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High-throughput screening

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https://www.readbyqxmd.com/read/28531227/different-microrna-profiles-reveal-the-diverse-outcomes-induced-by-ev71-and-ca16-infection-in-human-umbilical-vein-endothelial-cells-using-high-throughput-sequencing
#1
Jie Song, Yajie Hu, Jiaqi Li, Huiwen Zheng, Jingjing Wang, Lei Guo, Ruotong Ning, Hongzhe Li, Zening Yang, Haitao Fan, Longding Liu
Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) remain the predominant pathogens in hand, foot, and mouth disease (HFMD), but the factors underlying the pathogenesis of EV71 and CA16 infections have not been elucidated. Recently, the functions of microRNAs (miRNAs) in pathogen-host interactions have been highlighted. In the present study, we performed comprehensive miRNA profiling in EV71- and CA16-infected human umbilical vein endothelial cells (HUVECs) at multiple time points using high-throughput sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28530838/an-innovative-high-throughput-screening-approach-for-discovery-of-small-molecules-that-inhibit-tnf-receptors
#2
Chih Hung Lo, Nagamani Vunnam, Andrew K Lewis, Ting-Lan Chiu, Benjamin E Brummel, Tory M Schaaf, Benjamin D Grant, Prachi Bawaskar, David D Thomas, Jonathan N Sachs
Tumor necrosis factor receptor 1 (TNFR1) is a transmembrane receptor that binds tumor necrosis factor or lymphotoxin-alpha and plays a critical role in regulating the inflammatory response. Upregulation of these ligands is associated with inflammatory and autoimmune diseases. Current treatments reduce symptoms by sequestering free ligands, but this can cause adverse side effects by unintentionally inhibiting ligand binding to off-target receptors. Hence, there is a need for new small molecules that specifically target the receptors, rather than the ligands...
May 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28530188/simple-assay-for-screening-phytoestrogenic-compounds-using-the-oestrogen-receptor-immobilised-magnetite-nanoparticles
#3
Pimchanok Busayapongchai, Sineenat Siri
With increasing interests of phytoestrogens for their potential applications, a rapid and simple tool for screening these phytochemicals is still required. In this study, a simple assay to detect phytoestrogens was developed based on the competition binding between the tested samples and the fluorescently labelled oestrogen (E2) to the human ligand binding domain of oestrogen receptor (LBD-ER) that was immobilised on the magnetite nanoparticles (MNPs). The 40-kDa LBD-ER peptide was produced in an Escherichia coli system...
June 2017: IET Nanobiotechnology
https://www.readbyqxmd.com/read/28529634/novel-linear-peptides-with-high-affinity-to-%C3%AE-v%C3%AE-3-integrin-for-precise-tumor-identification
#4
Yi Ma, Guanhua Ai, Congying Zhang, Menglu Zhao, Xue Dong, Zhihao Han, Zhaohui Wang, Min Zhang, Yuxi Liu, Weidong Gao, Siwen Li, Yueqing Gu
Development of alternative linear peptides for targeting αvβ3 integrin has attracted much attention, as the traditional peptide ligand, cyclic RGD, is limited by inferior water-solubility and complex synthesis. Using pharmacophore-based virtual screening and high-throughput molecular docking, we identified two novel linear small peptides RWr and RWrNM with high affinity and specificity to αvβ3 integrin. The competitive binding with cyclic RGD (c(RGDyK)) and cellular uptake related to the integrin expression levels verified their affinity to αvβ3 integrin...
2017: Theranostics
https://www.readbyqxmd.com/read/28528669/modulation-of-ion-channels-by-cysteine-rich-peptides-from-sequence-to-structure
#5
Mehdi Mobli, Eivind A B Undheim, Lachlan D Rash
Venom peptides are natural ligands of ion channels and have been used extensively in pharmacological characterization of various ion channels and receptors. In this chapter, we survey all known venom peptide ion-channel modulators. Our survey reveals that the majority of venom peptides characterized to date target voltage-gated sodium or potassium channels. We further find that the majority of these peptides are found in scorpion and spider venoms. We discuss the influence of the pharmacological tools available in biasing discovery and the classical "toxin-to-sequence" approach to venom peptide biodiscovery...
2017: Advances in Pharmacology
https://www.readbyqxmd.com/read/28528648/copper-and-antibiotics-discovery-modes-of-action-and-opportunities-for-medicinal-applications
#6
Alex G Dalecki, Cameron L Crawford, Frank Wolschendorf
Copper is a ubiquitous element in the environment as well as living organisms, with its redox capabilities and complexation potential making it indispensable for many cellular functions. However, these same properties can be highly detrimental to prokaryotes and eukaryotes when not properly controlled, damaging many biomolecules including DNA, lipids, and proteins. To restrict free copper concentrations, all bacteria have developed mechanisms of resistance, sequestering and effluxing labile copper to minimize its deleterious effects...
2017: Advances in Microbial Physiology
https://www.readbyqxmd.com/read/28527947/embryonic-vascular-disruption-adverse-outcomes-linking-high-throughput-signaling-signatures-with-functional-consequences
#7
Robert G Ellis-Hutchings, Raja S Settivari, Alene T McCoy, Nicole Kleinstreuer, Jill Franzosa, Thomas B Knudsen, Edward W Carney
Embryonic vascular disruption is an important adverse outcome pathway (AOP) as chemical disruption of cardiovascular development induces broad prenatal defects. High throughput screening (HTS) assays aid AOP development although linking in vitro data to in vivo apical endpoints remains challenging. This study evaluated two anti-angiogenic agents, 5HPP-33 and TNP-470, across the ToxCastDB HTS assay platform and anchored the results to complex in vitro functional assays: the rat aortic explant assay (AEA), rat whole embryo culture (WEC), and the zebrafish embryotoxicity (ZET) assay...
May 17, 2017: Reproductive Toxicology
https://www.readbyqxmd.com/read/28527909/binding-assay-for-characterization-of-protein-kinase-inhibitors-possessing-sub-picomolar-to-sub-millimolar-affinity
#8
Hedi Sinijarv, Shanshan Wu, Taavi Ivan, Kaido Viht, Asko Uri
High demand for inhibitors regulating the activity of protein kinases has stimulated the quest for high throughput and reliable compound screening assays. Here we introduce a method applying a non-metal photoluminescent probe ARC-Lum(Fluo) for determination of dissociation constants of competitive inhibitors of protein kinases. Employing a single probe instead of a combination of antibody and fluorescent tracer makes the assay simpler, cheaper, and more accurate than several other inhibitor-screening technologies...
May 17, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28527783/identification-of-novel-selective-p2y6-receptor-antagonists-by-high-throughput-screening-assay
#9
Masaaki Ito, Shin-Ichiro Egashira, Kazuki Yoshida, Tomoko Mineno, Kazuo Kumagai, Hirotatsu Kojima, Takayoshi Okabe, Tetsuo Nagano, Michio Ui, Isao Matsuoka
AIMS: The P2Y6 nucleotide receptor is widely involved in inflammatory responses, and is a promising molecular target for the treatment of inflammatory diseases. Although several P2Y6 receptor antagonists have been developed and evaluated thus far, none has successfully been developed into a therapeutic drug. In this study, we explored new promising compounds that inhibit the human P2Y6 receptor. MAIN METHODS: High-throughput screening (HTS) was used to study the effects of various compounds on human P2Y6 receptors expressed in 1321N1 human astrocytoma cells by monitoring intracellular Ca(2+) concentration ([Ca(2+)]i) levels using an FDSS7000 real-time fluorescence detector...
May 17, 2017: Life Sciences
https://www.readbyqxmd.com/read/28526787/development-of-multi-well-plate-methods-using-pure-cultures-of-methanogens-to-identify-new-inhibitors-for-suppressing-ruminant-methane-emissions
#10
M R Weimar, J Cheung, D Dey, C McSweeney, M Morrison, Y Kobayashi, W B Whitman, V Carbone, L R Schofield, R S Ronimus, G M Cook
Hydrogenotrophic methanogens typically require strictly anaerobic culturing conditions in glass tubes with overpressures of H2 and CO2 that are both time-consuming and costly. To increase the throughput for screening chemical compound libraries, 96-well microtiter plate methods for the growth of a marine (environmental) methanogen Methanococcus maripaludis strain S2 and the rumen methanogen Methanobrevibacter species AbM4 were developed. A number of key parameters (inoculum size, reducing agents for media preparation, duration of assay, inhibitor solvents and culture volume) were optimised to achieve robust and reproducible growth in a high-throughput microtiter plate format...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28526655/digital-morphometrics-a-new-upper-airway-phenotyping-paradigm-in-obstructive-sleep-apnea
#11
Richard J Schwab, Sarah E Leinwand, Cary B Bearn, Greg Maislin, Ramya Bhat Rao, Adithya Nagaraja, Stephen Wang, Brendan T Keenan
BACKGROUND: Obstructive sleep apnea (OSA) is associated with changes in pharyngeal anatomy. The goal of this study was to objectively and reproducibly quantify pharyngeal anatomy using digital morphometrics based on a laser ruler, and to assess differences between apneics and controls and associations with AHI (apnea-hypopnea index). This is the first study to use digital morphometrics to quantify intraoral risk factors for OSA. METHODS: Digital photographs were obtained using an intraoral laser ruler and digital camera in 311 controls (mean AHI=4...
May 16, 2017: Chest
https://www.readbyqxmd.com/read/28526529/adding-biological-meaning-to-human-protein-protein-interactions-identified-by-yeast-two-hybrid-screenings-a-guide-through-bioinformatics-tools
#12
Juliana Felgueiras, Joana Vieira Silva, Margarida Fardilha
"A man is known by the company he keeps" is a popular expression that perfectly fits proteins. A common approach to characterize the function of a target protein is to identify its interacting partners and thus infer its roles based on the known functions of the interactors. Protein-protein interaction networks (PPINs) have been created for several organisms, including humans, primarily as results of high-throughput screenings, such as yeast two-hybrid (Y2H). Their unequivocal use to understand events underlying human pathophysiology is promising in identifying genes and proteins associated with diseases...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28526239/cellular-models-as-tools-for-the-study-of-the-role-of-alpha-synuclein-in-parkinson-s-disease
#13
REVIEW
Diana F Lázaro, Maria Angeliki S Pavlou, Tiago Fleming Outeiro
Neurodegenerative diseases are highly debilitating conditions characterised primarily by progressive neuronal loss and impairment of the nervous system. Parkinson's disease (PD) is one of the most common of these disorders, affecting 1-2% of the population above the age of 65. Although the underlying mechanisms of PD have been extensively studied, we still lack a full understanding of the molecular underpinnings of the disease. Thus, the in vitro and in vivo models currently used are able to only partially recapitulate the typical phenotypes of the disease...
May 16, 2017: Experimental Neurology
https://www.readbyqxmd.com/read/28524181/common-pitfalls-in-preclinical-cancer-target-validation
#14
REVIEW
William G Kaelin
An alarming number of papers from laboratories nominating new cancer drug targets contain findings that cannot be reproduced by others or are simply not robust enough to justify drug discovery efforts. This problem probably has many causes, including an underappreciation of the danger of being misled by off-target effects when using pharmacological or genetic perturbants in complex biological assays. This danger is particularly acute when, as is often the case in cancer pharmacology, the biological phenotype being measured is a 'down' readout (such as decreased proliferation, decreased viability or decreased tumour growth) that could simply reflect a nonspecific loss of cellular fitness...
May 19, 2017: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/28524079/assembly-of-hepatocyte-spheroids-using-magnetic-3d-cell-culture-for-cyp450-inhibition-induction
#15
Pujan K Desai, Hubert Tseng, Glauco R Souza
There is a significant need for in vitro methods to study drug-induced liver injury that are rapid, reproducible, and scalable for existing high-throughput systems. However, traditional monolayer and suspension cultures of hepatocytes are difficult to handle and risk the loss of phenotype. Generally, three-dimensional (3D) cell culture platforms help recapitulate native liver tissue phenotype, but suffer from technical limitations for high-throughput screening, including scalability, speed, and handling. Here, we developed a novel assay for cytochrome P450 (CYP450) induction/inhibition using magnetic 3D cell culture that overcomes the limitations of other platforms by aggregating magnetized cells with magnetic forces...
May 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28523501/peptide-imaging-maximizing-peptide-yield-optimization-of-the-peptide-mass-fingerprint
#16
Ekta Patel
In Matrix Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI), identification of observed proteins remains a challenge primarily due to the drop in sensitivity of time-of-flight (TOF) mass spectrometers beyond the mass range of 25-35 kDa (Francese et al. High Throughput Screen 12: 156-174, 2009) and inadequate mass resolving power at those molecular weights. To counteract this, a bottom-up proteomic approach is often employed. Proteolysis digests proteins into smaller peptide fragments, typically between 500 and 3000 Da which are easier to detect with a higher mass accuracy...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28523436/hrm-and-snapshot-as-alternative-forensic-snp-genotyping-methods
#17
Bhavik Mehta, Runa Daniel, Dennis McNevin
Single nucleotide polymorphisms (SNPs) have been widely used in forensics for prediction of identity, biogeographical ancestry (BGA) and externally visible characteristics (EVCs). Single base extension (SBE) assays, most notably SNaPshot® (Thermo Fisher Scientific), are commonly used for forensic SNP genotyping as they can be employed on standard instrumentation in forensic laboratories (e.g. capillary electrophoresis). High resolution melt (HRM) analysis is an alternative method and is a simple, fast, single tube assay for low throughput SNP typing...
May 18, 2017: Forensic Science, Medicine, and Pathology
https://www.readbyqxmd.com/read/28523286/synthetic-lethality-screens-using-rnai-in-combination-with-crispr-based-knockout-in-drosophila-cells
#18
Benjamin E Housden, Hilary E Nicholson, Norbert Perrimon
A synthetic lethal interaction is a type of genetic interaction where the disruption of either of two genes individually has little effect but their combined disruption is lethal. Knowledge of synthetic lethal interactions can allow for elucidation of network structure and identification of candidate drug targets for human diseases such as cancer. In Drosophila, combinatorial gene disruption has been achieved previously by combining multiple RNAi reagents. Here we describe a protocol for high-throughput combinatorial gene disruption by combining CRISPR and RNAi...
February 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28522750/inhibition-of-mitochondrial-matrix-chaperones-and-anti-apoptotic-bcl-2-family-proteins-empower-antitumor-therapeutic-responses
#19
Georg Karpel-Massler, Chiaki Tsuge Ishida, Elena Bianchetti, Chang Shu, Rolando Perez-Lorenzo, Basil Horst, Matei Banu, Kevin A Roth, Jeffrey N Bruce, Peter Canoll, Dario C Altieri, Markus D Siegelin
Rational therapeutic approaches based on synthetic lethality may improve cancer management. Based on a high-throughput drug screen, we provide preclinical proof of concept that targeting the mitochondrial Hsp90 chaperone network (mtHsp90) and inhibition of Bcl-2, Bcl-xL and Mcl-1 is sufficient to elicit synthetic lethality in tumors recalcitrant to therapy. Our analyses focused on BH3 mimetics that are broad acting (ABT263 and Obatoclax) or selective (ABT199, WEHI-539 and A1210477), along with the established mitochondrial matrix chaperone inhibitor Gamitrinib-TPP...
May 18, 2017: Cancer Research
https://www.readbyqxmd.com/read/28522407/high-throughput-screening-and-bioinformatic-analysis-to-ascertain-compounds-that-prevent-saturated-fatty-acid-induced-%C3%AE-cell-apoptosis
#20
Seung-Hee Lee, Daniel Cunha, Carlo Piermarocchi, Giovanni Paternostro, Anthony Pinkerton, Laurence Ladriere, Piero Marchetti, Decio L Eizirik, Miriam Cnop, Fred Levine
Pancreatic β-cell lipotoxicity is a central feature of the pathogenesis of type 2 diabetes. To study the mechanism by which fatty acids cause β-cell death and develop novel approaches to prevent it, a high-throughput screen on the β-cell line INS1 was carried out. The cells were exposed to palmitate to induce cell death and compounds that reversed palmitate-induced cytotoxicity were ascertained. Hits from the screen were analyzed by an increasingly more stringent testing funnel, ending with studies on primary human islets treated with palmitate...
May 15, 2017: Biochemical Pharmacology
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