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Selection of pairings reaching evenly across the data (SPREAD): A simple algorithm to design maximally informative fully crossed mating experiments.

ABSTRACT: We present a novel algorithm for the design of crossing experiments. The algorithm identifies a set of individuals (a 'crossing-set') from a larger pool of potential crossing-sets by maximizing the diversity of traits of interest, for example, maximizing the range of genetic and geographic distances between individuals included in the crossing-set. To calculate diversity, we use the mean nearest neighbor distance of crosses plotted in trait space. We implement our algorithm on a real dataset of Neurospora crassa strains, using the genetic and geographic distances between potential crosses as a two-dimensional trait space. In simulated mating experiments, crossing-sets selected by our algorithm provide better estimates of underlying parameter values than randomly chosen crossing-sets.

SUBMITTER: Zimmerman K

PROVIDER: S-EPMC4806887 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature

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Selection of pairings reaching evenly across the data (SPREAD): A simple algorithm to design maximally informative fully crossed mating experiments.

Zimmerman K K Levitis D D Addicott E E Pringle A A

Heredity 20150930 2

We present a novel algorithm for the design of crossing experiments. The algorithm identifies a set of individuals (a 'crossing-set') from a larger pool of potential crossing-sets by maximizing the diversity of traits of interest, for example, maximizing the range of genetic and geographic distances between individuals included in the crossing-set. To calculate diversity, we use the mean nearest neighbor distance of crosses plotted in trait space. We implement our algorithm on a real dataset of ...[more]

PMID: 26419337

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Project description:FRET biosensors have proven very useful tools for studying the activation of specific signalling pathways in living cells. Most biosensors designed to date have been predicated on fluorescent protein pairs that were identified by, and for use in, intensity based measurements, however fluorescence lifetime provides a more reliable measurement of FRET. Both the technology and fluorescent proteins available for FRET have moved on dramatically in the last decade. Lifetime imaging systems have become increasingly accessible and user-friendly, and there is an entire field of biology dedicated to refining and adapting different characteristics of existing and novel fluorescent proteins. This growing pool of fluorescent proteins includes the long-lifetime green and cyan fluorescent proteins Clover and mTurquoise2, the red variant mRuby2, and the dark acceptor sREACh. Here, we have tested these donors and acceptors in appropriate combinations against the standard or recommended norms (EGFP and mTFP as donors, mCherry and either Ypet or Venus as acceptors) to determine if they could provide more reliable, reproducible and quantifiable FLIM-FRET data to improve on the dynamic range compared to other donors and breadth of application of biosensor technologies. These tests were performed for comparison on both a wide-field, frequency domain system and a multiphoton, TCSPC time domain FLIM system. Clover proved to be an excellent donor with extended dynamic range in combination with mCherry on both platforms, while mRuby2 showed a high degree of variability and poor FRET efficiencies in all cases. mTFP-Venus was the most consistent cyan-yellow pair between the two FLIM methodologies, but mTurquoise2 has better dynamic range and transfers energy consistently over time to the dark acceptor sRCh. Combination of mTFP-sRCh with Clover-mCherry would allow the simultaneous use of two FLIM-FRET biosensors within one sample by eliminating the crosstalk between the yellow acceptor and green donor emissions.

Dataset Information

Selection of pairings reaching evenly across the data (SPREAD): A simple algorithm to design maximally informative fully crossed mating experiments.

Publications

Selection of pairings reaching evenly across the data (SPREAD): A simple algorithm to design maximally informative fully crossed mating experiments.

Similar Datasets

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