Literature DB >> 26977352

Frapid: achieving full automation of FRAP for chemical probe validation.

Clarence Yapp1, Catherine Rogers2, Pavel Savitsky3, Martin Philpott4, Susanne Müller2.   

Abstract

Fluorescence Recovery After Photobleaching (FRAP) is an established method for validating chemical probes against the chromatin reading bromodomains, but so far requires constant human supervision. Here, we present Frapid, an automated open source code implementation of FRAP that fully handles cell identification through fuzzy logic analysis, drug dispensing with a custom-built fluid handler, image acquisition & analysis, and reporting. We successfully tested Frapid on 3 bromodomains as well as on spindlin1 (SPIN1), a methyl lysine binder, for the first time.

Entities:  

Keywords:  (100.3008) Image recognition, algorithms and filters; (150.0150) Machine vision; (150.5758) Robotic and machine control; (170.1530) Cell analysis; (170.1790) Confocal microscopy; (170.2520) Fluorescence microscopy

Year:  2016        PMID: 26977352      PMCID: PMC4771461          DOI: 10.1364/BOE.7.000422

Source DB:  PubMed          Journal:  Biomed Opt Express        ISSN: 2156-7085            Impact factor:   3.732


  24 in total

1.  Identification and characterization of BPTF, a novel bromodomain transcription factor.

Authors:  M H Jones; N Hamana; M Shimane
Journal:  Genomics       Date:  2000-01-01       Impact factor: 5.736

2.  Ligation-independent cloning of PCR products (LIC-PCR).

Authors:  C Aslanidis; P J de Jong
Journal:  Nucleic Acids Res       Date:  1990-10-25       Impact factor: 16.971

3.  Fuzzy logic and maximum a posteriori-based image restoration for confocal microscopy.

Authors:  Giuseppe Vicidomini; Partha Pratim Mondal; Alberto Diaspro
Journal:  Opt Lett       Date:  2006-12-15       Impact factor: 3.776

Review 4.  Epigenetic chemical probes.

Authors:  S Müller; P J Brown
Journal:  Clin Pharmacol Ther       Date:  2012-10-24       Impact factor: 6.875

Review 5.  Bromodomains and their pharmacological inhibitors.

Authors:  Daniel Gallenkamp; Kathy A Gelato; Bernard Haendler; Hilmar Weinmann
Journal:  ChemMedChem       Date:  2014-02-04       Impact factor: 3.466

6.  Towards A Fully Automated High-Throughput Phototransfection System.

Authors:  David J Cappelleri; Adam Halasz; Jai-Yoon Sul; Tae Kyung Kim; James Eberwine; Vijay Kumar
Journal:  JALA Charlottesv Va       Date:  2010-08-01

7.  Systematic identification of mammalian regulatory motifs' target genes and functions.

Authors:  Jason B Warner; Anthony A Philippakis; Savina A Jaeger; Fangxue Sherry He; Jolinta Lin; Martha L Bulyk
Journal:  Nat Methods       Date:  2008-03-02       Impact factor: 28.547

8.  PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains.

Authors:  Sarah Picaud; David Da Costa; Angeliki Thanasopoulou; Panagis Filippakopoulos; Paul V Fish; Martin Philpott; Oleg Fedorov; Paul Brennan; Mark E Bunnage; Dafydd R Owen; James E Bradner; Philippe Taniere; Brendan O'Sullivan; Susanne Müller; Juerg Schwaller; Tatjana Stankovic; Stefan Knapp
Journal:  Cancer Res       Date:  2013-04-10       Impact factor: 12.701

9.  5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation.

Authors:  Richard J Hopkinson; Anthony Tumber; Clarence Yapp; Rasheduzzaman Chowdhury; WeiShen Aik; Ka Hing Che; Xuan Shirley Li; Jan B L Kristensen; Oliver N F King; Mun Chiang Chan; Kar Kheng Yeoh; Hwanho Choi; Louise J Walport; Cyrille C Thinnes; Jacob T Bush; Clarisse Lejeune; Anna M Rydzik; Nathan R Rose; Eleanor A Bagg; Michael A McDonough; Tobias Krojer; Wyatt W Yue; Stanley S Ng; Lars Olsen; Paul E Brennan; Udo Oppermann; Susanne Muller-Knapp; Robert J Klose; Peter J Ratcliffe; Christopher J Schofield; Akane Kawamura
Journal:  Chem Sci       Date:  2013-08-01       Impact factor: 9.825

10.  Software-aided automatic laser optoporation and transfection of cells.

Authors:  Hans Georg Breunig; Aisada Uchugonova; Ana Batista; Karsten König
Journal:  Sci Rep       Date:  2015-06-08       Impact factor: 4.379

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