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https://www.readbyqxmd.com/read/29786757/copy-number-abnormality-of-acute-lymphoblastic-leukemia-cell-lines-based-on-their-genetic-subtypes
#1
Chihiro Tomoyasu, Toshihiko Imamura, Toshihiro Tomii, Mio Yano, Daisuke Asai, Hiroaki Goto, Akira Shimada, Masashi Sanada, Shotaro Iwamoto, Junko Takita, Masayoshi Minegishi, Takeshi Inukai, Kanji Sugita, Hajime Hosoi
In this study, we performed genetic analysis of 83 B cell precursor acute lymphoblastic leukemia (B-ALL) cell lines. First, we performed multiplex ligation-dependent probe amplification analysis to identify copy number abnormalities (CNAs) in eight genes associated with B-ALL according to genetic subtype. In Ph+ B-ALL cell lines, the frequencies of IKZF1, CDKN2A/2B, BTG1, and PAX5 deletion were significantly higher than those in Ph- B-ALL cell lines. The frequency of CDKN2A/2B deletion in KMT2A rearranged cell lines was significantly lower than that in non-KMT2A rearranged cell lines...
May 21, 2018: International Journal of Hematology
https://www.readbyqxmd.com/read/29785012/multiplex-assessment-of-protein-variant-abundance-by-massively-parallel-sequencing
#2
Kenneth A Matreyek, Lea M Starita, Jason J Stephany, Beth Martin, Melissa A Chiasson, Vanessa E Gray, Martin Kircher, Arineh Khechaduri, Jennifer N Dines, Ronald J Hause, Smita Bhatia, William E Evans, Mary V Relling, Wenjian Yang, Jay Shendure, Douglas M Fowler
Determining the pathogenicity of genetic variants is a critical challenge, and functional assessment is often the only option. Experimentally characterizing millions of possible missense variants in thousands of clinically important genes requires generalizable, scalable assays. We describe variant abundance by massively parallel sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular abundance simultaneously. We apply VAMP-seq to quantify the abundance of 7,801 single-amino-acid variants of PTEN and TPMT, proteins in which functional variants are clinically actionable...
May 21, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29784904/differential-protein-profiling-as-a-potential-multi-marker-approach-for-obese-patients-with-heart-failure-a-retrospective-study
#3
Andrei Timotin, Mathieu Cinato, Frederic Boal, Sebastien Dejean, Rodica Anesia, Oleg Arnaut, Christine Lagente, Jerome Roncalli, Franck Desmoulin, Helene Tronchere, Oksana Kunduzova
Identification of novel circulating biomarkers predicting death and major cardio-metabolic events in obese patients with heart failure (HF) remains a research priority. In this study, we compared multi-marker profile of non-obese (NOB) and obese (OB) HF patients in relation to mortality outcome. The new multiplex proximity extension assay technology was used to analyze the levels of 92 proteins in plasma samples from HF patients according to body mass index (BMI) categories. At 2-year follow-up, all-cause mortality rates were significantly greater in NOB patients (BMI < 30 kg/m2 ) compared to the OB patients (BMI > 30 kg/m2 ) with HF (odds ratio 26; 95% CI: 1...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29783865/flow-cytometry-based-epitope-binning-using-competitive-binding-profiles-for-the-characterization-of-monoclonal-antibodies-against-cellular-and-soluble-protein-targets
#4
Brian M Chan, Anita Badh, Kelly A Berry, Stephanie A Grauer, Chadwick T King
A key step in the therapeutic antibody drug discovery process is early identification of diverse candidate molecules. Information comparing antibody binding epitopes can be used to classify antibodies within a large panel, guiding rational lead molecule selection. We describe a novel epitope binning method utilizing high-throughput flow cytometry (HTFC) that leverages cellular barcoding or spectrally distinct beads to multiplex samples to characterize antibodies raised against cell membrane receptor or soluble protein targets...
May 1, 2018: SLAS Discovery
https://www.readbyqxmd.com/read/29783746/an-electromagnetic-capacitive-composite-sensor-for-testing-of-thermal-barrier-coatings
#5
Yuan Ren, Mengchun Pan, Dixiang Chen, Wugang Tian
Thermal barrier coatings (TBCs) can significantly reduce the operating temperature of the aeroengine turbine blade substrate, and their testing technology is very urgently demanded. Due to their complex multi-layer structure, it is hard to evaluate TBCs with a single function sensor. In this paper, an electromagnetic/capacitive composite sensor is proposed for the testing of thermal barrier coatings. The dielectric material is tested with planar capacitor, and the metallic material is tested with electromagnetic coils...
May 19, 2018: Sensors
https://www.readbyqxmd.com/read/29783728/a-3d-printed-multichannel-viscometer-for-high-throughput-analysis-of-frying-oil-quality
#6
Sein Oh, Byeongyeon Kim, Sungyoung Choi
Viscosity as a sensitive measure of material changes is a potential quality-control parameter for simple and rapid assessment of frying oil quality. However, conventional viscometers require improvements in throughput, portability, cost-effectiveness and usability to be widely adopted for quality-control applications. Here we present a 3D-printed multichannel viscometer for simple, inexpensive and multiplexed viscosity measurement. The multichannel viscometer enables both parallel actuation of multiple fluid flows by pressing the plunger of the viscometer by hand and direct measurement of their relative volumes dispensed with naked eye...
May 19, 2018: Sensors
https://www.readbyqxmd.com/read/29783087/association-of-t-and-non-t-cell-cytokines-with-anhedonia-role-of-gender-differences
#7
Manish K Jha, Andrew H Miller, Abu Minhajuddin, Madhukar H Trivedi
OBJECTIVE: Among individual depressive symptoms, anhedonia has been reliably associated with activation of the innate immune response. However, it is unclear whether this association extends to T cell cytokines and if gender differentially affects this association. METHOD: Concentrations of T (IL-17, T-helper (Th) 1- and Th2-) and non-T cell cytokines were measured in plasma using the Bioplex Pro™ human cytokine multiplex kit in Combining Medications to Enhance Depression Outcomes (CO-MED) trial participants who provided plasma at baseline (n = 166)...
May 12, 2018: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/29783082/multiplexed-aptasensor-based-on-metal-ions-labels-for-simultaneous-detection-of-multiple-antibiotic-residues-in-milk
#8
Falan Li, Yemin Guo, Xiangyou Wang, Xia Sun
A dual-target electrochemical aptasensor was developed for the simultaneous detection of multiple antibiotics based on metal ions as signal tracers and nanocomposites as signal amplification strategy. Metal ions such as Cd2+ and Pb2+ could generate distinct differential pulse voltammetry (DPV) peaks. When targets were present, kanamycin (KAN) and streptomycin (STR) as models, the KAN aptamer (KAP) and STR aptamer (STP) were released from their complementary strands, with more change of Cd2+ and Pb2+ corresponding to peak currents...
April 13, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29783062/ykl-40-levels-increase-with-declining-ankle-brachial-index-and-are-associated-with-long-term-cardiovascular-mortality-in-peripheral-arterial-disease-patients
#9
Clemens Höbaus, Maximilian Tscharre, Carsten Thilo Herz, Gerfried Pesau, Thomas Wrba, Renate Koppensteiner, Gerit-Holger Schernthaner
BACKGROUND AND AIMS: YKL-40 is an inflammatory marker secreted by macrophages and is expressed in atherosclerotic plaques. YKL-40 increases in coronary artery disease (CAD) with poor coronary collateral vessel development. Higher levels are linked to reduced survival in CAD patients. Studies evaluating YKL-40 in patients with peripheral arterial disease (PAD) are scarce. This study aims to elucidate a possible link between YKL-40 and PAD severity as well as cardiovascular long-term mortality...
May 9, 2018: Atherosclerosis
https://www.readbyqxmd.com/read/29782964/an-in-vitro-approach-for-prioritization-and-evaluation-of-chemical-effects-on-glucocorticoid-receptor-mediated-adipogenesis
#10
Jessica K Hartman, Tyler Beames, Bethany Parks, Daniel Doheny, Gina Song, Alina Efremenko, Miyoung Yoon, Briana Foley, Chad Deisenroth, Patrick D McMullen, Rebecca A Clewell
Rising obesity rates worldwide have socio-economic ramifications. While genetics, diet, and lack of exercise are major contributors to obesity, environmental factors may enhance susceptibility through disruption of hormone homeostasis and metabolic processes. The obesogen hypothesis contends that chemical exposure early in development may enhance adipocyte differentiation, thereby increasing the number of adipocytes and predisposing for obesity and metabolic disease. We previously developed a primary human adipose stem cell (hASC) assay to evaluate the effect of environmental chemicals on PPARG-dependent adipogenesis...
May 18, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29782489/systematic-identification-of-factors-mediating-accelerated-mrna-degradation-in-response-to-changes-in-environmental-nitrogen
#11
Darach Miller, Nathan Brandt, David Gresham
Cellular responses to changing environments frequently involve rapid reprogramming of the transcriptome. Regulated changes in mRNA degradation rates can accelerate reprogramming by clearing or stabilizing extant transcripts. Here, we measured mRNA stability using 4-thiouracil labeling in the budding yeast Saccharomyces cerevisiae during a nitrogen upshift and found that 78 mRNAs are subject to destabilization. These transcripts include Nitrogen Catabolite Repression (NCR) and carbon metabolism mRNAs, suggesting that mRNA destabilization is a mechanism for targeted reprogramming of the transcriptome...
May 21, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29782292/evaluation-of-symptomatic-patients-with-resistant-discharge
#12
Cemile Sonmez, Selma Usluca, Ismail Hakki Usluca, Irem Kalipci, Figen Sezen, Cemal Resat Atalay, Selcuk Kilic
The aim of this study was to detect the presence of Chlamydia trachomatis, Neisseria (N.) gonorrhoeae, Mycoplasma (M.) hominis, M. genitalium, Ureaplasma (U.) urealyticum, and Trichomonas (T.) vaginalis in patients with resistant discharge. The study also evaluated the concordance of the diagnostic tests. Samples from 156 patients were tested by direct microscopy and culture for T. vaginalis and Mycoplasma IES for M. hominis and U. urealyticum. Multiplex Polymerase Chain Reaction (PCR) was used to determine the presence of six agents...
April 2018: Acta Dermatovenerologica Croatica: ADC
https://www.readbyqxmd.com/read/29782216/carbapenemase-producing-carbapenem-resistant-enterobacteriaceae-from-bangkok-thailand-and-their-detection-by-the-carba-np-and-modified-carbapenem-inactivation-method-tests
#13
Warawut Laolerd, Yukihiro Akeda, Likit Preeyanon, Panan Ratthawongjirakul, Pitak Santanirand
AIM: The purpose of the study was to determine the epidemiology of carbapenemase genes among carbapenem-resistant Enterobacteriaceae and evaluate the Carba NP and modified carbapenem inactivation method (mCIM) tests in their detection. MATERIALS AND METHODS: A total of 287 nonduplicated Enterobacteriaceae isolates, which were at least resistant to one of the carbapenems, were identified and detected for carbapenemase genes by multiplex PCR covering blaKPC , blaNDM , blaVIM , blaIMP , and blaOXA-48-like ...
May 21, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/29782012/a-microfluidic-platform-for-longitudinal-imaging-in-caenorhabditis-elegans
#14
Kyung Suk Lee, Erel Levine
In the last decade, microfluidic techniques have been applied to study small animals, including the nematode Caenorhabditis elegans, and have proved useful as a convenient live imaging platform providing capabilities for precise control of experimental conditions in real time. In this article, we demonstrate live imaging of individual worms employing WormSpa, a previously-published custom microfluidic device. In the device, multiple worms are individually confined to separate chambers, allowing multiplexed longitudinal surveillance of various biological processes...
May 2, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29782011/a-preclinical-mouse-model-of-osteosarcoma-to-define-the-extracellular-vesicle-mediated-communication-between-tumor-and-mesenchymal-stem-cells
#15
Tonny Lagerweij, Maria Pérez-Lanzón, S Rubina Baglio
Within the tumor microenvironment, resident or recruited mesenchymal stem cells (MSCs) contribute to malignant progression in multiple cancer types. Under the influence of specific environmental signals, these adult stem cells can release paracrine mediators leading to accelerated tumor growth and metastasis. Defining the crosstalk between tumor and MSCs is of primary importance to understand the mechanisms underlying cancer progression and identify novel targets for therapeutic intervention. Cancer cells produce high amounts of extracellular vesicles (EVs), which can profoundly affect the behavior of target cells in the tumor microenvironment or at distant sites...
May 6, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29781987/retrospective-microrna-sequencing-complementary-dna-library-preparation-protocol-using-formalin-fixed-paraffin-embedded-rna-specimens
#16
Olivier Loudig, Christina Liu, Thomas Rohan, Iddo Z Ben-Dov
-Archived, clinically classified formalin-fixed paraffin-embedded (FFPE) tissues can provide nucleic acids for retrospective molecular studies of cancer development. By using non-invasive or pre-malignant lesions from patients who later develop invasive disease, gene expression analyses may help identify early molecular alterations that predispose to cancer risk. It has been well described that nucleic acids recovered from FFPE tissues have undergone severe physical damage and chemical modifications, which make their analysis difficult and generally requires adapted assays...
May 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29780875/amyloid-%C3%AE-peptides-are-differentially-vulnerable-to-preanalytical-surface-exposure-an-effect-incompletely-mitigated-by-the-use-of-ratios
#17
Jamie Toombs, Martha S Foiani, Henrietta Wellington, Ross W Paterson, Charles Arber, Amanda Heslegrave, Michael P Lunn, Jonathan M Schott, Selina Wray, Henrik Zetterberg
Introduction: We tested the hypothesis that the amyloid β (Aβ) peptide ratios are more stable than Aβ42 alone when biofluids are exposed to two preanalytical conditions known to modify measurable Aβ concentration. Methods: Human cerebrospinal fluid (CSF) and culture media (CM) from human cortical neurons were exposed to a series of volumes and polypropylene surfaces. Aβ42 , Aβ40 , and Aβ38 peptide concentrations were measured using a multiplexed electrochemiluminescence immunoassay...
2018: Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring
https://www.readbyqxmd.com/read/29780847/community-acquired-respiratory-paramyxovirus-infection-after-allogeneic-hematopoietic-cell-transplantation-a-single-center-experience
#18
Yasmin Spahr, Sarah Tschudin-Sutter, Veronika Baettig, Francesca Compagno, Michael Tamm, Jörg Halter, Sabine Gerull, Jakob Passweg, Hans H Hirsch, Nina Khanna
Background: Paramyxoviruses include respiratory syncytial virus (RSV), parainfluenza virus (PIV), and human metapneumovirus (MPV), which may cause significant respiratory tract infectious disease (RTID) and mortality after allogeneic hematopoietic cell transplantation (HCT). However, clinical data regarding frequency and outcome are scarce. Methods: We identified all paramyxovirus RTIDs in allogeneic HCT recipients diagnosed by multiplex polymerase chain reaction between 2010 and 2014...
May 2018: Open Forum Infectious Diseases
https://www.readbyqxmd.com/read/29780522/a-single-electrode-electrochemical-system-for-multiplex-electrochemiluminescence-analysis-based-on-a-resistance-induced-potential-difference
#19
Wenyue Gao, Kateryna Muzyka, Xiangui Ma, Baohua Lou, Guobao Xu
Developing low-cost and simple electrochemical systems is becoming increasingly important but still challenged for multiplex experiments. Here we report a single-electrode electrochemical system (SEES) using only one electrode not only for a single experiment but also for multiplex experiments based on a resistance induced potential difference. SEESs for a single experiment and multiplex experiments are fabricated by attaching a self-adhesive label with a hole and multiple holes onto an ITO electrode, respectively...
April 28, 2018: Chemical Science
https://www.readbyqxmd.com/read/29780463/simultaneous-multiple-single-nucleotide-polymorphism-detection-based-on-click-chemistry-combined-with-dna-encoded-probes
#20
Qian-Yu Zhou, Fang Yuan, Xiao-Hui Zhang, Ying-Lin Zhou, Xin-Xiang Zhang
Single nucleotide polymorphisms (SNPs) are emerging as important biomarkers for disease diagnosis, prognostics and disease pathogenesis. As one type of disease is always connected to several SNP sites, there is great demand for a reliable multiple SNP detection method. Herein, we mimicked a ligation reaction based on DNA ligase and originally utilized an enzyme-free DNA template-directed click reaction for SNP detection. With 5'-alkyne and 3'-azide groups labelled on two oligonucleotide probes, the target DNA-directed Cu(i)-catalyzed alkyne-azide cycloaddition (CuAAC) click reaction produced a new DNA strand with a triazole backbone, as a mimic of a DNA phosphodiester linkage...
April 7, 2018: Chemical Science
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