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https://www.readbyqxmd.com/read/29228397/yeast-identification-by-sequencing-biochemical-kits-maldi-tof-ms-and-rep-pcr-dna-fingerprinting
#1
Ying Zhao, Chi-Ching Tsang, Meng Xiao, Jasper F W Chan, Susanna K P Lau, Fanrong Kong, Yingchun Xu, Patrick C Y Woo
No study has comprehensively evaluated the performance of 28S nrDNA and ITS sequencing, commercial biochemical test kits, MALDI-TOF MS platforms, and the emerging rep-PCR DNA fingerprinting technology using a cohort of yeast strains collected from a clinical microbiology laboratory. In this study, using 71 clinically important yeast isolates (excluding Candida albicans) collected from a single centre, we determined the concordance of 28S nrDNA and ITS sequencing and evaluated the performance of two commercial test kits, two MALDI-TOF MS platforms, and rep-PCR DNA fingerprinting...
December 8, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29228361/identification-of-clinical-isolates-of-aspergillus-including-cryptic-species-by-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-maldi-tof-ms
#2
M Reyes Vidal-Acuña, Maite Ruiz-Pérez de Pipaón, María José Torres-Sánchez, Javier Aznar
An expanded library of matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been constructed using the spectra generated from 42 clinical isolates and 11 reference strains, including 23 different species from 8 sections (16 cryptic plus 7 noncryptic species). Out of a total of 379 strains of Aspergillus isolated from clinical samples, 179 strains were selected to be identified by sequencing of beta-tubulin or calmodulin genes. Protein spectra of 53 strains, cultured in liquid medium, were used to construct an in-house reference database in the MALDI-TOF MS...
December 8, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29228202/activity-of-ceftazidime-avibactam-against-problem-enterobacteriaceae-and-pseudomonas-aeruginosa-in-the-uk-2015-16
#3
David M Livermore, Danièle Meunier, Katie L Hopkins, Michel Doumith, Robert Hill, Rachel Pike, Peter Staves, Neil Woodford
Background: Ceftazidime/avibactam combines an established oxyimino-cephalosporin with the first diazabicyclooctane β-lactamase inhibitor to enter clinical use. We reviewed its activity against Gram-negative isolates, predominantly from the UK, referred for resistance investigation in the first year of routine testing, beginning in July 2015. Methods: Isolates were as received from referring laboratories; there is a bias to submit those with suspected carbapenem resistance...
December 8, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29227188/clinical-strains-of-chryseobacterium-and-elizabethkingia-spp-isolated-from-pediatric-patients-in-a-university-hospital-performance-of-maldi-tof-ms-based-identification-antimicrobial-susceptibilities-and-baseline-patient-characteristics
#4
Hasan Cenk Mirza, Özlem Tuncer, Serpil Ölmez, Burçin Şener, Gökçen Dilşa Tuğcu, Uğur Özçelik, Nafia Canan Gürsoy, Barış Otlu, Ayşe Büyükçam, Ateş Kara, Banu Sancak
Our objective was to evaluate the performance of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for identification of the Chryseobacterium and Elizabethkingia spp. isolated from pediatric patients at Hacettepe University Hospital using 16S rRNA gene sequencing as the gold standard and to determine the antimicrobial susceptibility patterns of the isolates and baseline characteristics of patients. All stored Chryseobacterium and Elizabethkingia spp. isolated from various clinical specimens (sputum, blood, and urine) of pediatric patients at Hacettepe University Hospital between 2012 and 2016 were included in this study...
December 11, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29227110/itraq-quantitative-proteomic-profiling-and-maldi-msi-of-colon-cancer-spheroids-treated-with-combination-chemotherapies-in-a-3d-printed-fluidic-device
#5
Gabriel J LaBonia, Katelyn R Ludwig, C Bruce Mousseau, Amanda B Hummon
For a patient with metastatic colorectal cancer there are limited clinical options aside from chemotherapy. Unfortunately, the development of new chemotherapeutics is a long and costly process. New methods are needed to identify promising drug candidates earlier in the drug development process. Most chemotherapies are administered to patients in combinations. Here, an in vitro platform is used to assess the penetration and metabolism of combination chemotherapies in three-dimensional colon cancer cell cultures, or spheroids...
December 11, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29226683/permeability-barriers-for-nicotine-and-mannitol-in-porcine-buccal-mucosa-studied-by-high-resolution-maldi-mass-spectrometry-imaging
#6
Eva Marxen, Jette Jacobsen, Birgitte Hyrup, Christian Janfeldt
Improved nicotine permeability across buccal mucosa may enable more effective oromucosal nicotine replacement therapy products. It is essential to know the location and composition of the main barrier for drug diffusion to enhance the drug permeability. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) is a rapidly evolving technique that can be used to image the spatial distribution of drugs and drug metabolites in tissue cryo-sections, without prior labeling of the drug. In this study, the distribution of nicotine and mannitol in porcine buccal mucosa was imaged with 10 µm spatial resolution after apical as well as submucosal application of the drugs, in order to localize the main permeability barrier(s)...
December 11, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29226434/protein-identification-in-imaging-mass-spectrometry-through-spatially-targeted-liquid-micro-extractions
#7
Daniel J Ryan, David Nei, Boone M Prentice, Kristie L Rose, Richard M Caprioli, Jeffrey M Spraggins
RATIONALE: Liquid extraction surface analysis (LESA) can be used to generate spatially-directed protein identifications in an imaging mass spectrometry (IMS) workflow. This approach involves the use of robotic micro-extractions coupled to online liquid chromatography (LC). We have characterized the extraction efficiency of this method as well as its ability to identify proteins from a matrix assisted laser/desorption ionization (MALDI) IMS experiment. METHODS: Proteins and peptides were extracted from transverse sections of a rat brain and sagittal sections of a mouse pup using liquid surface extractions...
December 10, 2017: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/29225047/maldi-tof-ms-analysis-as-a-useful-tool-for-an-identification-of-legionella-pneumophila-a-facultatively-pathogenic-bacterium-interacting-with-free-living-amoebae-a-case-study-from-water-supply-system-of-hospitals-in-bratislava-slovakia
#8
Katarína Trnková, Martina Kotrbancová, Margita Špaleková, Miriam Fulová, Jana Boledovičová, Matej Vesteg
Legionellae, i.e. Legionella pneumophila, are human bacterial hydrophilic facultative pathogens causing pneumonia (Legionnaires' disease). Free-living amoebae (FLA) can serve as natural hosts and thus as reservoirs of many amoebae-resistant bacteria. An encysted amoeba can contribute to the resistance of intracellular L. pneumophila to various chemical and physical treatments. Humans can be infected by droplets containing bacteria from an environmental source or human-made devices such as shower heads, bathtubs, air-conditioning units or whirlpools...
December 7, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/29224965/concerted-action-of-dipeptidyl-peptidase-iv-and-glutaminyl-cyclase-results-in-formation-of-pyroglutamate-modified-amyloid-peptides-in-vitro
#9
Alvard Antonyan, Dagmar Schlenzig, Stephan Schilling, Marcel Naumann, Svetlana Sharoyan, Sona Mardanyan, Hans-Ulrich Demuth
Compelling evidence suggests a crucial role of amyloid beta peptides (Aβ(1-40/42)) in the etiology of Alzheimer's disease (AD). The N-terminal truncation of Aβ(1-40/42) and their modification, e.g. by glutaminyl cyclase (QC), is expected to enhance the amyloid toxicity. In this work, the MALDI-TOF mass spectrometry application proved N-terminal cleavage of Aβ(1-40/42) by purified dipeptidyl peptidase IV (DPPIV) in vitro observed earlier. The subsequent transformation of resulted Aβ(3-40/42) to pE-Aβ(3-40/42) in QC catalyzed glutamate cyclization was manifested...
December 7, 2017: Neurochemistry International
https://www.readbyqxmd.com/read/29224733/validated-maldi-tof-ms-method-for-anthrax-lethal-factor-provides-early-diagnosis-and-evaluation-of-therapeutics
#10
Maribel Gallegos-Candela, Anne E Boyer, Adrian R Woolfitt, Judy Brumlow, Renato C Lins, Conrad P Quinn, Alex R Hoffmaster, Gabriel Meister, John R Barr
Anthrax lethal factor (LF) is a zinc-dependent endoprotease and a critical virulence factor for Bacillus anthracis, the causative agent of anthrax. The mass spectrometry (MS) method for total-LF quantification includes three steps; 1) LF specific antibody capture/concentration, 2) LF-specific hydrolysis of a peptide substrate, and 3) detection and quantification of LF-cleaved peptides by isotope-dilution MALDI-TOF/MS. Recombinant LF spiked plasma was used for calibration and quality control (QC) materials. Specificity was 100% from analysis of serum and plasma from 383 non-infected humans, 31 rabbits, and 24 rhesus macaques...
December 7, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/29224161/quantitative-region-specific-dna-methylation-analysis-by-the-epityper%C3%A2-technology
#11
Sonja Kunze
DNA methylation plays a profound role in development and health as well as development and progression of disease. High-throughput quantitative DNA methylation analysis is therefore crucial for the study of the normal physiology of the epigenome and its dysregulation in disease. Many target areas are identified by a range of emerging genome-wide cytosine methylation techniques, but these whole genome scans usually only provide methylation data for a few individual CpG sites (CpGs) within a region. The EpiTYPER™ assay is a region-specific method for the detection and quantitative analysis of DNA methylation that allows performing a high-resolution scan of selected regions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224050/maldi-imaging-combined-with-laser-microdissection-based-microproteomics-for-protein-identification-application-to-intratumor-heterogeneity-studies
#12
Rémi Longuespée, Deborah Alberts, Dominique Baiwir, Gabriel Mazzucchelli, Nicolas Smargiasso, Edwin De Pauw
Matrix-assisted laser desorption ionization (MALDI) imaging is widely used for in situ proteomic mapping and finds multiple applications in pathology. However, low fragmentation yields in MALDI avoid an optimal identification of peptides from tissues. On the other hand, LMD-based microproteomic analyses allow for the identification of hundreds to thousands of proteins from small tissue regions. Herein, we present the combination of MALDI imaging and LMD-based microproteomic approaches for parallel identification...
December 10, 2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223927/biochemical-characterization-of-the-ybpci-miniprotein-the-first-carboxypeptidase-inhibitor-isolated-from-yellow-bell-pepper-capsicum-annuum-l-a-novel-contribution-to-the-knowledge-of-miniproteins-stability
#13
Juliana Cotabarren, Mariana Edith Tellechea, Francesc Xavier Avilés, Julia Lorenzo, Walter David Obregón
The cystine-knot metallocarboxypeptidase inhibitors (MCPIs) are peptides that contribute to control proteolytic activity, involved in storage, growth and maintenance of plants. Lately studies reported several MCPIs with potential use in biomedical applications; as anti-cancer, anti-thrombotic, anti-malaric and anti-angiogenic agents. We report the isolation, purification, chemical stability and biochemical characterization of a novel carboxypeptidase A inhibitor (YBPCI) isolated from Capsicum annuum L. var...
December 6, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/29223155/recombinant-human-erythropoietin-with-additional-processable-protein-domains-purification-of-protein-synthesized-in-escherichia-coli-heterologous-expression-system
#14
T M Grunina, A V Demidenko, A M Lyaschuk, M S Poponova, Z M Galushkina, L A Soboleva, S A Cherepushkin, N B Polyakov, D A Grumov, A I Solovyev, V G Zhukhovitsky, I S Boksha, M E Subbotina, A V Gromov, V G Lunin, A S Karyagina
Three variants of human recombinant erythropoietin (rhEPO) with additional N-terminal protein domains were obtained by synthesis in an Escherichia coli heterologous expression system. These domains included (i) maltose-binding protein (MBP), (ii) MBP with six histidine residues (6His) in N-terminal position, (iii) s-tag (15-a.a. oligopeptide derived from bovine pancreatic ribonuclease A) with N-terminal 6His. Both variants of the chimeric protein containing MBP domain were prone to aggregation under nondenaturing conditions, and further purification of EPO after the domain cleavage by enterokinase proved to be impossible...
November 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29223016/application-of-single-nucleotide-extension-and-maldi-tof-mass-spectrometry-in-proofreading-and-dna-repair-assay
#15
Kang-Yi Su, Hung-Ming Lai, Steven D Goodman, Wei-Yao Hu, Wern-Cherng Cheng, Liang-In Lin, Ya-Chien Yang, Woei-Horng Fang
Proofreading and DNA repair are important factors in maintaining the high fidelity of genetic information during DNA replication. Herein, we designed a non-labeled and non-radio-isotopic simple method to measure proofreading. An oligonucleotide primer is annealed to a template DNA forming a mismatched site and is proofread by Klenow fragment of Escherichia coli DNA polymerase I (pol I) in the presence of all four dideoxyribonucleotide triphosphates. The proofreading excision products and re-synthesis products of single nucleotide extension are subjected to MALDI-TOF mass spectrometry (MS)...
December 2, 2017: DNA Repair
https://www.readbyqxmd.com/read/29223009/influence-of-spermatozoal-lipidomic-profile-on-the-cryoresistance-of-frozen-spermatozoa-from-stallions
#16
T Cabrera, C Ramires-Neto, K R A Belaz, C P Freitas-Dell'aqua, D Zampieri, A Tata, M N Eberlin, M A Alvarenga, F F Souza
The membrane of spermatozoa, which contributes to cellular cryoresistance, contains numerous lipids with a composition that directly affects membrane fluidity and the fertilization process. In light of variations in the degree of sensitivity in equine seminal freezing, this study aimed to correlate equine semen lipids with post-thawing characteristics of spermatozoa. We used ejaculates from 34 stallions, which were evaluated (total motility ≥ 60%), frozen and thawed and reevaluated for motility of spermatozoa, membrane integrity and lipid peroxidation...
November 26, 2017: Theriogenology
https://www.readbyqxmd.com/read/29222021/identification-and-validation-of-salivary-proteomic-signatures-for-non-invasive-detection-of-ovarian-cancer
#17
Md Tajmul, Farhat Parween, Lata Singh, Sandeep R Mathur, J B Sharma, Sunesh Kumar, D N Sharma, Savita Yadav
Ovarian cancer (OC) is one of the most lethal cancers among all gynecological malignancies. An effective and non-invasive screening approach is needed urgently to reduce high mortality rate. The purpose of this study was to identify the salivary protein signatures (SPS) for non-invasive detection of ovarian cancer. Differentially expressed SPS were identified by fluorescence-based 2D-DIGE coupled with MALDI/TOF-MS. The expression levels of three differential proteins (Lipocalin-2, indoleamine-2, 3-dioxygenase1 (IDO1) and S100A8) were validated using western blotting and ELISA...
December 5, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29221866/a-capillary-zone-electrophoresis-method-for-detection-of-apolipoprotein-c-iii-glycoforms-and-other-related-artifactually-modified-species
#18
Coralie Ruel, Marco Morani, Arnaud Bruneel, Christophe Junot, Myriam Taverna, François Fenaille, Thuy Tran
ApolipoproteinC-III (ApoC-III) is a human plasma glycoprotein whose O-glycosylation can be altered as a result of congenital disorders of glycosylation (CDG). ApoC-III exhibits three major glycoforms whose relative quantification is of utmost importance for the diagnosis of CDG patients. Considering the very close structures of these glycoforms and their tendency to adsorb on the capillary, a thorough optimization of capillary electrophoresis (CE) parameters including preconditioning and in-between rinsing procedures was required to efficiently separate all the ApoC-III glycoforms...
December 5, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29221301/matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-a-powerful-tool-for-identification-of-corynebacterium-species
#19
Rong Bao, Xiaodong Gao, Bijie Hu, Zhaoyan Zhou
Background: Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful tool that has initiated a revolution in the clinical microbiology laboratory for identification of nosocomial pathogens. The efficacy of MALDI-TOF MS produced by bioMerieux, Marcy l'Etoile, France (VITEK MS) for detecting Corynebacterium remains unknown. Methods: Corynebacterium isolates were isolated from clinical specimen in a tertial teaching hospital from 2012 to 2013...
September 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29220567/the-structural-basis-of-the-histone-demethylase-kdm6b-histone-3-lysine-27-specificity
#20
Sarah Elizabeth Jones, Lars Olsen, Michael Gajhede
KDM subfamily 6 enzymes KDM6A and KDM6B specifically catalyse demethylation of di-/tri-methylated lysine on Histone 3 lysine 27 (H3K27me3/2) and play an important role in repression of developmental genes. Despite identical amino acid sequence in the immediate surroundings of H3K9me3/2 (ARKS) the enzymes do not catalyse demethylation of this general marker of repression. In order to address this question for KDM6B we used computational methods to identify H3(17-33) derived peptides with improved binding affinity, that would enable co-crystallization with the catalytic core of human KDM6B (ccKDM6B)...
December 8, 2017: Biochemistry
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