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https://www.readbyqxmd.com/read/28108354/abcs-of-dna-aptamer-and-related-assay-development
#1
REVIEW
Tarun Kumar Sharma, John G Bruno, Abhijeet Dhiman
This review is intended to guide the novice in aptamer research and development to understand virtually all of the aptamer development options and currently available assay modalities. Aptamer development topics range from discussions of basic and advanced versions of Systematic Evolution of Ligands by EXponential Enrichment (SELEX) and SELEX variations involving incorporation of exotic unnatural nucleotides to expand library diversity for even greater aptamer affinity and specificity to improved next generation methods of DNA sequencing, screening and tracking aptamer development throughout the SELEX process and characterization of lead aptamer candidates...
January 17, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28108183/evaluation-of-multiplex-assay-platforms-for-detection-of-influenza-hemagglutinin-subtype-specific-antibody-responses-influenza-ha-subtype-specific-antibody-detection-platform
#2
Zhu-Nan Li, Kimberly M Weber, Rebecca A Limmer, Bobbi J Horne, James Stevens, Joy Schwerzmann, Jens Wrammert, Megan McCausland, Andrew J Phipps, Kathy Hancock, Daniel B Jernigan, Min Levine, Jacqueline M Katz, Joseph D Miller
Influenza hemagglutination inhibition (HI) and virus microneutralization assays (MN) are widely used for seroprevalence studies. However, these assays have limited field portability and are difficult to fully automate for high throughput laboratory testing. To address these issues, three multiplex influenza subtype-specific antibody detection assays were developed using recombinant hemagglutinin antigens in combination with Chembio, Luminex(®), and ForteBio(®) platforms. Assay sensitivity, specificity, and subtype cross-reactivity were evaluated using a panel of well characterized human sera...
January 17, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28107998/multiplex-and-accurate-quantification-of-acute-kidney-injury-biomarker-candidates-in-urine-using-protein-standard-absolute-quantification-psaq-and-targeted-proteomics
#3
Benoît Gilquin, Mathilde Louwagie, Michel Jaquinod, Alexandre Cez, Guillaume Picard, Leila El Kholy, Brigitte Surin, Jérôme Garin, Myriam Ferro, Thomas Kofman, Caroline Barau, Emmanuelle Plaisier, Pierre Ronco, Virginie Brun
There is a need for multiplex, specific and quantitative methods to speed-up the development of acute kidney injury biomarkers and allow a more specific diagnosis. Targeted proteomic analysis combined with stable isotope dilution has recently emerged as a powerful option for the parallelized evaluation of candidate biomarkers. This article presents the development of a targeted proteomic assay to quantify 4 acute kidney injury biomarker candidates in urine samples. The proteins included in the assessed panel consisted of myo-inositol oxygenase (MIOX), phosphoenolpyruvate carboxykinase 1 (PCK1), neutrophil gelatinase-associated lipocalin (NGAL) and liver fatty acid-binding protein (L-FABP)...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107959/use-of-quantum-dot-beads-labeled-monoclonal-antibody-to-improve-the-sensitivity-of-a-quantitative-and-simultaneous-immunochromatographic-assay-for-neuron-specific-enolase-and-carcinoembryonic-antigen
#4
Kun Xiao, Kan Wang, Weijian Qin, Yafei Hou, Wenting Lu, Hao Xu, Yan Wo, Daxiang Cui
Detection of multiplex tumor markers was of great importance for cancer diagnosis. Immunochromatographic test strip (ICTS) was the most frequently-used point-of-care detection means. Herein, a convenient and fast method for simultaneous quantitative detection of neuron specific enolase (NSE) and carcinoembryonic antigen (CEA) was developed based on ICTS using quantum dot beads (QBs) as marking material. Good monodispersity, high colloidal stability and carboxyl-modified (COOH-) QBs were used. For this method, two test lines were applied to the NC membrane for simultaneous analysis of CEA and NSE respectively...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107943/development-of-a-nanoarray-capable-of-the-rapid-and-simultaneous-detection-of-zearalenone-t2-toxin-and-fumonisin
#5
Sara E McNamee, Francesca Bravin, Giulia Rosar, Christopher T Elliott, Katrina Campbell
Fusarium mycotoxins such as trichothecenes, zearalenone and fumonisins occur on a worldwide basis in cereal grains, animal feeds and forages. Practical solutions for multiple mycotoxin determination in samples are required by industry and regulators for cost effective screening purposes. The feasibility of developing a novel multiplex nanoarray for the simultaneous and semi-quantitative detection of three regulated mycotoxins: zearalenone (ZEA), T2-toxin (T2) and fumonisin B1 (FUM) was examined. Additionally, the assay was also able to detect HT2 toxin and fumonisin B2 and B3 due to the cross reactivity profiles of the antibodies used...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107927/electrochemical-detection-of-magnetically-entrapped-dna-sequences-from-complex-samples-by-multiplexed-enzymatic-labelling-application-to-a-transgenic-food-feed-quantitative-survey
#6
C L Manzanares-Palenzuela, J P Martín-Clemente, M J Lobo-Castañón, B López-Ruiz
Monitoring of genetically modified organisms in food and feed demands molecular techniques that deliver accurate quantitative results. Electrochemical DNA detection has been widely described in this field, yet most reports convey qualitative data and application in processed food and feed samples is limited. Herein, the applicability of an electrochemical multiplex assay for DNA quantification in complex samples is assessed. The method consists of the simultaneous magnetic entrapment via sandwich hybridisation of two DNA sequences (event-specific and taxon-specific) onto the surface of magnetic microparticles, followed by bienzymatic labelling...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107781/a-rare-hla-genotype-in-two-siblings-with-type-1-diabetes-in-a-japanese-family-clustered-with-type-1-diabetes
#7
Yujiro Ina, Yumiko Kawabata, Ryuichi Sakamoto, Naotaka Sekiguchi, Hiroshi Ikegami
Multiplex families with type 1 diabetes are important for identification of rare variants that cannot be identified in case-control association studies. Very low incidence of type 1 diabetes in Japanese population, however, makes identification of such families difficult. We identified a Japanese family in which three members developed type 1 diabetes, and studied the genotype of the HLA. All three members with type 1 diabetes had the DRB1*08:02-DQB1*03:02 haplotype, which is specific to the Asian population and strongly susceptible for type 1 diabetes...
January 20, 2017: Journal of Diabetes Investigation
https://www.readbyqxmd.com/read/28107671/recent-sequence-variation-in-probe-binding-site-affected-detection-of-respiratory-syncytial-virus-group-b-by-real-time-rt-pcr
#8
Everlyn Kamau, Charles N Agoti, Clement S Lewa, John Oketch, Betty E Owor, Grieven P Otieno, Anne Bett, Patricia A Cane, D James Nokes
BACKGROUND: Direct immuno-fluorescence test (IFAT) and multiplex real-time RT-PCR have been central to RSV diagnosis in Kilifi, Kenya. Recently, these two methods showed discrepancies with an increasing number of PCR undetectable RSV-B viruses. OBJECTIVES: Establish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity. STUDY DESIGN: Nucleoprotein (N) and glycoprotein (G) genes were sequenced for real-time RT-PCR positive and negative samples...
January 5, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28107507/a-multiplex-rt-pcr-assay-for-detection-and-differentiation-of-avian-origin-canine-h3n2-equine-origin-h3n8-human-origin-h3n2-and-h1n1-2009-canine-influenza-viruses
#9
Chenxi Wang, Qian Wang, Junyi Hu, Honglei Sun, Juan Pu, Jinhua Liu, Yipeng Sun
Virological and serological surveys have documented that H1N1/2009, avian-origin canine H3N2 (cH3N2), seasonal human-origin H3N2 (hH3N2), and equine-origin H3N8 influenza viruses are consistently circulating in dogs. In the present study, a multiplex reverse-transcriptase polymerase chain reaction (mRT-PCR) assay was developed for simultaneous detection and differentiation of these influenza viruses. Four primer sets were designed to target the hemagglutinin genes of H1N1/2009, cH3N2, hH3N2, and H3N8 canine influenza viruses (CIVs)...
2017: PloS One
https://www.readbyqxmd.com/read/28106562/plasma-amyloid-%C3%AE-peptides-in-type-2-diabetes-a-matched-case-control-study
#10
Kirsten E Peters, Wendy A Davis, Kevin Taddei, Ralph N Martins, Colin L Masters, Timothy M E Davis, David G Bruce
BACKGROUND: Plasma amyloid-β (Aβ) levels have rarely been investigated in type 2 diabetes despite its known associations with Alzheimer's disease. OBJECTIVE: To compare blood plasma Aβ concentrations (Aβ40 and Aβ42) in cognitively normal individuals with and without type 2 diabetes. METHODS: Plasma Aβ40 and Aβ42 were measured in 194 participants with diabetes recruited from the community-based Fremantle Diabetes Study Phase II cohort (mean age 71 years, 59% males) and 194 age-, sex-, and APOEɛ4 allele-matched, control subjects without diabetes from the Australian Imaging, Biomarkers and Lifestyle Study using a multiplex microsphere-based immunoassay...
January 19, 2017: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/28106132/m-otdr-sensing-system-based-on-3d-encoded-microstructures
#11
Qizhen Sun, Fan Ai, Deming Liu, Jianwei Cheng, Hongbo Luo, Kuan Peng, Yiyang Luo, Zhijun Yan, Perry Ping Shum
In this work, a quasi-distributed sensing scheme named as microstructured OTDR (M-OTDR) by introducing ultra-weak microstructures along the fiber is proposed. Owing to its relative higher reflectivity compared with the backscattered coefficient in fiber and three dimensional (3D) i.e. wavelength/frequency/time encoded property, the M-OTDR system exhibits the superiorities of high signal to noise ratio (SNR), high spatial resolution of millimeter level and high multiplexing capacity up to several ten thousands theoretically...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28106114/multiplexing-pka-and-erk1-2-kinases-fret-biosensors-in-living-cells-using-single-excitation-wavelength-dual-colour-flim
#12
Claire Demeautis, François Sipieter, Julien Roul, Catherine Chapuis, Sergi Padilla-Parra, Franck B Riquet, Marc Tramier
Monitoring of different signalling enzymes in a single assay using multiplex biosensing provides a multidimensional workspace to elucidate biological processes, signalling pathway crosstalk, and determine precise sequence of events at the single living cell level. In this study, we interrogate the complexity in cAMP/PKA-MAPK/ERK1&2 crosstalk by using multi-parameter biosensing experiments to correlate biochemical activities simultaneously in time and space. Using a single excitation wavelength dual colour FLIM method we are able to detect fluorescence lifetime images of two donors to simultaneously measure PKA and ERK1&2 kinase activities in the same cellular localization by using FRET biosensors...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28105835/silver-nanoclusters-beacon-as-stimuli-responsive-versatile-platform-for-multiplex-dnas-detection-and-aptamer-substrate-complexes-sensing
#13
Guoliang Liu, Jingjing Li, Da-Qian Feng, Jun-Jie Zhu, Wei Wang
An activatable silver nanoclusters beacon (ASNCB) was synthesized through a facile one-pot approach and applied for multiplex DNAs, small molecule, and protein sensing. Multifunctional single-stranded DNA sequences are rationally designed and used for ASNCB in situ synthesis. Via target-responsive structure transformation of ASNCB, target recognition induced ASNCB conformational transition and lit up the fluorescent signal of silver nanoclusters. By further implementing two different color ASNCBs (520 and 600 nm), the parallel multiplexed analysis of two target genes (Influenza A virus genes H1N1 and H5N1) is achieved...
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28105353/isolated-extramedullary-cutaneous-relapse-despite-concomitant-severe-graft-vs-host-disease-and-tissue-chimerism-analysis-in-a-patient-with-acute-lymphoblastic-leukemia-after-allogeneic-hematopoietic-stem-cell-transplantation-a-case-report
#14
Bulent Kantarcioglu, Huseyin Saffet Bekoz, Yeliz Duvarci Ogret, Asli Cakir, Demet Kivanc, Fatma Savran Oguz, Deniz Sargin
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a potentially curative treatment option for patients with acute lymphoblastic leukemia (ALL). The curative potential of allo-HSCT for ALL is, in part, due to the graft-vs.-leukemia (GVL) effect, in addition to the intensive conditioning chemo-radiotherapy. However, relapse remains the major cause of treatment failure following allo-HSCT for ALL. In the allo-HSCT setting, testing for genetic markers of hematopoietic chimerism has become a part of the routine diagnostic program...
December 2016: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/28104717/clinical-targeted-exome-based-sequencing-in-combination-with-genome-wide-copy-number-profiling-precision-medicine-analysis-of-203-pediatric-brain-tumors
#15
Shakti H Ramkissoon, Pratiti Bandopadhayay, Jaeho Hwang, Lori A Ramkissoon, Noah F Greenwald, Steven E Schumacher, Ryan O'Rourke, Nathan Pinches, Patricia Ho, Hayley Malkin, Claire Sinai, Mariella Filbin, Ashley Plant, Wenya Linda Bi, Michael S Chang, Edward Yang, Karen D Wright, Peter E Manley, Matthew Ducar, Sanda Alexandrescu, Hart Lidov, Ivana Delalle, Liliana C Goumnerova, Alanna J Church, Katherine A Janeway, Marian H Harris, Laura E MacConaill, Rebecca D Folkerth, Neal I Lindeman, Charles D Stiles, Mark W Kieran, Azra H Ligon, Sandro Santagata, Adrian M Dubuc, Susan N Chi, Rameen Beroukhim, Keith L Ligon
BACKGROUND: Clinical genomics platforms are needed to identify targetable alterations, but implementation of these technologies and best practices in routine clinical pediatric oncology practice are not yet well established. METHODS: Profile is an institution-wide prospective clinical research initiative that uses targeted sequencing to identify targetable alterations in tumors. OncoPanel, a multiplexed targeted exome-sequencing platform that includes 300 cancer-causing genes, was used to assess single nucleotide variants and rearrangements/indels...
January 19, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28103272/prevalence-and-determinants-of-oral-human-papillomavirus-infection-in-500-young-adults-from-italy
#16
Valentina Lupato, Dana Holzinger, Daniela Höfler, Anna Menegaldo, Paolo Giorgi Rossi, Annarosa Del Mistro, Maria Cristina Da Mosto, Michael Pawlita, Paolo Boscolo-Rizzo
Although the prevalence of human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma (OPSCC) is increasing in developed countries and becoming a relevant health issue, the natural history of oral HPV infection is still unclear. Estimating the infection's prevalence in specific populations and identifying risk factors can widen our understanding of its natural history and help to delineate appropriate prevention strategies. This study sought to (i) determine oral HPV prevalence and genotype distribution in a large series of young Italian adults, (ii) validate an oral rinse sampling/storage protocol, and (iii) pinpoint factors associated with oral HPV infection...
2017: PloS One
https://www.readbyqxmd.com/read/28103008/quantitative-tracking-of-combinatorially-engineered-populations-with-multiplexed-binary-assemblies
#17
Ramsey Zeitoun, Gur Pines, William C Grau, Ryan T Gill
Advances in synthetic biology and genomics have enabled full-scale genome engineering efforts on laboratory timescales. However, the absence of sufficient approaches for mapping engineered genomes at system-wide scales onto performance has limited the adoption of more sophisticated algorithms for engineering complex biological systems. Here we report on the development and application of a robust approach to quantitatively map combinatorially engineered populations at scales up to several dozen target sites...
January 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28102949/simultaneous-pet-mr-imaging-with-a-radio-frequency-penetrable-pet-insert
#18
Alexander M Grant, Brian J Lee, Chen-Ming Chang, Craig S Levin
PURPOSE: A brain sized radio frequency (RF)-penetrable PET insert has been designed for simultaneous operation with MRI systems. This system takes advantage of electro-optical coupling and battery power to electrically float the PET insert relative to the MRI ground, permitting RF signals to be transmitted through small gaps between the modules that form the PET ring. This design facilitates the use of the built-in body coil for RF transmission and thus could be inserted into any existing MR site wishing to achieve simultaneous PET/MR imaging...
January 2017: Medical Physics
https://www.readbyqxmd.com/read/28102419/towards-encoded-particles-for-highly-multiplexed-colorimetric-point-of-care-autoantibody-detection
#19
Gustav Svedberg, Yunjin Jeong, Hunjong Na, Jisung Jang, Peter Nilsson, Sunghoon Kwon, Jesper Gantelius, Helene Andersson Svahn
Highly multiplexed point of care tests could improve diagnostic accuracy and differential diagnostic capacity in for instance emergency medicine and low resource environments. Available technology platforms for POC biomarker detection are typically simplex or low-plexed, whereas common lab-based microarray systems allow for the simultaneous detection of thousands of DNA or protein biomarkers. In this study, we demonstrate a novel suspension particle array platform that utilizes 900 μm bricks for POC amenable colorimetric biomarker detection with an encoding capacity of over two million...
January 19, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28102343/individualised-multiplexed-circulating-tumour-dna-assays-for-monitoring-of-tumour-presence-in-patients-after-colorectal-cancer-surgery
#20
Sarah B Ng, Clarinda Chua, Matthew Ng, Anna Gan, Polly Sy Poon, Melissa Teo, Cherylin Fu, Wei Qiang Leow, Kiat Hon Lim, Alexander Chung, Si-Lin Koo, Su Pin Choo, Danliang Ho, Steve Rozen, Patrick Tan, Mark Wong, William F Burkholder, Iain Beehuat Tan
Circulating tumour DNA (ctDNA) has the potential to be a specific biomarker for the monitoring of tumours in patients with colorectal cancer (CRC). Here, our aim was to develop a personalised surveillance strategy to monitor the clinical course of CRC after surgery. We developed patient-specific ctDNA assays based on multiplexed detection of somatic mutations identified from patient primary tumours, and applied them to detect ctDNA in 44 CRC patients, analysing a total of 260 plasma samples. We found that ctDNA detection correlated with clinical events - it is detectable in pre-operative but not post-operative plasma, and also in patients with recurrent CRC...
January 19, 2017: Scientific Reports
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