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https://www.readbyqxmd.com/read/28432350/enhancing-the-throughput-and-multiplexing-capabilities-of-next-generation-sequencing-for-efficient-implementation-of-pooled-shrna-and-crispr-screens
#1
Md Fahmid Islam, Atsushi Watanabe, Lai Wong, Conor Lazarou, Frederick S Vizeacoumar, Omar Abuhussein, Wayne Hill, Maruti Uppalapati, C Ronald Geyer, Franco J Vizeacoumar
Next generation sequencing is becoming the method of choice for functional genomic studies that use pooled shRNA or CRISPR libraries. A key challenge in sequencing these mixed-oligo libraries is that they are highly susceptible to hairpin and/or heteroduplex formation. This results in polyclonal, low quality, and incomplete reads and reduces sequencing throughput. Unfortunately, this challenge is significantly magnified in low-to-medium throughput bench-top sequencers as failed reads significantly perturb the maximization of sequence coverage and multiplexing capabilities...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432289/simultaneous-detection-of-egfr-and-vegf-in-colorectal-cancer-using-fluorescence-raman-endoscopy
#2
Yong-Il Kim, Sinyoung Jeong, Kyung Oh Jung, Myung Geun Song, Chul-Hee Lee, Seock-Jin Chung, Ji Yong Park, Myeong Geun Cha, Sung Gun Lee, Bong-Hyun Jun, Yun-Sang Lee, Do Won Hwang, Hyewon Youn, Keon Wook Kang, Yoon-Sik Lee, Dae Hong Jeong, Dong Soo Lee
Fluorescence endomicroscopy provides quick access to molecular targets, while Raman spectroscopy allows the detection of multiple molecular targets. Using a simultaneous fluorescence-Raman endoscopic system (FRES), we herein demonstrate its potential in cancer diagnosis in an orthotopically induced colorectal cancer (CRC) xenograft model. In the model, epidermal growth factor receptor (EGFR) and vascular endothelial growth factor (VEGF) were targeted with antibody-conjugated fluorescence and surface-enhanced Raman scattering (F-SERS) dots...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28431057/quantitative-analysis-of-pkp2-and-neighbouring-genes-in-a-patient-with-arrhythmogenic-right-ventricular-cardiomyopathy-caused-by-heterozygous-pkp2-deletion
#3
Keiko Sonoda, Seiko Ohno, Sou Otuki, Koichi Kato, Nobue Yagihara, Hiroshi Watanabe, Takeru Makiyama, Tohru Minamino, Minoru Horie
Aims: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a disease mainly caused by desmosome gene mutations. The genetic culprit, however, remains elusive in ∼50% of ARVC patients. One of the reasons for missing genetic abnormalities is the difficulty in detecting large deletions/duplications, which are called as copy number variation (CNV) by the Sanger sequencing method. This study aimed to identify CNVs in PKP2 and a part of other desmosome genes in ARVC patients. Methods and Results: The study cohort consisted of 71 ARVC probands who were diagnosed as definite or borderline cases based on 2010 Task Force Criteria...
April 1, 2017: Europace: European Pacing, Arrhythmias, and Cardiac Electrophysiology
https://www.readbyqxmd.com/read/28430750/elevated-immune-response-among-children-4-years-of-age-with-pronounced-local-adverse-events-after-the-fifth-dtap-vaccination
#4
Saskia van der Lee, Jeanet M Kemmeren, Lia G H de Rond, Kemal Öztürk, Anneke Westerhof, Hester E de Melker, Elisabeth A M Sanders, Guy A M Berbers, Nicoline A T van der Maas, Hans C Rümke, Anne-Marie Buisman
BACKGROUND: In the Netherlands, acellular pertussis vaccines replaced the more reactogenic whole-cell pertussis vaccines. This replacement in the primary immunization schedule of infants coincided with a significant increase in pronounced local adverse events (AEs) in 4 years old children shortly after the administration of a fifth diphtheria, tetanus, acellular pertussis and inactivated polio (DTaP-IPV) vaccine. The objective of this study was to investigate possible differences in vaccine antigen-specific immune responses between children with and without a pronounced local AE after the fifth DTaP-IPV vaccination...
April 19, 2017: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/28430279/microcontact-printing-with-aminosilanes-creating-biomolecule-micro-and-nanoarrays-for-multiplexed-microfluidic-bioassays
#5
Shivani Sathish, Sébastien G Ricoult, Kazumi Toda-Peters, Amy Q Shen
Microfluidic systems integrated with protein and DNA micro- and nanoarrays have been the most sought-after technologies to satisfy the growing demand for high-throughput disease diagnostics. As the sensitivity of these systems relies on the bio-functionalities of the patterned recognition biomolecules, the primary concern has been to develop simple technologies that enable biomolecule immobilization within microfluidic devices whilst preserving bio-functionalities. To address this concern, we introduce a two-step patterning approach to create micro- and nanoarrays of biomolecules within microfluidic devices...
April 21, 2017: Analyst
https://www.readbyqxmd.com/read/28430277/rapid-single-cell-detection-and-identification-of-pathogens-by-using-surface-enhanced-raman-spectroscopy
#6
N E Dina, H Zhou, A Colniţă, N Leopold, T Szoke-Nagy, C Coman, C Haisch
For the successful treatment of infections, real-time analysis and enhanced multiplex capacity, sensitivity and cost-effectiveness of the developed detection method are critical. In this work, surface-enhanced Raman scattering (SERS) was employed with the final aim of identification and discrimination of pathogenic bacteria, based on their detected SERS fingerprint at the single-cell level. Several genera of bacteria that are found in most of the isolated infections in bacteraemia were successfully identified in less than 5 minutes without the use of antibodies or other specific receptors...
April 21, 2017: Analyst
https://www.readbyqxmd.com/read/28430266/machine-learning-approach-to-oam-beam-demultiplexing-via-convolutional-neural-networks
#7
Timothy Doster, Abbie T Watnik
Orbital angular momentum (OAM) beams allow for increased channel capacity in free-space optical communication. Conventionally, these OAM beams are multiplexed together at a transmitter and then propagated through the atmosphere to a receiver where, due to their orthogonality properties, they are demultiplexed. We propose a technique to demultiplex these OAM-carrying beams by capturing an image of the unique multiplexing intensity pattern and training a convolutional neural network (CNN) as a classifier. This CNN-based demultiplexing method allows for simplicity of operation as alignment is unnecessary, orthogonality constraints are loosened, and costly optical hardware is not required...
April 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/28430256/all-fiber-optic-acoustic-sensor-array-for-real-time-sound-source-localization
#8
Jian Wang, Hongyan Wu, Bo Jia
Real-time sound source localization has been widely realized by the conventional microphone array for the present. In addition, fiber-optic microphones have many advantages over conventional microphones. In the present work, an all-fiber-optic acoustic array system with a wavelength-division multiplexing scheme is proposed, which has a high sensitivity and significant superiority in high-frequency signal detection and can be applied in harsh environments. The system also has the advantages of simple construction and low cost...
April 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/28430157/development-of-user-friendly-method-to-distinguish-subspecies-of-the-korean-medicinal-herb-perilla-frutescens-using-multiplex-pcr
#9
Yonguk Kim, Ah-Young Kim, Ara Jo, Hakjoon Choi, Seung-Sik Cho, Chulyung Choi
Perilla (Perilla frutescens) is an economically and culturally important plant in East Asia. Plant breeding between cultivars has enhanced the genetic diversity of perilla overall, but means that functionally diverse subspecies are more difficult to identify and distinguish. In this study, we developed gene-based DNA markers to distinguish between the Korean herbal medicinal perilla varieties. We identified informative simple sequence repeat (SSR) regions on the promoter regions of the Myb-P1 and dihydroflavonol 4-reductase (DFR) genes, as well as a large insertion-deletion (indel) region in the limonene synthase (LS) gene, and developed markers to characterize the distinct subspecies differences (PfMyb-P1pro, PfDFRpro, and PfLS, respectively)...
April 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28430087/modification-of-two-capripoxvirus-quantitative-real-time-pcr-assays-to-improve-diagnostic-sensitivity-and-include-beta-actin-as-an-internal-positive-control
#10
Amaresh Das, Ming Y Deng, Shawn Babiuk, Michael T McIntosh
Capripoxviruses (CaPVs), consisting of Sheeppox virus (SPV), Goatpox virus (GPV), and Lumpy skin disease virus (LSDV) species, cause economically significant diseases in sheep, goats, and cattle, respectively. Quantitative real-time polymerase chain reaction (qPCR) assays are routinely used for rapid detection of CaPVs in surveillance and outbreak management programs. We further modified and optimized 2 previously published CaPV qPCR assays, referred to as the Balinsky and Bowden assays, by changing commercial PCR reagents used in the tests...
May 2017: Journal of Veterinary Diagnostic Investigation
https://www.readbyqxmd.com/read/28429586/bubble-mediated-ultrasensitive-multiplex-detection-of-metal-ions-in-three-dimensional-dna-nanostructure-encoded-microchannels
#11
Xiangmeng Qu, Fan Yang, Hong Chen, Jiang Li, Hongbo Zhang, Guo-Jun Zhang, Li Li, Lihua Wang, Shiping Song, Yang Tian, Hao Pei
The development of rapid and sensitive point-of-test devices for the on-site monitoring of heavy-metal contamination has great scientific and technological importance. However, developing fast, inexpensive, and sensitive microarray sensors to achieve such goal remains challenging. In this work, we present a DNA nanostructured microarray (DNM) with tubular three-dimensional (3D) sensing surface and ordered nanotopography. This microarray enables enhanced molecular interaction toward the rapid and sensitive multiplex detection of heavy-metal ions...
April 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28429164/detection-of-gastrointestinal-pathogens-in-oncology-patients-by-highly-multiplexed-molecular-panels
#12
C C Otto, L H Chen, T He, Y-W Tang, N E Babady
We compared the frequency of gastrointestinal (GI) pathogen detection in an oncology patient population by two multiplexed molecular assays, the Luminex xTAG® Gastrointestinal Pathogen Panel (GPP, which identifies 14 GI pathogens) and the BioFire Gastrointestinal Panel (BFGP, which identifies 22 GI pathogens). We additionally reviewed the clinical characteristics of patients tested with both panels. A total of 200 prospectively collected and 81 archived stool samples were tested by both panels. In the prospective cohort, the GPP and BFGP identified a pathogen in 33...
April 20, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28428694/a-microarray-immunoassay-for-serum-thyrotropin-and-thyroglobulin-using-antibodies-immobilized-on-track-etched-membranes
#13
Bharti Jain, J Kumarasamy, Chandrakala Gholve, Savita Kulkarni, M G R Rajan
Serum thyroglobulin (Tg) and thyroid stimulating hormone (TSH) measurements have evolved as important analytes for monitoring the prognosis of patients with differentiated thyroid cancer, post-thyroidectomy. Individual analyte immunoassay is the current practice in clinical pathology, but the simultaneous assay for all relevant analytes for a given disease, can reduce assay costs, improve patient compliance and give the clinician more information for an unequivocal diagnosis. Microarray immunoassay (MI) can achieve this goal and, hence, we have developed and validated a immuno-radiometric MI for quantitation of serum TSH and Tg by using highly micro-porous polycarbonate (PC) track-etched membranes (TEM) to immobilize the monoclonal anti-TSH and polyclonal anti-Tg antibodies in ~1 mm diameter spots...
June 2017: Indian Journal of Clinical Biochemistry: IJCB
https://www.readbyqxmd.com/read/28428361/single-tube-dodecaplex-pcr-panel-of-polymorphic-microsatellite-markers-closely-linked-to-the-dmpk-ctg-repeat-for-preimplantation-genetic-diagnosis-of-myotonic-dystrophy-type-1
#14
Mulias Lian, Mingjue Zhao, Caroline G Lee, Samuel S Chong
BACKGROUND: Preimplantation genetic diagnosis (PGD) of myotonic dystrophy type 1 (DM1) currently uses conventional PCR to detect nonexpanded dystrophia myotonica protein kinase (DMPK) alleles or triplet-primed PCR to detect the CTG-expanded alleles, coupled with analysis of linked microsatellite markers to increase diagnostic accuracy. We aimed to simplify the process of identification and selection of informative linked markers for application to DM1 PGD. METHODS: An in silico search was performed to identify all markers within 1-1...
April 20, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28428354/multiplex-tandem-mass-spectrometry-enzymatic-activity-assay-for-newborn-screening-of-the-mucopolysaccharidoses-and-type-2-neuronal-ceroid-lipofuscinosis
#15
Yang Liu, Fan Yi, Arun Babu Kumar, Naveen Kumar Chennamaneni, Xinying Hong, C Ronald Scott, Michael H Gelb, Frantisek Turecek
BACKGROUND: We expanded the use of tandem mass spectrometry combined with liquid chromatography (LC-MS/MS) for multiplex newborn screening of seven lysosomal enzymes in dried blood spots (DBS). The new assays are for enzymes responsible for the mucopolysaccharidoses (MPS-I, -II, -IIIB, -IVA, -VI, and -VII) and type 2 neuronal ceroid lipofuscinosis (LINCL). METHODS: New substrates were prepared and char-acterized for tripeptidyl peptidase 1 (TPP1), α-N-acetylglucosaminidase (NAGLU), and lysosomal β-glucuronidase (GUSB)...
April 20, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28427842/predominance-of-international-clone-2-oxa-23-producing-acinetobacter-baumannii-clinical-isolates-in-greece-2015-results-of-a-nationwide-study
#16
Spyros Pournaras, Konstantina Dafopoulou, Mariateresa Del Franco, Olympia Zarkotou, Evangelia Dimitroulia, Efi Protonotariou, Aggeliki Poulou, Raffaele Zarrilli, Athanasios Tsakris
In a previous nationwide study in Greece, OXA-58 was the sole carbapenemase present among carbapenem-resistant Acinetobacter baumannii (CRAB) isolated between 2000 and 2009. In this study, the antibiotic resistances, carbapenemase gene content and clonal relatedness of 194 single-patient CRAB clinical isolates collected randomly during 2015 from 11 tertiary hospitals located throughout Greece were investigated. Antimicrobial susceptibility was determined using commercial and dilution methods. PCR for carbapenemase genes were performed...
April 18, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28427756/human-tissue-kallikreins-blood-levels-and-response-to-radiotherapy-in-intermediate-risk-prostate-cancer
#17
Nicola J Nasser, John Thoms, Antoninus Soosaipillai, Melania Pintilie, Ri Wang, Eleftherios P Diamandis, Robert G Bristow
OBJECTIVES: Kallikreins are serine proteases over expressed in many malignancies. In this study, we measure changes in serum kallikrein (KLKs) levels during intensity-modulated radiotherapy (IMRT) in prostate cancer patients, and find potential correlations between serum kallikrein level and normal tissues toxicity during radiation. METHODS: Forty-nine patients with prostate cancer were recruited as follows: group 1, definitive standard fractionation IMRT (78Gy in 39 fractions, n=15); group 2, definitive hypofractionated IMRT (60Gy in 20 fractions, n=15); and group 3, IMRT postprostatectomy (66Gy in 33 fractions, n=19)...
April 17, 2017: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
https://www.readbyqxmd.com/read/28427715/multiplexed-dynamic-imaging-of-genomic-loci-by-combined-crispr-imaging-and-dna-sequential-fish
#18
Yodai Takei, Sheel Shah, Sho Harvey, Lei S Qi, Long Cai
Visualization of chromosome dynamics allows the investigation of spatiotemporal chromatin organization and its role in gene regulation and other cellular processes. However, current approaches to label multiple genomic loci in live cells have a fundamental limitation in the number of loci that can be labeled and uniquely identified. Here we describe an approach we call "track first and identify later" for multiplexed visualization of chromosome dynamics by combining two techniques: CRISPR imaging and DNA sequential fluorescence in situ hybridization...
April 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28427352/point-of-sampling-detection-of-zika-virus-within-a-multiplexed-kit-capable-of-detecting-dengue-and-chikungunya
#19
Ozlem Yaren, Barry W Alto, Priyanka V Gangodkar, Shatakshi R Ranade, Kunal N Patil, Kevin M Bradley, Zunyi Yang, Nikhil Phadke, Steven A Benner
BACKGROUND: Zika, dengue, and chikungunya are three mosquito-borne viruses having overlapping transmission vectors. They cause diseases having similar symptoms in human patients, but requiring different immediate management steps. Therefore, rapid (< one hour) discrimination of these three viruses in patient samples and trapped mosquitoes is needed. The need for speed precludes any assay that requires complex up-front sample preparation, such as extraction of nucleic acids from the sample...
April 20, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28426525/gstm1-and-gstt1-genes-are-associated-with-dna-damage-of-p53-gene-in-coke-oven-workers
#20
Yuefeng He, Jun Qi, Fang He, Yongchang Zhang, Youlian Wang, Ruobing Zhang, Gang Li
OBJECTIVES: This study investigated whether variations in GSTT1 and GSTM1 gene are associated with the DNA damage level of p53 gene. METHODS: We quantified urinary 1-hydroxypyrene using high-performance liquid chromatography, and examined the DNA damage level of p53 gene by real-time quantitative PCR in 756 coke-oven workers. Multiplex PCR was used to detect the presence or absence of genes. RESULTS: DNA damage levels of p53 gene in the high exposure group and intermediate exposure group were significantly higher than that of p53 gene in the low exposure group (P < 0...
April 19, 2017: Journal of Occupational and Environmental Medicine
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