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High-throughput screening

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https://www.readbyqxmd.com/read/28213220/receptor-based-screening-assays-for-the-detection-of-antibiotics-residues-a-review
#1
REVIEW
Saeed Ahmed, Jianan Ning, Guyue Cheng, Ijaz Ahmad, Jun Li, Liu Mingyue, Wei Qu, Mujahid Iqbal, M A B Shabbir, Zonghui Yuan
Consumer and regulatory agencies have a high concern to antibiotic residues in food producing animals, so appropriate screening assays of fast, sensitive, low cost, and easy sample preparation for the identification of these residues are essential for the food-safety insurance. Great efforts in the development of a high-throughput antibiotic screening assay have been made in recent years. Concerning the screening of antibiotic residue, this review elaborate an overview on the availability, advancement and applicability of antibiotic receptor based screening assays for the safety assessment of antibiotics usage (i...
May 1, 2017: Talanta
https://www.readbyqxmd.com/read/28212541/analysis-of-variability-in-high-throughput-screening-data-applications-to-melanoma-cell-lines-and-drug-responses
#2
Kuan-Fu Ding, Darren Finlay, Hongwei Yin, William P D Hendricks, Chris Sereduk, Jeffrey Kiefer, Aleksandar Sekulic, Patricia M LoRusso, Kristiina Vuori, Jeffrey M Trent, Nicholas J Schork
High-throughput screening (HTS) strategies and protocols have undergone significant development in the last decade. It is now possible to screen hundreds of thousands of compounds, each exploring multiple biological phenotypes and parameters, against various cell lines or model systems in a single setting. However, given the vast amount of data such studies generate, the fact that they use multiple reagents, and are often technician-intensive, questions have been raised about the variability, reliability and reproducibility of HTS results...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28212410/a-high-throughput-genetic-screen-identifies-previously-uncharacterized-borrelia-burgdorferi-genes-important-for-resistance-against-reactive-oxygen-and-nitrogen-species
#3
Meghan E Ramsey, Jenny A Hyde, Diana N Medina-Perez, Tao Lin, Lihui Gao, Maureen E Lundt, Xin Li, Steven J Norris, Jon T Skare, Linden T Hu
Borrelia burgdorferi, the causative agent of Lyme disease in humans, is exposed to reactive oxygen and nitrogen species (ROS and RNS) in both the tick vector and vertebrate reservoir hosts. B. burgdorferi contains a limited repertoire of canonical oxidative stress response genes, suggesting that novel gene functions may be important for protection of B. burgdorferi against ROS or RNS exposure. Here, we use transposon insertion sequencing (Tn-seq) to conduct an unbiased search for genes involved in resistance to nitric oxide, hydrogen peroxide, and tertiary-butyl hydroperoxide in vitro...
February 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28212015/discovery-and-preclinical-characterization-of-3-4-4-chlorophenyl-7-fluoroquinoline-3-yl-sulfonyl-benzonitrile-a-novel-non-acetylenic-metabotropic-glutamate-receptor-5-mglur5-negative-allosteric-modulator-for-psychiatric-indications
#4
János Galambos, Attila Bielik, Mikhail Krasavin, Zoltán Orgován, György Domány, Katalin Nógrádi, Gábor Wágner, György T Balogh, Zoltán Béni, János Koti, Zoltán Szakács, Amrita Bobok, Sándor Kolok, Mónika L Miko-Bakk, Mónika Vastag, Katalin Sághy, Judit Laszy, Attila Sándor Halász, Ottilia Balázs, Krisztina Gál, István Greiner, Zsolt Szombathelyi, György M Keserű
Negative allosteric modulators (NAM) of metabotropic glutamate receptor 5 (mGluR5) have been implicated as potential pharmacotherapy for a number of psychiatric diseases including anxiety and depression. Most of the mGluR5 NAM clinical candidates can be characterized by the central acetylenic moiety that connects the terminal pharmacophores. Identification of a sulfoquinoline hit via high throughput screening (HTS) followed by optimization provided a 4-phenyl-3-aryl-sulfoquinoline lead compound with the minimal pharmacophore...
February 17, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28211892/high-throughput-in-situ-cell-electroporation-microsystem-for-parallel-delivery-of-single-guide-rnas-into-mammalian-cells
#5
Shengtai Bian, Yicen Zhou, Yawei Hu, Jing Cheng, Xiaofang Chen, Youchun Xu, Peng Liu
Arrayed genetic screens mediated by the CRISPR/Cas9 technology with single guide RNA (sgRNA) libraries demand a high-throughput platform capable of transfecting diverse cell types at a high efficiency in a genome-wide scale for detection and analysis of sophisticated cellular phenotypes. Here we developed a high-throughput in situ cell electroporation (HiCEP) microsystem which leveraged the superhydrophobic feature of the microwell array to achieve individually controlled conditions in each microwell and coupled an interdigital electrode array chip with the microwells in a modular-based scheme for highly efficient delivery of exogenous molecules into cells...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211844/a-tool-named-iris-for-versatile-high-throughput-phenotyping-in-microorganisms
#6
George Kritikos, Manuel Banzhaf, Lucia Herrera-Dominguez, Alexandra Koumoutsi, Morgane Wartel, Matylda Zietek, Athanasios Typas
Advances in our ability to systematically introduce and track controlled genetic variance in microorganisms have, in the past decade, fuelled high-throughput reverse genetics approaches. When coupled to quantitative readouts, such approaches are extremely powerful at elucidating gene function and providing insights into the underlying pathways and the overall cellular network organization. Yet, until now, all efforts to quantify microbial macroscopic phenotypes have been restricted to monitoring growth in a small number of model microorganisms...
February 17, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28211678/high-throughput-screening-of-sulfated-proteins-by-using-a-genome-wide-proteome-microarray-and-protein-tyrosine-sulfation-system
#7
Bo-Yu Huang, Po-Chung Chen, Bo-Han Chen, Chen-Chu Wang, Hsuan-Fu Liu, Yi-Zao Chen, Chien-Sheng Chen, Yuh-Shyong Yang
Protein tyrosine sulfation (PTS) is a widespread posttranslational modification that induces intercellular and extracellular responses by regulating protein-protein interactions and enzymes activities. Although PTS affects numerous physiological and pathological processes, only a small fraction of the total predicted sulfated proteins has been identified to date. Here, we localized the potential sulfation sites of Escherichia coli proteins on a proteome microarray by using a 3'-phosphoadenosine 5'-phosphosulfate (PAPS) synthase-coupled tyrosylprotein sulfotransferase (TPST) catalysis system that involves in situ PAPS generation and TPST catalysis...
February 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28211071/accurate-robust-and-reliable-calculations-of-poisson-boltzmann-binding-energies
#8
Duc D Nguyen, Bao Wang, Guo-Wei Wei
Poisson-Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, ΔGel, and binding free energy, ΔΔGel, is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with solvent excluded surfaces for estimating both electrostatic solvation free energies and electrostatic binding free energies...
February 16, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28209627/characterization-of-a-blood-spot-creatine-kinase-skeletal-muscle-isoform-immunoassay-for-high-throughput-newborn-screening-of-duchenne-muscular-dystrophy
#9
Stuart J Moat, Teemu Korpimäki, Petra Furu, Harri Hakala, Hanna Polari, Liisa Meriö, Pauliina Mäkinen, Ian Weeks
BACKGROUND: Duchenne muscular dystrophy (DMD) is a progressive, lethal X-linked neuromuscular disorder with an average worldwide incidence of 1:5000. Blood spot creatine kinase (CK) enzyme assays previously used in newborn screening programs for DMD are nonspecific because measured CK enzyme activity is attributable to 3 isoenzyme forms of CK (CK-MM, CK-MB, and CK-BB) and it is the CK-MM isoform that is found predominantly in skeletal muscle. CK-MM is increased in boys with DMD owing to muscle damage...
February 16, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28208291/growth-based-bacterial-viability-assay-for-interference-free-and-high-throughput-toxicity-screening-of-nanomaterials
#10
Tian A Qiu, Thu Ha Thi Nguyen, Natalie V Hudson-Smith, Peter L Clement, Dona-Carla Forester, Hilena Frew, Mimi N Hang, Catherine J Murphy, Robert J Hamers, Z Vivian Feng, Christy L Haynes
Current high-throughput approaches evaluating toxicity of chemical agents toward bacteria typically rely on optical assays, such as luminescence and absorbance, to probe the viability of the bacteria. However, when applied to toxicity induced by nanomaterials, scattering and absorbance from the nanomaterials act as interferences that complicate quantitative analysis. Herein, we describe a bacterial viability assay that is free of optical interference from nanomaterials and can be performed in a high-throughput format on 96-well plates...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28207264/steering-orbital-optimization-out-of-local-minima-and-saddle-points-toward-lower-energy
#11
Alain C Vaucher, Markus Reiher
The general procedure underlying Hartree-Fock and Kohn-Sham density functional theory calculations consists in optimizing orbitals for a self-consistent solution of the Roothaan-Hall equations in an iterative process. It is often ignored that multiple self-consistent solutions can exist, several of which may correspond to minima of the energy functional. In addition to the difficulty sometimes encountered to converge the calculation to a self-consistent solution, one must ensure that the correct self-consistent solution was found, typically the one with the lowest electronic energy...
February 16, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28204945/spectrum-of-mutations-in-chinese-children-with-steroid-resistant-nephrotic-syndrome
#12
Fang Wang, Yanqin Zhang, Jianhua Mao, Zihua Yu, Zhuwen Yi, Li Yu, Jun Sun, Xiuxiu Wei, Fangrui Ding, Hongwen Zhang, Huijie Xiao, Yong Yao, Weizhen Tan, Svjetlana Lovric, Jie Ding, Friedhelm Hildebrandt
BACKGROUND: The aim of this study was to elucidate whether genetic screening test results of pediatric patients with steroid-resistant nephrotic syndrome (SRNS) vary with ethnicity. METHODS: Using high-throughput DNA sequencing, 28 nephrotic syndrome-related genes were analyzed in 110 chil-dren affected by SRNS and 10 children with isolated proteinuria enrolled by 5 centers in China (67 boys, 53 girls). Their age at disease onset ranged from 1 day to 208 months (median, 48...
February 15, 2017: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/28202772/high-throughput-screening-of-tyrosine-kinase-inhibitor-cardiotoxicity-with-human-induced-pluripotent-stem-cells
#13
Arun Sharma, Paul W Burridge, Wesley L McKeithan, Ricardo Serrano, Praveen Shukla, Nazish Sayed, Jared M Churko, Tomoya Kitani, Haodi Wu, Alexandra Holmström, Elena Matsa, Yuan Zhang, Anusha Kumar, Alice C Fan, Juan C Del Álamo, Sean M Wu, Javid J Moslehi, Mark Mercola, Joseph C Wu
Tyrosine kinase inhibitors (TKIs), despite their efficacy as anticancer therapeutics, are associated with cardiovascular side effects ranging from induced arrhythmias to heart failure. We used human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), generated from 11 healthy individuals and 2 patients receiving cancer treatment, to screen U.S. Food and Drug Administration-approved TKIs for cardiotoxicities by measuring alterations in cardiomyocyte viability, contractility, electrophysiology, calcium handling, and signaling...
February 15, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28202375/generation-and-characterization-of-west-nile-pseudo-infectious-reporter-virus-for-antiviral-screening
#14
Hong-Lei Zhang, Han-Qing Ye, Cheng-Lin Deng, Si-Qing Liu, Pei-Yong Shi, Cheng-Feng Qin, Zhi-Ming Yuan, Bo Zhang
West Nile virus (WNV), a mosquito-borne flavivirus, is an important neurotropic human pathogen. As a biosafety level-3 (BSL-3) agent, WNV is strictly to BSL-3 laboratories for experimentations, thus greatly hindering the development of vaccine and antiviral drug. Here, we developed a novel pseudo-infectious WNV reporter virus expressing the Gaussia luciferase (Gluc). A stable 293TNS1 cell line expressing NS1 was selected for trans-supplying NS1 protein to support the replication of WNV-ΔNS1 virus and WNV-ΔNS1-Gluc reporter virus with large-fragment deletion of NS1...
February 12, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28199790/an-integrated-microfluidic-processor-for-dna-encoded-combinatorial-library-functional-screening
#15
Andrew B MacConnell, Alexander K Price, Brian M Paegel
DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables whole-library functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits...
February 15, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28199182/one-reporter-for-in-cell-activity-profiling-of-majority-of-protein-kinase-oncogenes
#16
Iva Gudernova, Silvie Foldynova-Trantirkova, Barbora El Ghannamova, Bohumil Fafilek, Miroslav Varecha, Lukas Balek, Eva Hruba, Lucie Jonatova, Iva Jelinkova, Michaela Kunova Bosakova, Lukas Trantirek, Jiri Mayer, Pavel Krejci
In-cell profiling enables the evaluation of receptor tyrosine activity in a complex environment of regulatory networks that affect signal initiation, propagation and feedback. We used FGF-receptor signaling to identify EGR1 as a locus that strongly responds to the activation of a majority of the recognized protein kinase oncogenes, including 30 receptor tyrosine kinases and 154 of their disease-associated mutants. The EGR1 promoter was engineered to enhance trans-activation capacity and optimized for simple screening assays with luciferase or fluorescent reporters...
February 15, 2017: ELife
https://www.readbyqxmd.com/read/28198902/microvalve-based-bioprinting-process-bio-inks-and-applications
#17
REVIEW
Wei Long Ng, Jia Min Lee, Wai Yee Yeong, May Win Naing
Bioprinting is an emerging research field that has attracted tremendous attention for various applications; it offers a highly automated, advanced manufacturing platform for the fabrication of complex bioengineered constructs. Different bio-inks comprising multiple types of printable biomaterials and cells are utilized during the bioprinting process to improve the homology to native tissues and/or organs in a highly reproducible manner. This paper, presenting a first-time comprehensive yet succinct review of microvalve-based bioprinting, provides an in-depth analysis and comparison of different drop-on-demand bioprinting systems and highlights the important considerations for microvalve-based bioprinting systems...
February 15, 2017: Biomaterials Science
https://www.readbyqxmd.com/read/28198897/metal-oxide-semiconductor-based-gas-sensors-screening-preparation-and-integration
#18
Jian Zhang, Ziyu Qin, Dawen Zeng, Changsheng Xie
Metal-oxide-semiconductor (MOS) based gas sensors have been considered a promising candidate for gas detection over the past few years. However, the sensing properties of MOS-based gas sensors also need to be further enhanced to satisfy the higher requirements for specific applications, such as medical diagnosis based on human breath, gas detection in harsh environments, etc. In these fields, excellent selectivity, low power consumption, a fast response/recovery rate, low humidity dependence and a low limit of detection concentration should be fulfilled simultaneously, which pose great challenges to the MOS-based gas sensors...
February 15, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28198471/machine-learned-approximations-to-density-functional-theory-hamiltonians
#19
Ganesh Hegde, R Chris Bowen
Large scale Density Functional Theory (DFT) based electronic structure calculations are highly time consuming and scale poorly with system size. While semi-empirical approximations to DFT result in a reduction in computational time versus ab initio DFT, creating such approximations involves significant manual intervention and is highly inefficient for high-throughput electronic structure screening calculations. In this letter, we propose the use of machine-learning for prediction of DFT Hamiltonians. Using suitable representations of atomic neighborhoods and Kernel Ridge Regression, we show that an accurate and transferable prediction of DFT Hamiltonians for a variety of material environments can be achieved...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198412/a-screening-strategy-for-the-discovery-of-drugs-that-reduce-c-ebp%C3%AE-lip-translation-with-potential-calorie-restriction-mimetic-properties
#20
Mohamad A Zaini, Christine Müller, Tobias Ackermann, Jeanette Reinshagen, Gertrud Kortman, Ole Pless, Cornelis F Calkhoven
An important part of the beneficial effects of calorie restriction (CR) on healthspan and lifespan is mediated through regulation of protein synthesis that is under control of the mechanistic target of rapamycin complex 1 (mTORC1). As one of its activities, mTORC1 stimulates translation into the metabolic transcription factor CCAAT/Enhancer Binding Protein β (C/EBPβ) isoform Liver-specific Inhibitory Protein (LIP). Regulation of LIP expression strictly depends on a translation re-initiation event that requires a conserved cis-regulatory upstream open reading frame (uORF) in the C/EBPβ-mRNA...
February 15, 2017: Scientific Reports
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