting of ammonium sulfate precipitation and Protein A affinity chromatography was developed...
May 1, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/29757692/integrative-omics-from-data-to-biology
#19
Hassan Dihazi, Abdul R Asif, Tim Beißbarth, Rainer Bohrer, Kirstin Feussner, Ivo Feussner, Olaf Jahn, Christof Lenz, Andrzej Majcherczyk, Bernhard Schmidt, Kerstin Schmitt, Henning Urlaub, Oliver Valerius
Multi-omic approaches are promising a broader view on cellular processes and a deeper understanding of biological systems. With strongly improved high-throughput methods the amounts of data generated have become huge, and their handling challenging. New bioinformatic tools and pipelines for the integration of data from different omics disciplines continue to emerge, and will support scientists to reliably interpret data in the context of biological processes. Comprehensive data integration strategies will fundamentally improve systems biology and systems medicine...
May 14, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29757429/allofinder-a-strategy-for-allosteric-modulator-discovery-and-allosterome-analyses
#20
Min Huang, Kun Song, Xinyi Liu, Shaoyong Lu, Qiancheng Shen, Renxiao Wang, Jingze Gao, Yuanyuan Hong, Qian Li, Duan Ni, Jianrong Xu, Guoqiang Chen, Jian Zhang
Allostery tweaks innumerable biological processes and plays a fundamental role in human disease and drug discovery. Exploration of allostery has thus been regarded as a crucial requirement for research on biological mechanisms and the development of novel therapeutics. Here, based on our previously developed allosteric data and methods, we present an interactive platform called AlloFinder that identifies potential endogenous or exogenous allosteric modulators and their involvement in human allosterome. AlloFinder automatically amalgamates allosteric site identification, allosteric screening and allosteric scoring evaluation of modulator-protein complexes to identify allosteric modulators, followed by allosterome mapping analyses of predicted allosteric sites and modulators in human proteome...
May 11, 2018: Nucleic Acids Research
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