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High-throughput screening

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https://www.readbyqxmd.com/read/28727807/digoxin-reveals-a-functional-connection-between-hiv-1-integration-preference-and-t-cell-activation
#1
Alexander Zhyvoloup, Anat Melamed, Ian Anderson, Delphine Planas, Chen-Hsuin Lee, Janos Kriston-Vizi, Robin Ketteler, Andy Merritt, Jean-Pierre Routy, Petronela Ancuta, Charles R M Bangham, Ariberto Fassati
HIV-1 integrates more frequently into transcribed genes, however the biological significance of HIV-1 integration targeting has remained elusive. Using a selective high-throughput chemical screen, we discovered that the cardiac glycoside digoxin inhibits wild-type HIV-1 infection more potently than HIV-1 bearing a single point mutation (N74D) in the capsid protein. We confirmed that digoxin repressed viral gene expression by targeting the cellular Na+/K+ ATPase, but this did not explain its selectivity. Parallel RNAseq and integration mapping in infected cells demonstrated that digoxin inhibited expression of genes involved in T-cell activation and cell metabolism...
July 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28727449/the-use-of-maldi-ms-combined-with-differential-hydrogen-deuterium-exchange-for-semi-automated-protein-global-conformational-screening
#2
Gregory F Pirrone, Heather Wang, Nicole Canfield, Alexander S Chin, Timothy A Rhodes, Alexey A Makarov
Matrix-assisted laser desorption/ionization (MALDI) coupled with a time-of-flight (TOF) mass-spectrometry (MS) detector is acknowledged to be very useful for analysis of biological molecules. At the same time, hydrogen-deuterium exchange (HDX) is a well-known technique for studying protein higher-order structure. However, coupling MALDI with HDX may be challenging due to undesired back-exchange reactions during analysis. In this report, we survey an approach that utilizes MALDI coupled with automated sample preparation to compare global conformational changes of proteins under different solution conditions using differential HDX...
July 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28727445/an-antibiotic-that-inhibits-the-atpase-activity-of-an-abc-transporter-by-binding-to-a-remote-extracellular-site
#3
Leigh Morgan Matano, Heidi Gabrielle Morris, Anthony R Hesser, Sara E S Martin, Wonsik Lee, Tristan W Owens, Emaline Laney, Hidemasa Nakaminami, David Hooper, Timothy C Meredith, Suzanne Walker
Antibiotic-resistant strains of Staphylococcus aureus pose a major threat to human health and there is an ongoing need for new antibiotics to treat resistant infections. In a high throughput screen (HTS) of 230,000 small molecules designed to identify bioactive wall teichoic acid (WTA) inhibitors, we identified one hit, which was expanded through chemical synthesis into a small panel of potent compounds. We showed that these compounds target TarG, the transmembrane component of the two-component ATP-binding cassette (ABC) transporter TarGH, which exports WTA precursors to the cell surface for attachment to peptidoglycan...
July 20, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28727427/high-throughput-synthesis-and-structure-of-zeolite-zsm-43-with-two-directional-8-ring-channels
#4
Tom Willhammar, Jie Su, Yifeng Yun, Xiaodong Zou, Mobae Afeworki, Simon C Weston, Hilda B Vroman, William W Lonergan, Karl G Strohmaier
The aluminosilicate zeolite ZSM-43 (where ZSM = Zeolite Socony Mobil) was first synthesized more than 3 decades ago, but its chemical structure remained unsolved because of its poor crystallinity and small crystal size. Here we present optimization of the ZSM-43 synthesis using a high-throughput approach and subsequent structure determination by the combination of electron crystallographic methods and powder X-ray diffraction. The synthesis required the use of a combination of both inorganic (Cs(+) and K(+)) and organic (choline) structure-directing agents...
July 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28725491/ds16570511-is-a-small-molecule-inhibitor-of-the-mitochondrial-calcium-uniporter
#5
Naohiro Kon, Michiko Murakoshi, Aya Isobe, Katsuji Kagechika, Naoki Miyoshi, Takahiro Nagayama
In cardiac myocytes, regulation of mitochondrial Ca(2+) is important for cellular signaling and cardiac contraction. Ca(2+) entry into the mitochondria is mediated by a highly selective Ca(2+) channel called the mitochondrial calcium uniporter, which consists of a pore-forming subunit MCU and regulatory subunits such as MICU1. Although pharmacological regulation of the mitochondrial Ca(2+) influx is a promising approach to controlling the cellular functions, a cell-permeable and specific inhibitor of the mitochondrial calcium uniporter has not yet been developed...
2017: Cell Death Discovery
https://www.readbyqxmd.com/read/28724938/a-novel-role-for-rar%C3%AE-agonists-as-apolipoprotein-ciii-inhibitors-identified-from-high-throughput-screening
#6
Sang Jun Lee, Madhupriya Mahankali, Abdallah Bitar, Huafei Zou, Elizabeth Chao, Hung Nguyen, Jose Gonzalez, Dawna Caballero, Mitch Hull, Danling Wang, Peter G Schultz, Weijun Shen
Elevated triglyceride (TG) levels are well-correlated with the risk for cardiovascular disease (CVD). Apolipoprotein CIII (ApoC-III) is a key regulator of plasma TG levels through regulation of lipolysis and lipid synthesis. To identify novel regulators of TG levels, we carried out a high throughput screen (HTS) using an ApoC-III homogenous time resolved fluorescence (HTRF) assay. We identified several retinoic acid receptor (RAR) agonists that reduced secreted ApoC-III levels in human hepatic cell lines. The RARα specific agonist AM580 inhibited secreted ApoC-III by >80% in Hep3B cells with an EC50 ~2...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28724888/crosscheck-an-open-source-web-tool-for-high-throughput-screen-data-analysis
#7
Jamil Najafov, Ayaz Najafov
Modern high-throughput screening methods allow researchers to generate large datasets that potentially contain important biological information. However, oftentimes, picking relevant hits from such screens and generating testable hypotheses requires training in bioinformatics and the skills to efficiently perform database mining. There are currently no tools available to general public that allow users to cross-reference their screen datasets with published screen datasets. To this end, we developed CrossCheck, an online platform for high-throughput screen data analysis...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28723269/identification-of-antipneumococcal-molecules-effective-against-different-streptococcus-pneumoniae-serotypes-using-a-resazurin-based-high-throughput-screen
#8
Hyung Jun Kim, Namyoul Kim, David Shum, Srigouri Huddar, Chul Min Park, Soojin Jang
Streptococcus pneumoniae is a major human pathogen, causing around 1.6 million deaths worldwide each year. By optimizing a resazurin-based assay to detect S. pneumoniae growth in 384-well microplates, we developed a new high-throughput screening (HTS) system for the discovery of antipneumococcal molecules, which was unsuccessful using conventional absorbance measurements. Before applying our protocol to a large-scale screen, we validated the system through a pilot screen targeting about 7,800 bioactive molecules using three different S...
July 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/28722773/radh-a-versatile-halogenase-for-integration-into-synthetic-pathways
#9
Binuraj Menon, Eileen Brandenburger, Humera Sharif, Ulrike Klemstein, Sarah Shepherd, Michael Greaney, Jason Micklefield
Flavin-dependent halogenases are useful enzymes providing halogenated molecules with improved biological activity or intermediates for synthetic derivatization. Here we demonstrate how the fungal halogenase RadH can be used to regioselectively halogenate a range of bioactive aromatic scaffolds. Site-directed mutagenesis of RadH was used to identify catalytic residues and provide insights into the mechanism of fungal halogenases. A high throughput fluorescence screen was also developed enabling a RadH mutant to be evolved with improved properties...
July 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28722296/a-ligand-based-nmr-screening-approach-for-identification-and-characterization-of-inhibitors-and-promoters-of-amyloid-peptide-aggregation
#10
Reinhard Werner Neier, Claudio Dalvit, Sara Santi
Over the years a great effort has been put into the development of rapid and reliable methods to monitor in real-time the aggregation dynamics of the β1-42 amyloid peptide. We present an alternative approach based on a suitable reporter or spy molecule and three different NMR experiments, WaterLOGSY, 1H Selective T1 filter and 19F T2 filter, for monitoring the initial self-aggregation process kinetics of the β1-42 amyloid peptide and identifying molecules that retard or accelerate the self-aggregation process...
July 19, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28722137/precise-and-arbitrary-deposition-of-biomolecules-onto-biomimetic-fibrous-matrices-for-spatially-controlled-cell-distribution-and-functions
#11
Chao Jia, Bowen Luo, Haoyu Wang, Yongqian Bian, Xueyong Li, Shaohua Li, Hongjun Wang
Advances in nano-/microfabrication allow the fabrication of biomimetic substrates for various biomedical applications. In particular, it would be beneficial to control the distribution of cells and relevant biomolecules on an extracellular matrix (ECM)-like substrate with arbitrary micropatterns. In this regard, the possibilities of patterning biomolecules and cells on nanofibrous matrices are explored here by combining inkjet printing and electrospinning. Upon investigation of key parameters for patterning accuracy and reproducibility, three independent studies are performed to demonstrate the potential of this platform for: i) transforming growth factor (TGF)-β1-induced spatial differentiation of fibroblasts, ii) spatiotemporal interactions between breast cancer cells and stromal cells, and iii) cancer-regulated angiogenesis...
July 19, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28721653/comparison-of-flow-cytometry-and-elasa-for-screening-of-proper-candidate-aptamer-in-cell-selex-pool
#12
Maryam Sadat Nabavinia, Fahimeh Charbgoo, Mona Alibolandi, Fatemeh Mosaffa, Aida Gholoobi, Mohammad Ramezani, Khalil Abnous
Aptamers are single-stranded RNA or DNA, which bind to their target with high affinity and specificity. Method of isolating aptamers against cell surface protein is called cell-SELEX. Common approach for monitoring cell-SELEX developed aptamers is flow cytometry. Since flow cytometry is costly and requires sophisticated equipments, we suggested implementing easy access, high throughput enzyme-link apta-sorbent assay test (ELASA) to confirm the specificity of aptamers selected through cell-SELEX process. In this regard, we compared ELASA and flow cytometry techniques in order to screen potent candidate aptamers against A2780 Rcis cell line, which were selected by cell-SELEX...
July 19, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28718848/label-free-high-throughput-holographic-screening-and-enumeration-of-tumor-cells-in-blood
#13
Dhananjay Kumar Singh, Caroline C Ahrens, Wei Li, Siva A Vanapalli
We introduce inline digital holographic microscopy (in-line DHM) as a label-free technique for detecting tumor cells in blood. The optimized DHM platform fingerprints every cell flowing through a microchannel at 10 000 cells per second, based on three features - size, maximum intensity and mean intensity. To identify tumor cells in a background of blood cells, we developed robust gating criteria using machine-learning approaches. We established classifiers from the features extracted from 100 000-cell training sets consisting of red blood cells, peripheral blood mononuclear cells and tumor cell lines...
July 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28718799/zebrafish-as-a-model-organism-for-the-development-of-drugs-for-skin-cancer
#14
REVIEW
Fatemeh Bootorabi, Hamed Manouchehri, Reza Changizi, Harlan Barker, Elisabetta Palazzo, Annalisa Saltari, Mataleena Parikka, Carlo Pincelli, Ashok Aspatwar
Skin cancer, which includes melanoma and squamous cell carcinoma, represents the most common type of cutaneous malignancy worldwide, and its incidence is expected to rise in the near future. This condition derives from acquired genetic dysregulation of signaling pathways involved in the proliferation and apoptosis of skin cells. The development of animal models has allowed a better understanding of these pathomechanisms, with the possibility of carrying out toxicological screening and drug development. In particular, the zebrafish (Danio rerio) has been established as one of the most important model organisms for cancer research...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28718678/discovery-of-novel-isoflavone-derivatives-as-ache-buche-dual-targeted-inhibitors-synthesis-biological-evaluation-and-molecular-modelling
#15
Bo Feng, Xinpeng Li, Jie Xia, Song Wu
AChE and BuChE are druggable targets for the discovery of anti-Alzheimer's disease drugs, while dual-inhibition of these two targets seems to be more effective. In this study, we synthesised a series of novel isoflavone derivatives based on our hit compound G from in silico high-throughput screening and then tested their activities by in vitro AChE and BuChE bioassays. Most of the isoflavone derivatives displayed moderate inhibition against both AChE and BuChE. Among them, compound 16 was identified as a potent AChE/BuChE dual-targeted inhibitor (IC50: 4...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28718373/screening-of-specific-nucleic-acid-aptamers-binding-tumor-markers-in-the-serum-of-the-lung-cancer-patients-and-identification-of-their-activities
#16
Kun Li, Chen-Lin Xiu, Li-Ming Gao, Hua-Gang Liang, Shu-Feng Xu, Ming Shi, Jian Li, Zhi-Wei Liu
Lung cancer is by far the leading cause of cancer death in the world. Despite the improvements in diagnostic methods, the status of early detection was not achieved. So, a new diagnostic method is needed. The aim of this study is to obtain the highly specific nucleic acid aptamers with strong affinity to tumor markers in the serum of the lung cancer patients for targeting the serum. Aptamers specifically binding to tumor markers in the serum of the lung cancer patients were screened from the random single-stranded DNA library with agarose beads as supports and the serum as a target by target-substituting subtractive SELEX technique and real-time quantitative polymerase chain reaction technique...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28717593/short-reads-from-honey-bee-apis-sp-sequencing-projects-reflect-microbial-associate-diversity
#17
Michael Gerth, Gregory D D Hurst
High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome...
2017: PeerJ
https://www.readbyqxmd.com/read/28717411/skeletal-muscle-generated-from-induced-pluripotent-stem-cells-induction-and-application
#18
REVIEW
Yuko Miyagoe-Suzuki, Shin'ichi Takeda
Human induced pluripotent stem cells (hiPS cells or hiPSCs) can be derived from cells of patients with severe muscle disease. If skeletal muscle induced from patient-iPSCs shows disease-specific phenotypes, it can be useful for studying the disease pathogenesis and for drug development. On the other hand, human iPSCs from healthy donors or hereditary muscle disease-iPSCs whose genomes are edited to express normal protein are expected to be a cell source for cell therapy. Several protocols for the derivation of skeletal muscle from human iPSCs have been reported to allow the development of efficient treatments for devastating muscle diseases...
June 26, 2017: World Journal of Stem Cells
https://www.readbyqxmd.com/read/28717384/accelerating-root-system-phenotyping-of-seedlings-through-a-computer-assisted-processing-pipeline
#19
Lionel X Dupuy, Gladys Wright, Jacqueline A Thompson, Anna Taylor, Sebastien Dekeyser, Christopher P White, William T B Thomas, Mark Nightingale, John P Hammond, Neil S Graham, Catherine L Thomas, Martin R Broadley, Philip J White
BACKGROUND: There are numerous systems and techniques to measure the growth of plant roots. However, phenotyping large numbers of plant roots for breeding and genetic analyses remains challenging. One major difficulty is to achieve high throughput and resolution at a reasonable cost per plant sample. Here we describe a cost-effective root phenotyping pipeline, on which we perform time and accuracy benchmarking to identify bottlenecks in such pipelines and strategies for their acceleration...
2017: Plant Methods
https://www.readbyqxmd.com/read/28717245/development-and-validation-of-a-three-gene-prognostic-signature-for-patients-with-hepatocellular-carcinoma
#20
Binghua Li, Wendu Feng, Ouyang Luo, Tiancheng Xu, Yajuan Cao, Hongyan Wu, Decai Yu, Yitao Ding
Hepatocellular carcinoma (HCC) is the leading cause of cancer-related death worldwide, because recurrence often occurs in most HCC patients undergoing hepatectomy. It is necessary to identify patients with high risk for recurrence and adopt effective therapies. An obstacle to monitor patients at high risk for poor prognosis has been the lack of useful predictive biomarkers. Fortunately, recent progress in system biology allows to screen the biomarkers for HCC prognosis in a high-throughput manner. In this study, we performed systematic Kaplan-Meier survival analysis of the whole mRNA transcriptomics based on the Cancer Genome Atlas project (TCGA) and developed a three-gene prognostic signature composing of three genes UPB1, SOCS2 and RTN3...
July 17, 2017: Scientific Reports
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