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Plant Cytomics: Novel Methods to View Molecules on the Move

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PlantOmics: The Omics of Plant Science

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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.

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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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Authors and Affiliations

  1. Department of Plant Biology, North Carolina State University, Raleigh, NC, USA

    Eric Davies Ph.D.

  2. University for Information Science and Technology “St. Paul the Apostle”, Partizanska bb, 6000, Ohrid, Republic of Macedonia

    Bratislav Stankovic Ph.D.

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  1. Eric Davies Ph.D.
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  2. Bratislav Stankovic Ph.D.
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Correspondence to Eric Davies Ph.D. .

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Editors and Affiliations

  1. Department of Genomics, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, West Bengal, India

    Debmalya Barh

  2. University of Agriculture, Centre of Biochemistry and Biotechnology, Faisalabad, Pakistan

    Muhammad Sarwar Khan

  3. Department of Plant Biology, North Carolina State University, Raleigh, North Carolina, USA

    Eric Davies

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Davies, E., Stankovic, B. (2015). Plant Cytomics: Novel Methods to View Molecules on the Move. In: Barh, D., Khan, M., Davies, E. (eds) PlantOmics: The Omics of Plant Science. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2172-2_14

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