Functional characterization of RNA fragments using high-throughput interactome screening

2019 ◽  
Vol 193 ◽  
pp. 173-183 ◽  
Author(s):  
Paulina Jackowiak ◽  
Angelika Lis ◽  
Magdalena Luczak ◽  
Ireneusz Stolarek ◽  
Marek Figlerowicz
Keyword(s):  
High Throughput ◽  
Functional Characterization ◽  
Rna Fragments

scholarly journals Formulation, High Throughput In Vitro Screening and In Vivo Functional Characterization of Nanoemulsion-Based Intranasal Vaccine Adjuvants

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0126120 ◽  
Author(s):  
Pamela T. Wong ◽  
Pascale R. Leroueil ◽  
Douglas M. Smith ◽  
Susan Ciotti ◽  
Anna U. Bielinska ◽  
...  
Keyword(s):  
High Throughput ◽  
Functional Characterization ◽  
In Vitro Screening ◽  
Vaccine Adjuvants ◽  
Intranasal Vaccine

scholarly journals All-Optical Electrophysiology for High-Throughput Functional Characterization of a Human iPSC-Derived Motor Neuron Model of ALS

2018 ◽  
Vol 10 (6) ◽  
pp. 1991-2004 ◽  
Author(s):  
Evangelos Kiskinis ◽  
Joel M. Kralj ◽  
Peng Zou ◽  
Eli N. Weinstein ◽  
Hongkang Zhang ◽  
...  
Keyword(s):  
Motor Neuron ◽  
High Throughput ◽  
Neuron Model ◽  
Functional Characterization ◽  
All Optical ◽  
Human Ipsc

scholarly journals Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

2016 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefano Campanaro ◽  
Laura Treu ◽  
Panagiotis G. Kougias ◽  
Davide De Francisci ◽  
Giorgio Valle ◽  
...  
Keyword(s):  
High Throughput ◽  
Functional Characterization ◽  
Shotgun Sequencing ◽  
Metagenomic Analysis

scholarly journals Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular sensors

2019 ◽  
Author(s):  
Johan O. L. Andreasson ◽  
Michael R. Gotrik ◽  
Michelle J. Wu ◽  
Hannah K. Wayment-Steele ◽  
Wipapat Kladwang ◽  
...  
Keyword(s):  
High Throughput ◽  
Online Community ◽  
Large Scale ◽  
Functional Characterization ◽  
New Paradigm ◽  
Molecular Sensors ◽  
Rna Switches ◽  
Rna Sensors ◽  
Rna Design

AbstractInternet-based scientific communities promise a means to apply distributed, diverse human intelligence towards previously intractable scientific problems. However, current implementations have not allowed communities to propose experiments to test all emerging hypotheses at scale or to modify hypotheses in response to experiments. We report high-throughput methods for molecular characterization of nucleic acids that enable the large-scale videogame-based crowdsourcing of functional RNA sensor design, followed by high-throughput functional characterization. Iterative design testing of thousands of crowdsourced RNA sensor designs produced near-thermodynamically optimal and reversible RNA switches that act as self-contained molecular sensors and couple five distinct small molecule inputs to three distinct protein binding and fluorogenic outputs—results that surpass computational and expert-based design. This work represents a new paradigm for widely distributed experimental bioscience.One Sentence SummaryOnline community discovers standalone RNA sensors.

High-throughput functional characterization of miRNAs in cytogenetically defined AML subgroups

2013 ◽  
Vol 225 (03) ◽  
Author(s):  
R Jammal ◽  
S Emmrich ◽  
K Henke ◽  
J Kuipers ◽  
M Heuvel vd ◽  
...  
Keyword(s):  
High Throughput ◽  
Functional Characterization

scholarly journals High-Throughput Recovery and Characterization of Metagenome-Derived Glycoside Hydrolase-Containing Clones as a Resource for Biocatalyst Development

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Zachary Armstrong ◽  
Feng Liu ◽  
Sam Kheirandish ◽  
Hong-Ming Chen ◽  
Keith Mewis ◽  
...  
Keyword(s):  
High Throughput ◽  
Glycoside Hydrolase ◽  
Plant Biomass ◽  
Functional Characterization ◽  
Environmental Dna ◽  
Functional Screening ◽  
Biomass Degradation ◽  
Genomic Context ◽  
Or Gene

ABSTRACT Functional metagenomics is a powerful tool for both the discovery and development of biocatalysts. This study presents the high-throughput functional screening of 22 large-insert fosmid libraries containing over 300,000 clones sourced from natural and engineered ecosystems, characterization of active clones, and a demonstration of the utility of recovered genes or gene cassettes in the development of novel biocatalysts. Screening was performed in a 384-well-plate format with the fluorogenic substrate 4-methylumbelliferyl cellobioside, which releases a fluorescent molecule when cleaved by β-glucosidases or cellulases. The resulting set of 164 active clones was subsequently interrogated for substrate preference, reaction mechanism, thermal stability, and optimal pH. The environmental DNA harbored within each active clone was sequenced, and functional annotation revealed a cornucopia of carbohydrate-degrading enzymes. Evaluation of genomic-context information revealed both synteny and polymer-targeting loci within a number of sequenced clones. The utility of these fosmids was then demonstrated by identifying clones encoding activity on an unnatural glycoside (4-methylumbelliferyl 6-azido-6-deoxy-β-d-galactoside) and transforming one of the identified enzymes into a glycosynthase capable of forming taggable disaccharides. IMPORTANCE The generation of new biocatalysts for plant biomass degradation and glycan synthesis has typically relied on the characterization and investigation of one or a few enzymes at a time. By coupling functional metagenomic screening and high-throughput functional characterization, we can progress beyond the current scale of catalyst discovery and provide rapid annotation of catalyst function. By functionally screening environmental DNA from many diverse sources, we have generated a suite of active glycoside hydrolase-containing clones and demonstrated their reaction parameters. We then demonstrated the utility of this collection through the generation of a new catalyst for the formation of azido-modified glycans. Further interrogation of this collection of clones will expand our biocatalytic toolbox, with potential application to biomass deconstruction and synthesis of glycans.

scholarly journals Green fluorescent protein-based assays for high-throughput functional characterization and ligand-binding studies of biotin protein ligase

2016 ◽  
Vol 8 (2) ◽  
pp. 418-424 ◽  
Author(s):  
Samuel P. Askin ◽  
Thomas E. H. Bond ◽  
Patrick M. Schaeffer
Keyword(s):  
Green Fluorescent Protein ◽  
Ligand Binding ◽  
High Throughput ◽  
Fluorescent Protein ◽  
Functional Characterization ◽  
Binding Studies ◽  
Biotin Protein Ligase ◽  
Green Fluorescent

Rapid functional characterization of GFP-tagged biotin protein ligase (BirA-GFP) with a high-throughput DSF-GTP assay.

scholarly journals Functional characterization of MCAK/Kif2C cancer mutations using high-throughput microscopic analysis

2020 ◽  
Vol 31 (7) ◽  
pp. 580-588 ◽  
Author(s):  
Mike Wagenbach ◽  
Juan Jesus Vicente ◽  
Yulia Ovechkina ◽  
Sarah Domnitz ◽  
Linda Wordeman
Keyword(s):  
High Throughput ◽  
Karyotype Evolution ◽  
Functional Characterization ◽  
Microscopic Analysis ◽  
Missense Mutations ◽  
Cancer Mutations

MCAK/Kif2C is a microtubule-depolymerizing kinesin. Its activity can be rapidly quantified in fluorescently labeled cells using Cell Profiler. This method was used to interrogate MCAK/Kif2C missense mutations catalogued in the cBioPortal database. A majority of the mutations tested are deleterious and likely to increase karyotype evolution in cancer.

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