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Plant Cytomics: Novel Methods to View Molecules on the Move

  • Eric Davies
  • Bratislav Stankovic
Chapter

Abstract

We provide our definition and the brief history of “cytomics” followed by an overview of general methodological approaches of optical imaging, especially fluorescence microscopy. We then go into detail on novel fluor-linking agents (nanobodies, aptamers, and aldehydes) and the array of novel fluors available. We describe many of the new techniques developed for superfast, super-resolution microscopy (photoreactivated localization microscopy, structured illumination microscopy, stimulated emission depletion microscopy, and stochastic optical reconstruction microscopy) followed by quantitative microscopy and image analysis. We then delve into unconventional methods, novel light systems, and alternatives to fluorescence (non-liner optical imaging, single-molecule light absorption, luminescent proteins). We then describe how these systems have been employed recently for proteins, nucleic acids, the cytoskeleton, and also small molecules of major interest to plants. We finish with a description of recent findings specific to plant cytomics and furnish several impressive images and other illustrations from the recent plant literature.

Keywords

Green Fluorescent Protein Complementary Metal Oxide Semiconductor Yellow Fluorescent Protein Structure Illumination Microscopy Stimulate Emission Depletion 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Abbreviations

3B

Bayesian analysis of bleaching and blinking

CCD

Charged couple devices

CFP

Cyano fluorescent protein

CMOS

Complementary metal oxide semiconductor

CNOI

Coherent nonlinear optical imaging

DNA

Deoxyribonucleic acid

dSTORM

Direct stochastic optical reconstruction microscopy

FLISM

Fluorescence light sheet microscopy

FOV

Field of view

FRET

Fluorescence (or Förster) resonance energy transfer

FPALM

Fluorescence photoactivation localization microscopy

GFP

Green fluorescent protein

LED

Light-emitting diode

NLDOM

Nonlinear dissipation optical microscopy

OMERO

Open microscopy environment remote objects

PALM

Photoactivation localization microscopy

PGS

Parametric generation spectroscopy

PM

Plasma membrane

PPS

Pump–probe spectroscopy

PY1-ME

Peroxy yellow 1 methyl ester

RNA

Ribonucleic acid

ROS

Reactive oxygen species

RUM

Really unconventional microscopy

SELEX

Systemic evolution of ligands by exponential enrichment

SIM

Structured illumination microscopy

SNAP

Soluble N-ethylmaleimide-sensitive factor-attachment proteins

SPIM

Selective plane illumination microscopy

SR

Super-resolution

SSIM

Saturated structured illumination microscopy

STED

Stimulated emission depletion

STORM

Stochastic optical reconstruction microscopy

tFT

tandem Fluorescent protein timer

TRUE

Time-reversed ultrasound encoded

TULIP

Tunable light-inducible protein tag

YFP

Yellow fluorescent protein

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© Springer India 2015

Authors and Affiliations

  1. 1.Department of Plant BiologyNorth Carolina State UniversityRaleighUSA
  2. 2.University for Information Science and Technology “St. Paul the Apostle”OhridRepublic of Macedonia

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