FPCount protocol - Full protocol v1

2021 ◽  
Author(s):  
Eszter Csibra ◽  
Guy-Bart Stan
Keyword(s):  
Protein Concentration ◽  
Fluorescent Protein ◽  
R Package ◽  
Protein Storage ◽  
Concentration Determination ◽  
Plate Reader ◽  
Full Protocol ◽  
Microplate Reader

FPCount is a complete protocol for fluorescent protein calibration, consisting of: 1. FP expression/purification using Thermo's HisPur Cobalt Resin. 2. FP concentration determination in a microplate reader. 3. FP fluorescence quantification in a microplate reader. Results can be analysed with the corresponding R package, FPCountR. --- Summary 1. Expression 2. Harvesting/Washing 3. Lysis 4. Fractionation 5. Gel1: Verification of Expression/Fractions 6. Purification 7. Gel2: Verification of Purification 8. Protein concentration and buffer exchange 9. Quantification of FP concentration (part1) 10. Quantification of FP fluorescence 11. Quantification of FP concentration (part2) 12. Protein Storage 13. Calibration of Plate Reader

FPCount protocol - in-lysate (purification free) protocol v1

2021 ◽  
Author(s):  
Eszter Csibra ◽  
Guy-Bart Stan
Keyword(s):  
Protein Concentration ◽  
Fluorescent Protein ◽  
R Package ◽  
Protein Quantification ◽  
Protein Storage ◽  
Cell Lysates ◽  
Concentration Determination ◽  
His Tag ◽  
Plate Reader ◽  
Microplate Reader

FPCount is a complete protocol for fluorescent protein calibration, consisting of: 1. FP expression and production of cell lysates. 2. FP concentration determination in a microplate reader. 3. FP fluorescence quantification in a microplate reader. Results can be analysed with the corresponding R package, FPCountR. This in-lysate version of the protocol uses the ECmax protein quantification protocol of FPs in lysates and does not require His-tag purification of the FPs. Note that it is only suitable for FPs with entries in FPbase. If you want to verify or validate results, it's recommended you follow the 'short' protocol, which requires FP purification, or the 'complete' protocol, which requires FP purification and compares three protein quantification methods. --- Summary 1. Expression 2. Harvesting/Washing 3. Lysis 4. Fractionation 8. Protein concentration and buffer exchange 9. Quantification of FP concentration (part1) 10. Quantification of FP fluorescence 12. Protein storage 13. Calibration of Plate Reader

FPCount protocol - Short protocol v1

2021 ◽  
Author(s):  
Eszter Csibra ◽  
Guy-Bart Stan
Keyword(s):  
Protein Concentration ◽  
Fluorescent Protein ◽  
R Package ◽  
Protein Quantification ◽  
Short Version ◽  
Protein Storage ◽  
Concentration Determination ◽  
Sds Page ◽  
Plate Reader ◽  
Microplate Reader

FPCount is a complete protocol for fluorescent protein calibration, consisting of: 1. FP expression/purification using Thermo's HisPur Cobalt Resin. 2. FP concentration determination in a microplate reader. 3. FP fluorescence quantification in a microplate reader. Results can be analysed with the corresponding R package, FPCountR. This short version uses the ECmax protein quantification protocol, and is only suitable for FPs with entries in FPbase. If you want to verify or validate results, it's recommended you follow the complete protocol, which describes three protein quantification methods. The short protocol also skips the SDS-PAGE steps. If you require these, please see the complete protocol. --- Summary 1. Expression 2. Harvesting/Washing 3. Lysis 4. Fractionation 6. Purification 8. Protein concentration and buffer exchange 9. Quantification of FP concentration (part1) 10. Quantification of FP fluorescence 12. Protein storage 13. Calibration of Plate Reader

Targeting and processing of membrane-anchored YFP fusion proteins to protein storage vacuoles in transgenic tobacco seeds

2005 ◽  
Vol 15 (4) ◽  
pp. 361-364 ◽  
Author(s):  
Ka Leung Fung ◽  
Yin Fun Yim ◽  
Yu Chung Tse ◽  
Yansong Miao ◽  
Samuel S.M. Sun ◽  
...  
Keyword(s):  
Transgenic Tobacco ◽  
Fusion Proteins ◽  
Seed Protein ◽  
Fluorescent Protein ◽  
Yellow Fluorescent Protein ◽  
Protein Storage ◽  
Protein Storage Vacuoles ◽  
Pharmaceutical Proteins ◽  
Tobacco Seeds ◽  
Foreign Proteins

Seeds that store proteins in protein storage vacuoles are attractive bioreactors for producing and storing large amounts of pharmaceutical proteins. However, foreign proteins expressed in transgenic plants are subjected to the delivery and modification processes present within plant cells. Here, it is demonstrated that unique membrane sequences deliver a yellow fluorescent protein (YFP) to the seed protein storage vacuoles in transgenic tobacco (Nicotiana tabacum L.) plants, where the YFP is then separated from its membrane anchors. This precise targeting and separation is required for the successful delivery of useful proteins to seed protein storage vacuoles for their stable accumulation in transgenic crops.

scholarly journals A Genetic Toolkit for Investigating Clavibacter Species: Markerless Deletion, Permissive Site Identification, and an Integrative Plasmid

2021 ◽  
Author(s):  
Danielle M. Stevens ◽  
Andrea Tang ◽  
Gitta Coaker
Keyword(s):  
Fluorescent Protein ◽  
Genetic Manipulation ◽  
Region Of Interest ◽  
R Package ◽  
Clavibacter Michiganensis ◽  
Gram Positive ◽  
Integrative Plasmid ◽  
Tomato Pathogen ◽  
Green Fluorescent ◽  
Markerless Deletion

The development of knockout mutants and expression variants are critical for understanding genotype-phenotype relationships. However, advances in these techniques in gram-positive actinobacteria have stagnated over the last decade. Actinobacteria in the Clavibacter genus are composed of diverse crop pathogens that cause a variety of wilt and cankering diseases. Here, we present a suite of tools for genetic manipulation in the tomato pathogen Clavibacter michiganensis including a markerless deletion system, an integrative plasmid, and an R package for identification of permissive sites for plasmid integration. The vector pSelAct-KO is a recombination-based, markerless knockout system that uses dual selection to engineer seamless deletions of a region of interest, providing opportunities for repeated higher-order genetic knockouts. The efficacy of pSelAct-KO was demonstrated in C. michiganensis and was confirmed using whole-genome sequencing. We developed permissR, an R package to identify permissive sites for chromosomal integration, which can be used in conjunction with pSelAct-Express, a nonreplicating integrative plasmid that enables recombination into a permissive genomic location. Expression of enhanced green fluorescent protein by pSelAct-Express was verified in two candidate permissive regions predicted by permissR in C. michiganensis. These molecular tools are essential advances for investigating gram-positive actinobacteria, particularly for important pathogens in the Clavibacter genus. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

scholarly journals FPCountR: Absolute quantification of fluorescent proteins for synthetic biology

2021 ◽  
Author(s):  
Eszter Csibra ◽  
Guy-Bart Stan
Keyword(s):  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
R Package ◽  
Absolute Quantification ◽  
Cellular Protein ◽  
Cell Counts ◽  
Time Calibration ◽  
Quantitative Characterisation ◽  
First Time ◽  
Cell Volumes

AbstractThis paper presents a generalisable method for the calibration of fluorescence readings on microplate readers, in order to convert arbitrary fluorescence units into absolute units. FPCountR relies on the generation of bespoke fluorescent protein (FP) calibrants, assays to determine protein concentration and activity, and a corresponding analytical workflow. We systematically characterise the assay protocols for accuracy, sensitivity and simplicity, and describe a novel ‘ECmax’ assay that outperforms the others and even enables accurate calibration without requiring the purification of FPs. To obtain cellular protein concentrations, we consider methods for the conversion of optical density to either cell counts or alternatively to cell volumes, as well as examining how cells can interfere with protein counting via fluorescence quenching, which we quantify and correct for the first time. Calibration across different instruments, disparate filter sets and mismatched gains is demonstrated to yield equivalent results. It can also reveal that mCherry absorption at 600nm does not confound cell density measurements unless expressed to over 100,000 proteins per cell. FPCountR is presented as pair of open access tools (protocol and R package) to enable the community to use this method, and ultimately to facilitate the quantitative characterisation of synthetic microbial circuits.

Research highlights: nanopore protein detection and analysis

Lab on a Chip ◽  
2015 ◽  
Vol 15 (17) ◽  
pp. 3424-3427 ◽  
Author(s):  
Shiv Acharya ◽  
Shayson Edwards ◽  
Jacob Schmidt
Keyword(s):  
Protein Folding ◽  
Protein Concentration ◽  
Protein Detection ◽  
Specific Protein ◽  
Protein Species ◽  
Concentration Determination

Nanopore detection of specific protein species using carrier DNA – Quantitative protein concentration determination using aptamers – Protein folding studied with unfoldase-coupled nanopores.

scholarly journals Dependence of fluorescent protein brightness on protein concentration in solution and enhancement of it

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Takamitsu J. Morikawa ◽  
Hideaki Fujita ◽  
Akira Kitamura ◽  
Takashi Horio ◽  
Johtaro Yamamoto ◽  
...  
Keyword(s):  
Protein Concentration ◽  
Fluorescent Protein
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