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https://www.readbyqxmd.com/read/28732357/profiling-cancer-related-gene-mutations-in-oral-squamous-cell-carcinoma-from-japanese-patients-by-targeted-amplicon-sequencing
#1
Takafumi Nakagaki, Miyuki Tamura, Kenta Kobashi, Ryota Koyama, Hisayo Fukushima, Tomoko Ohashi, Masashi Idogawa, Kazuhiro Ogi, Hiroyoshi Hiratsuka, Takashi Tokino, Yasushi Sasaki
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95...
July 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28732346/multiplexed-aptasensor-for-simultaneous-detection-of-carcinoembryonic-antigen-and-mucin-1-based-on-metal-ion-electrochemical-labels-and-ru-nh3-6-3-electronic-wires
#2
Chao Ma, Haiyun Liu, Lina Zhang, Hao Li, Mei Yan, Xianrang Song, Jinghua Yu
In this paper, a dual-target electrochemical aptasensor has been developed for simultaneous detection of carcinoembryonic antigen and mucin-1 based on metal ion electrochemical labels and Ru(NH3)6(3+) electronic wires. When targets are present, the interaction between targets and their respective aptamers leads to the dissociation of double-strand DNA because the targets have higher affinity to its aptamer than the complementary strand. And the qualitative and quantitative analyses of the two targets are realized by the differential pulse voltammetry (DPV) peaks generated by metal ion electrochemical labels...
July 13, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28732207/a-crispr-resource-for-individual-combinatorial-or-multiplexed-gene-knockout
#3
Nicolas Erard, Simon R V Knott, Gregory J Hannon
We have combined a machine-learning approach with other strategies to optimize knockout efficiency with the CRISPR/Cas9 system. In addition, we have developed a multiplexed sgRNA expression strategy that promotes the functional ablation of single genes and allows for combinatorial targeting. These strategies have been combined to design and construct a genome-wide, sequence-verified, arrayed CRISPR library. This resource allows single-target or combinatorial genetic screens to be carried out at scale in a multiplexed or arrayed format...
July 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28731711/identification-of-proteomic-features-to-distinguish-benign-pulmonary-nodules-from-lung-adenocarcinoma
#4
Simona G Codreanu, Megan D Hoeksema, Robbert J C Slebos, Lisa J Zimmerman, S M Jamshedur Rahman, Ming Li, Sheau-Chiann Chen, Heidi Chen, Rosana Eisenberg, Daniel C Liebler, Pierre P Massion
We hypothesized that distinct protein expression features of benign and malignant pulmonary nodules may reveal novel candidate biomarkers for the early detection of lung cancer. We performed proteome profiling by liquid chromatography-tandem mass spectrometry to characterize 34 resected benign lung nodules, 24 early stage untreated lung adenocarcinomas (ADCs) and biopsies of bronchial epithelium. Group comparisons identified 65 proteins that differentiate nodules from ADCs and normal bronchial epithelium, and 66 proteins that differentiate ADCs from nodules and normal bronchial epithelium...
July 21, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28731574/rapid-buffer-and-ligand-screening-for-affinity-chromatography-by-multiplexed-surface-plasmon-resonance-imaging
#5
Karin P M Geuijen, Daniëlle E J W van Wijk-Basten, David F Egging, Richard B M Schasfoort, Michel H Eppink
Protein purifications are often based on the principle of affinity chromatography, where the protein of interest selectively binds to an immobilized ligand. The development of affinity purification requires selecting proper wash and elution conditions. In recent years, miniaturization of the purification process is applied to speed up the development (e.g. microtiterplates, robocolumns). We have studied the application of surface plasmon resonance imaging (SPRi) as a tool to simultaneously screen many buffer conditions for wash and elution steps in an affinity-based purification process...
July 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28730502/establishment-of-11-linked-x-str-loci-within-1-1-mb-to-assist-with-kinship-testing
#6
James Chun-I Lee, Chun-Yen Lin, Li-Chin Tsai, Yu-Jen Yu, Keng-Hsien Liao, Adrian Linacre, Hsing-Mei Hsieh
This report identifies and characterizes 10 novel short tandem repeat (STR) loci on the human X chromosome, all of which are within a range of 1.1 Mb. These newly characterized loci were developed to aid in kinship assignment when the X chromosome is specifically required. The repeat DNA sequences were identified initially using data in GenBank and are located immediately upstream and downstream from the previously described locus DXS6807. Only those loci with seven or more observed alleles were used for further study resulting in the identification of 10 new loci...
July 20, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28730487/a-methodology-for-comprehensive-analysis-of-toll-like-receptor-signaling-in-macrophages
#7
Marijke Koppenol-Raab, Aleksandra Nita-Lazar
A combination of high-throughput, multiplexed, quantitative methods with computational modeling and statistical approaches is required to obtain system-level understanding of biological function. Mass spectrometry (MS)-based proteomics has emerged as a preferred tool for the analysis of changes in protein abundance and their post-translational modification (PTM) levels at a global scale, comparable with genomic experiments and generating data suitable for use in mathematical modeling of signaling pathways. Here we describe a set of parallel bottom-up proteomic approaches to detect and quantify the global protein changes in total intracellular proteins, their phosphorylation, and the proteins released by active and passive secretion or shedding mechanisms (referred to as the secretome as reviewed in Makridakis and Vlahou, J Proteome 73:2291-2305, 2010) in response to the stimulation of Toll-like receptors (TLRs) with specific ligands in cultured macrophages...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730477/utilizing-the-luminex-magnetic-bead-based-suspension-array-for-rapid-multiplexed-phosphoprotein-quantification
#8
Adam Stewart, Udai Banerji
The study of protein phosphorylation is critical for the advancement of our understanding of cellular responses to external and internal stimuli. Phosphorylation, the addition of phosphate groups, most often occurs on serine, threonine, or tyrosine residues due to the action of protein kinases. This structural change causes the protein to become activated (or deactivated) and enables it in turn to initiate the phosphorylation of other proteins in a cascade, eventually causing cell-wide changes such as apoptosis, cell differentiation, and growth (among others)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730135/clinical-characteristics-and-ultrasonographic-findings-of-acute-bacterial-enterocolitis-in-children
#9
Peter Chun, Taek Jin Lim, Eun Ha Hwang, Sang Wook Mun, Yeoun Joo Lee, Jae Hong Park
PURPOSE: This study clarified the bacterial pathogens currently causing acute infectious enterocolitis (AIE) in children and evaluated the clinical characteristics and ultrasonographic findings according to the different pathogens. METHODS: Medical records regarding age, sex, clinical symptoms, laboratory data, identified enteropathogens, ultrasonographic findings, treatment, and outcome of 34 patients who were diagnosed with AIE via stool examination using multiplex polymerase chain reaction (PCR) or culture, were retrospectively reviewed...
June 2017: Pediatric Gastroenterology, Hepatology & Nutrition
https://www.readbyqxmd.com/read/28729664/spectral-function-modulation-based-on-nonlinear-frequency-division-multiplexing
#10
Guangqiang He, Luning Wang, Chenyang Li, Siyu Liu, Weisheng Hu
A combination of phase and amplitude modulation in nonlinear discrete spectrum is proposed based on nonlinear frequency division multiplexing. Here the integrable nonlinear Schrodinger equation is used as the channel model. We propose the transmission system with designed transmitting signals and implement our scheme with simulation. We use 8QAM constellation and 2 eigenvalues to generate 5 bit signals, which greatly improve spectral efficiency. This method can be expanded for higher order modulation and further improve transmission capacity in limited bandwidth...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729548/multiplex-polymerase-chain-reaction-for-pathogen-detection-in-donor-recipient-corneal-transplant-tissue-and-donor-storage-solution
#11
Takehiro Hariya, Kazuichi Maruyama, Sunao Sugita, Masayo Takahashi, Shunji Yokokura, Kota Sato, Yasuhiro Tomaru, Norio Shimizu, Toru Nakazawa
Corneal transplantation is a safe, reliable method of restoring visual acuity in patients with corneal disorders. Although it has a very high success rate, rejection can still occur, especially if the site is infected. Therefore, seeking to find better ways to manage infection risk, this study investigated a new technique, based on multiplex polymerase chain reaction (mPCR), to identify pathogens, including viruses, bacteria, and fungi, in corneal transplantation recipient sites, donor corneas and the donor cornea storage solution...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28728979/ploc-mvirus-predict-subcellular-localization-of-multi-location-virus-proteins-via-incorporating-the-optimal-go-information-into-general-pseaac
#12
Xiang Cheng, Xuan Xiao, Kuo-Chen Chou
Knowledge of subcellular locations of proteins is crucially important for in-depth understanding their functions in a cell. With the explosive growth of protein sequences generated in the postgenomic age, it is highly demanded to develop computational tools for timely annotating their subcellular locations based on the sequence information alone. The current study is focused on virus proteins. Although considerable efforts have been made in this regard, the problem is far from being solved yet. Most existing methods can be used to deal with single-location proteins only...
July 17, 2017: Gene
https://www.readbyqxmd.com/read/28728899/machine-learning-enabled-discovery-and-design-of-membrane-active-peptides
#13
Ernest Y Lee, Gerard C L Wong, Andrew L Ferguson
Antimicrobial peptides are a class of membrane-active peptides that form a critical component of innate host immunity and possess a diversity of sequence and structure. Machine learning approaches have been profitably employed to efficiently screen sequence space and guide experiment towards promising candidates with high putative activity. In this mini-review, we provide an introduction to antimicrobial peptides and summarize recent advances in machine learning-enabled antimicrobial peptide discovery and design with a focus on a recent work Lee et al...
July 8, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28728835/a-multiplex-pcr-for-detection-of-six-viruses-in-ducks
#14
Yongjuan Wang, Shanyuan Zhu, Weiming Hong, Anping Wang, Weiyong Zuo
In this study, six pairs of specific primers that can amplify DNA fragments of different sizes were designed and synthesized according to viral protein gene sequences published in GenBank. Then, a multiplex PCR method was established for rapid detection of duck hepatitis virus 1, duck plague virus, duck Tembusu virus, muscovy duck parvovirus, muscovy duck reovirus, and duck H9N2 avian influenza virus, and achieve simple and rapid detection of viral diseases in ducks. Single PCR was used to confirm primer specificity, and PCR conditions were optimized to construct a multiplex PCR system...
July 17, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28728056/sequence-based-diversity-of-23-autosomal-str-loci-in-koreans-investigated-using-an-in-house-massively-parallel-sequencing-panel
#15
Eun Hye Kim, Hwan Young Lee, So Yeun Kwon, Eun Young Lee, Woo Ick Yang, Kyoung-Jin Shin
As DNA databases continue to grow and international cooperation increases, forensic STR loci have expanded to increase the discriminatory power and inter-database compatibility. Current capillary electrophoresis (CE) and/or massively parallel sequencing (MPS)-based commercial STR analysis systems reflect such changing trends of expanding STR loci. Due to the general gains of larger multiplexing and the detection of sequence variation, the application of MPS technology to STR analysis has further improved discrimination and is expected to aid in mixture interpretation by increasing the effective number of alleles...
July 9, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28727877/genetic-predisposition-to-breast-cancer-due-to-mutations-other-than-brca1-and-brca2-founder-alleles-among-ashkenazi-jewish-women
#16
Tom Walsh, Jessica B Mandell, Barbara M Norquist, Silvia Casadei, Suleyman Gulsuner, Ming K Lee, Mary-Claire King
Importance: Among Ashkenazi Jewish women, 3 mutations in BRCA1 and BRCA2 severely increase the risk of breast and ovarian cancer. However, among Ashkenazi Jewish patients with breast cancer who do not carry one of these founder mutations, the likelihood of carrying another pathogenic mutation in BRCA1 or BRCA2 or another breast cancer gene is not known. This information would be valuable to the patient and family for cancer prevention and treatment. Objective: To determine the frequency of cancer-predisposing mutations other than the BRCA1 and BRCA2 founder alleles among patients of Ashkenazi Jewish ancestry with breast cancer...
July 20, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28727615/multiplexing-prisms-for-field-expansion
#17
Eli Peli, Jae-Hyun Jung
PURPOSE: Prisms used for field expansion are limited by the optical scotoma at a prism apex (apical scotoma). For a patient with two functioning eyes, fitting prisms unilaterally allows the other eye to compensate for the apical scotoma. A monocular patient's field loss cannot be expanded with a conventional or Fresnel prism because of the apical scotoma. A newly invented optical device, the multiplexing prism (MxP), was developed to overcome the apical scotoma limitation in monocular field expansion...
July 19, 2017: Optometry and Vision Science: Official Publication of the American Academy of Optometry
https://www.readbyqxmd.com/read/28727605/in-vitro-compatibility-of-contact-lenses-with-corneal-epithelial-cells
#18
Ajay K Vijay, Zohra Fadli, Carol Lakkis, Chantal Coles-Brennan, Mark D P Willcox
PURPOSE: To determine the interaction of contact lenses of different materials with corneal epithelial cells grown in tissue culture. METHODS: Two different corneal epithelial cell lines were grown to confluence in culture media. Two hydrogel contact lenses with and without polyvinylpyrrolidone (PVP) {1-DAY ACUVUE MOIST (1-Day ACUVUE [hydrogel lenses]) and a silicone hydrogel contact lens, AIR OPTIX NIGHT & DAY} were removed from their blister packs, washed in phosphate-buffered saline, and applied to the cells...
July 18, 2017: Eye & Contact Lens
https://www.readbyqxmd.com/read/28726914/3d-printed-smartphone-based-point-of-care-tool-for-fluorescence-and-magnetophoresis-based-cytometry
#19
Stephanie Knowlton, Ashwini Joshi, Philip Syrrist, Ahmet F Coskun, Savas Tasoglu
In developing countries, there are often limited resources available to provide important medical diagnostics, which severely limits our ability to diagnose conditions and administer proper treatment, leading to high mortality rates for treatable conditions. Here, we propose a multiplex tool capable of density-based cell sorting via magnetic focusing in parallel with fluorescence imaging to provide highly specific clinical assays. While many cell sorting techniques and fluorescence microscopes generally are costly and require extensive user training, limiting accessibility and usability in developing countries, this device is compact, low-cost, and portable...
July 20, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28726912/3d-material-cytometry-3dmac-a-very-high-replicate-high-throughput-analytical-method-using-microfabricated-shape-specific-cell-material-niches
#20
Kirsten Parratt, Jenny Jeong, Peng Qiu, Krishnendu Roy
Studying cell behavior within 3D material niches is key to understanding cell biology in health and diseases, and developing biomaterials for regenerative medicine applications. Current approaches to studying these cell-material niches have low throughput and can only analyze a few replicates per experiment resulting in reduced measurement assurance and analytical power. Here, we report 3D material cytometry (3DMaC), a novel high-throughput method based on microfabricated, shape-specific 3D cell-material niches and imaging cytometry...
July 20, 2017: Lab on a Chip
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