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High-throughput screening

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https://www.readbyqxmd.com/read/28440957/the-role-of-high-throughput-screening-in-ecotoxicology-and-engineered-nanomaterials
#1
REVIEW
Andrew Barrick, Amélie Châtel, Mélanie Bruneau, Catherine Mouneyrac
The field of environmental toxicology developed as a result of growing concerns about anthropogenic influences on the environment and how to ameliorate ecological impact. Many governmental bodies are beginning to emphasize prevention rather than mitigation when addressing novel products, leading to more of a focus on identifying potential toxicity prior to release. With the exponential advances in their development and sale, novel metamaterials and biotechnology are set to dramatically outpace the capabilities of current testing strategies...
April 25, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28440616/discovery-and-characterization-of-a-eukaryotic-initiation-factor-4a-3-selective-inhibitor-that-suppresses-nonsense-mediated-mrna-decay
#2
Misa Iwatani-Yoshihara, Masahiro Ito, Yoshihiro Ishibashi, Hideyuki Oki, Toshio Tanaka, Daisuke Morishita, Takashi Ito, Hiromichi Kimura, Yasuhiro Imaeda, Samuel A Aparicio, Atsushi Nakanishi, Tomohiro Kawamoto
Eukaryotic initiation factor 4A-3 (eIF4A3) is an Asp-Glu-Ala-Asp (DEAD) box-family adenosine triphosphate (ATP)-dependent RNA helicase. Subtypes eIF4A1 and eIF4A2 are required for translation initiation, but eIF4A3 participates in the exon junction complex (EJC) and functions in RNA metabolism including nonsense-mediated RNA decay (NMD). No small molecules for NMD inhibition via selective inhibition of eIF4A3 have been discovered. Here we identified allosteric eIF4A3 inhibitors from a high-throughput screening campaign...
April 25, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28440476/exploration-of-mir-1202-and-mir-196a-in-human-endometrial-cancer-based-on-high-throughout-gene-screening-analysis
#3
Hong Chen, Yujuan Fan, Wensheng Xu, Junying Chen, Yugang Meng, Di Fang, Jingran Wang
Altered microRNA (miRNA) expression has been reported to participate in the pathogenesis of several human diseases, and particularly cancer. The present study examined the involvement of various miRNAs in the pathophysiology of endometrial cancer (EC) and atypical endometrial hyperplasia (AEH). We performed a high-throughput analysis of the miRNAs (miRNA microarray) found in samples of endometrial tissue obtained from 45 patients; among whom, 15 patients were diagnosed with EC, 15 patients were diagnosed with AEH, and the remainder were healthy donors...
April 24, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28439871/application-of-chemical-genomics-to-plant-bacteria-communication-a-high-throughput-system-to-identify-novel-molecules-modulating-the-induction-of-bacterial-virulence-genes-by-plant-signals
#4
Elodie Vandelle, Maria Rita Puttilli, Andrea Chini, Giulia Devescovi, Vittorio Venturi, Annalisa Polverari
The life cycle of bacterial phytopathogens consists of a benign epiphytic phase, during which the bacteria grow in the soil or on the plant surface, and a virulent endophytic phase involving the penetration of host defenses and the colonization of plant tissues. Innovative strategies are urgently required to integrate copper treatments that control the epiphytic phase with complementary tools that control the virulent endophytic phase, thus reducing the quantity of chemicals applied to economically and ecologically acceptable levels...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439865/identification-of-protein-dna-interactions-using-enhanced-yeast-one-hybrid-assays-and-a-semiautomated-approach
#5
Allison Gaudinier, Michelle Tang, Anne-Maarit Bågman, Siobhan M Brady
Yeast one-hybrid assays are an in vitro gene-centered approach to map transcription factor-DNA interactions. Here we describe this method and adaptations to screen for interactions between plant transcriptional regulators and their targets. Of particular note, the use of yeast one-hybrid assays fills in an important gap in available methodologies. When one is interested in a specific biological process of interest, the yeast one-hybrid assay is the only method that allows researchers to identify upstream regulators of the biological process of interest...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439239/development-of-automated-patch-clamp-technique-to-investigate-cftr-chloride-channel-function
#6
Arnaud Billet, Lionel Froux, John W Hanrahan, Frederic Becq
The chloride (Cl(-)) channel cystic fibrosis transmembrane conductance regulator (CFTR) is defective in cystic fibrosis (CF), and mutation of its encoding gene leads to various defects such as retention of the misfolded protein in the endoplasmic reticulum, reduced stability at the plasma membrane, abnormal channel gating with low open probability, and thermal instability, which leads to inactivation of the channel at physiological temperature. Pharmacotherapy is one major therapeutic approach in the CF field and needs sensible and fast tools to identify promising compounds...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28438642/diagnostic-microarray-for-14-water-and-foodborne-pathogens-using-a-flatbed-scanner
#7
Vidya Srinivasan, Robert D Stedtfeld, Dieter M Tourlousse, Samuel W Baushke, Yu Xin, Sarah M Miller, Trinh Pham, Jean-Marie Rouillard, Erdogan Gulari, James M Tiedje, Syed A Hashsham
Parallel detection approaches are of interest to many researchers interested in identifying multiple water and foodborne pathogens simultaneously. Availability and cost-effectiveness are two key factors determining the usefulness of such approaches for laboratories with limited resources. In this study, we developed and validated a high-density microarray for simultaneous screening of 14 bacterial pathogens using an approach that employs gold labeling with silver enhancement (GLS) protocol. In total, 8887 probes (50-mer) were designed using an in-house database of virulence and marker genes (VMGs), and synthesized in quadruplicate on glass slides using an in-situ synthesis technology...
April 21, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28438393/use-of-the-entericbio-gastro-panel-ii-in-a-diagnostic-microbiology-laboratory-challenges-and-opportunities
#8
Gary McAuliffe, Liselle Bissessor, Deborah Williamson, Sharon Moore, Janet Wilson, Muriel Dufour, Susan Taylor, Arlo Upton
We sought to verify the performance of the EntericBio real-time Gastro Panel 2 (GP2; Serosep, Ireland) assay targeting Salmonella, Shigella, Campylobacter, verotoxin producing E. coli (VTEC), Giardia, and Cryptosporidium in a high-throughput diagnostic laboratory. Following a technical verification period where 237 faecal samples were tested in parallel, guided culture and discrepancy analysis were performed. A total of 13,223 faecal samples were screened by the GP2 assay. During technical verification, sensitivity, specificity, negative and positive predictive value of the GP2 assay compared with conventional methods were 100% (83-100%), 98% (96...
April 21, 2017: Pathology
https://www.readbyqxmd.com/read/28437628/advanced-biomaterials-and-microengineering-technologies-to-recapitulate-the-stepwise-process-of-cancer-metastasis
#9
REVIEW
Nitish Peela, Danh Truong, Harpinder Saini, Hunghao Chu, Samaneh Mashaghi, Stephanie L Ham, Sunil Singh, Hossein Tavana, Bobak Mosadegh, Mehdi Nikkhah
Cancer is one of the leading causes of death globally according to the World Health Organization. Although improved treatments and early diagnoses have reduced cancer related mortalities, metastatic disease remains a major clinical challenge. The local tumor microenvironment plays a significant role in cancer metastasis, where tumor cells respond and adapt to a plethora of biochemical and biophysical signals from stromal cells and extracellular matrix (ECM) proteins. Due to these complexities, there is a critical need to understand molecular mechanisms underlying cancer metastasis to facilitate the discovery of more effective therapies...
April 21, 2017: Biomaterials
https://www.readbyqxmd.com/read/28436560/development-of-a-high-throughput-genotoxicity-assay-using-umu-test-strains-expressing-human-cytochrome-p450s-and-nadph-p450-reductase-and-bacterial-o-acetyltransferase
#10
Hisako Hori, Daisuke Hirata, Wataru Fujii, Yoshimitsu Oda
Umu test is one of the in vitro genotoxicity test that has been used widely. It was developed as a high-throughput test system using the 96-well microplate. We have previously constructed new umu test strains for the evaluation of genotoxicity of procarcinogenic metabolic products formed by cytochrome P450 (CYP) enzymes. In this study, a highly sensitive high-throughput genotoxicity test was developed using four umu test strains (OY1002/1A1, OY1002/1B1, OY1002/1A2, and OY1002/3A4) that express human CYPs and NADPH-P450 reductase...
April 24, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28436458/development-of-a-fluorescent-asfv-strain-that-retains-the-ability-to-cause-disease-in-swine
#11
Manuel V Borca, Vivian O'Donnell, Lauren G Holinka, Brent Sanford, Paul A Azzinaro, Guillermo R Risatti, Douglas P Gladue
African swine fever is a contagious and often lethal disease for domestic pigs with a significant economic impact for the swine industry. The etiological agent, African swine fever virus (ASFV), is a highly structurally complex double stranded DNA virus. No effective vaccines or antiviral treatment are currently commercially available. We present here the development of a strain of ASFV that has been shown to retain its ability to cause disease in swine, efficiently replicate in swine macrophage and that is fluorescently tagged...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28434976/compartmentalized-microfluidic-perfusion-system-to-culture-human-induced-pluripotent-stem-cell-aggregates
#12
Yuki Kondo, Koji Hattori, Shota Tashiro, Eri Nakatani, Ryosuke Yoshimitsu, Taku Satoh, Shinji Sugiura, Toshiyuki Kanamori, Kiyoshi Ohnuma
Microfluidic perfusion systems enable small-volume cell cultures under precisely controlled microenvironments, and are typically developed for cell-based high-throughput screening. However, most such systems are designed to manipulate dissociated single cells, not cell aggregates, and are thus unsuitable to induce differentiation in human induced pluripotent stem cells (hiPSCs), which is conventionally achieved by using cell aggregates to increase cell-cell interactions. We have now developed a compartmentalized microfluidic perfusion system with large flow channels to load, culture, and observe cell aggregates...
April 20, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28433629/a-novel-strategy-to-dissect-endogenous-gene-transcriptional-regulation-in-live-cells
#13
Wenqing Yang, Siliang Zhang, Yi Zhang, Xin Huang
Gene transcription is a central tenet of biology, traditionally measured by RT-PCR, microarray, or more recently, RNA sequencing. However, these measurements only provide a snapshot of the state of gene transcription and only represent an overall readout of complex transcriptional networks that regulate gene expression. In this report, we describe a novel strategy to dissect endogenous gene transcription regulation in live cells by knocking in a reporter gene, EGFP, under the control of the endogenous gene promoter, using the ARID1A gene as an example...
April 19, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28433511/design-synthesis-and-pharmacological-evaluation-of-4-azolyl-benzamide-derivatives-as-novel-gpr52-agonists
#14
Kazuyuki Tokumaru, Yoshiteru Ito, Izumi Nomura, Takashi Nakahata, Yuji Shimizu, Emi Kurimoto, Kazunobu Aoyama, Kazuyoshi Aso
G protein-coupled receptor 52 (GPR52) agonists are expected to improve the symptoms of psychiatric disorders. During exploration for a novel class of GPR52 agonists with good pharmacokinetic profiles, we synthesized 4-(3-(3-fluoro-5-(trifluoromethyl)benzyl)-5-methyl-1H-1,2,4-triazol-1-yl)-2-methylbenzamide (4u; half maximal effective concentration (EC50)=75nM, maximal response (Emax)=122%) starting from a high-throughput screening hit 3 (EC50=470nM, Emax=56%). The structural features of a reported GPR52 agonist were applied to 3, led to design 4-azolylbenzamides as novel GPR52 agonists...
April 1, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28433059/an-entropy-driven-signal-amplifying-strategy-for-real-time-monitoring-of-dna-methylation-process-and-high-throughput-screening-of-methyltransferase-inhibitors
#15
Siyi Chen, Huan Ma, Wang Li, Zhou Nie, Shouzhuo Yao
Based on the entropy-driven toehold-mediated hairpin displacement (ETHDA), a facile and sensitive one-step fluorescence sensing platform has been proposed for the evaluation DNA methylation process catalyzed by methyltransferase (MTase). In this designed system, a hairpin probe is methylated by DNA adenine methylation (Dam) MTase and cleaved by DpnI endonuclease successively, liberating a catalyzer strand to initiate the signal amplification. The fluorescence intensity is increasing upon the catalyzer strand triggered circulating procedure of the ETHDA process...
June 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28432618/the-identification-of-key-genes-and-pathways-in-hepatocellular-carcinoma-by-bioinformatics-analysis-of-high-throughput-data
#16
Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma (HCC) initiation and progression. HCC-associated gene expression dataset was downloaded from Gene Expression Omnibus database. Statistical software R was used for significance analysis of differentially expressed genes (DEGs) between liver cancer samples and normal samples. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, based on R software, were applied for the identification of pathways in which DEGs significantly enriched...
June 2017: Medical Oncology
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
#17
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/28431245/host-microbe-co-metabolism-dictates-cancer-drug-efficacy-in-c-%C3%A2-elegans
#18
Timothy A Scott, Leonor M Quintaneiro, Povilas Norvaisas, Prudence P Lui, Matthew P Wilson, Kit-Yi Leung, Lucia Herrera-Dominguez, Sonia Sudiwala, Alberto Pessia, Peter T Clayton, Kevin Bryson, Vidya Velagapudi, Philippa B Mills, Athanasios Typas, Nicholas D E Greene, Filipe Cabreiro
Fluoropyrimidines are the first-line treatment for colorectal cancer, but their efficacy is highly variable between patients. We queried whether gut microbes, a known source of inter-individual variability, impacted drug efficacy. Combining two tractable genetic models, the bacterium E. coli and the nematode C. elegans, we performed three-way high-throughput screens that unraveled the complexity underlying host-microbe-drug interactions. We report that microbes can bolster or suppress the effects of fluoropyrimidines through metabolic drug interconversion involving bacterial vitamin B6, B9, and ribonucleotide metabolism...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431229/functional-enhancer-screening-in-single-cells
#19
Joris van Arensbergen, Bas van Steensel
In this issue of Molecular Cell, Xie et al. (2017) introduce Mosaic-seq, a powerful technology that combines CRISPRi and single-cell RNA-seq. This method enables the high-throughput assessment of contributions of enhancers to gene regulation.
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28431096/a-new-rapid-resazurin-based-microdilution-assay-for-antimicrobial-susceptibility-testing-of-neisseria-gonorrhoeae
#20
Sunniva Foerster, Valentino Desilvestro, Lucy J Hathaway, Christian L Althaus, Magnus Unemo
Objectives: Rapid, cost-effective and objective methods for antimicrobial susceptibility testing of Neisseria gonorrhoeae would greatly enhance surveillance of antimicrobial resistance. Etest, disc diffusion and agar dilution methods are subjective, mostly laborious for large-scale testing and take ∼24 h. We aimed to develop a rapid broth microdilution assay using resazurin (blue), which is converted into resorufin (pink fluorescence) in the presence of viable bacteria. Methods: The resazurin-based broth microdilution assay was established using 132 N...
April 19, 2017: Journal of Antimicrobial Chemotherapy
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