APOPTOSIS: Associated plasma membrane structural changes include translocation of the anionic phosphatidyl serine (PS) from the inner to the outer leaflet of the lipid bilayer where it can bind Annexin V, a Ca
2+-dependent phospholipid-binding protein with high affinity for PS. By labelling Annexin V with fluorescent dyes (e.g., FITC
[40]), one can image, for example, via wide-field or confocal microscopy, and/or flow cytometry, Annexin V-positive cells to determine the rate of apoptosis
[41]. Fluorescent Annexin V conjugates provide a quick and reliable detection method of the early stages of apoptosis
[42]. Apoptosis in cells can also be detected, for example, by imaging fluorescence conjugates of Bax as it translocates from the cytosol to the outer mitochondrial membrane, and/or cytochrome C as it is released from the mitochondria into the cytosol
[43].
ENDOCYTOSIS: Immunostaining against endosomal protein markers
[44] includes against early endosome proteins (Syntaxin 6 and Rab5
[45], and EEA1
[46]), recycling endosome markers (e.g., Rab25
[47]), and late endosome/lysosomal markers (Rab7
[48], LAMP1 and LAMP2
[49], cathepsin D, and LIMPII
[50]). Primary or secondary antibodies can be conjugated with dyes of different colours (e.g., Alexa 488, Alexa 594, or Alexa 647). Typical endosomes (~100 nm) are smaller than optical resolution (~250 nm), hence endosomes look like puncta under a wide-field or confocal fluorescence microscope. To image EGFR endocytic traffic, one can, for example, label an EGFR cognate ligand (e.g., EGF) with organic dyes, both visible and infrared
[51], or clone EGFR with tags, such as Halo
[52] and SNAP
[53], which are subsequently labelled with Alexa or Cyanine dyes. In live cells, one can use fluorescent protein (FP) fusions of the endosomal markers and/or of other proteins (e.g., clathrin
[54]). To image in the nucleus, a popular method is fluorescence in situ hybridisation (FISH) assays
[55].
AUTOPHAGY: FP constructs of the 17 kDa soluble microtubule-associated protein 1A/1B-Light Chain 3 (LC3)
[56] are commonly used (e.g., eGFP-LC3, mCherry-LC3, or RFP-LC3). During autophagy, the cytoplasmic form of LC3 (LC3-I) becomes covalently ligated to phosphatidyl ethanolamine (PE). The appearance of fluorescent puncta of the lipidated LC3-II form allow determination via wide-field or confocal fluorescence microscopy of the number of autophagosomes (dia. 500–900 nm
[57]), where LC3-II is recruited to
[58]. Serum depletion and the autophagic inhibitor 3-methyladenine (chloroquine) are often used as positive controls
[59]. Colocalisation of red and green probes (e.g., RFP-LC3 and LysoSensor Green) allows for the morphological observation and quantification of autophagosome maturation and fusion with the lysosome
[60]. pH-responsive FPs (and organic dyes) allow the evaluation of intracellular pH and interrogation of specific subcellular compartments
[61].
SINGLE PARTICLE TRACKING (SPT): A direct probe of fluorescent particle movement in live cells
[62]. In two colours, SPT can report molecular association and dissociation events in real time from which kinetic and dynamic interaction parameters can be determined (e.g.,
[63][64]). At the plasma membrane, SPT exploits total internal reflection fluorescence (TIRF) illumination to improve contrast
[65]. Suitable organic dyes and other probes have to be selected to ensure specific interactions with the proteins of interest and to minimise non-specific staining of the (typically) glass surface where the TIRF evanescent wave illuminating the adjacent basolateral cell surface is concentrated
[66][67]. SPT can also be used to track particles in endosomes and at the nucleus using probes, such as adaptamers and FPs, and/or bright organic dyes, such as Atto 647N (e.g.,
[68][69]).
NEAR-FIELD SCANNING OPTICAL MICROSCOPY (NSOM)
[70]: The resolution of NSOM is defined by the size of the point light source used (typically 50–100 nm). NSOM breaks the far-field optical resolution limit (~250 nm) by exploiting the properties of evanescent waves in close vicinity (i.e., ~nanometres) of the aperture defining the size of the point light source, which must therefore be brought within nanometres of the surface to collect the near-field optical signal. The point source is scanned over the surface, without touching it. The distance between the point light source and the sample surface is usually controlled through a feedback mechanism that is unrelated to the NSOM signal (e.g., as in AFM)
[71]).
STOCHASTIC OPTICAL RECONSTRUCTION MICROSCOPY (STORM)
[72]: A single-molecule localisation microscopy (SMLM) method with a resolution of ~20 nm. It reports on the number of proteins that form nanoclusters and on the size of the clusters (example shown in Figure 6). STORM is compatible with many commonly used organic dyes, which can be converted to an off state using specific excitation parameters combined with oxygen-scavenging imaging buffers. Fluorophores for STORM should be bright, have a high rate of photo-switching, and exhibit minimal photo-bleaching in thiol-containing buffers. Normally used to analyse clusters in chemically fixed cells, sub-12 nm resolution is possible in cryo-vitrified samples using solid immersion lenses
[73].
FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET): A spectroscopic ruler useful for measuring intra-molecular and inter-molecular separations in the range ~2–8 nm
[74]. It is based on the transfer of excitation energy between two fluorescent molecules through non-radiative dipole–dipole coupling
[75][76]. The rate of energy transfer, from which the separation between donor and acceptor molecules can be measured, is determined chiefly from the overlap between the emission spectra of the donor and the excitation spectra of the acceptor. FRET can be combined with SPT
[77][78][79] (Figure 6E), fluorescence lifetime imaging (FLIM)
[80], and fluorescence polarisation
[81]. The combination can be used to detect dimers and oligomers, and/or to determine separations between two planes, as a proxy for molecular orientation at the plasma membrane
[82].
FLUOROPHORE LOCALISATION IMAGING WITH PHOTOBLEACHING (FLImP)
[83][84]: Based on SMLM, the position of a cluster of fluorescent molecules changes upon each individual photobleaching event. The shift in the position of the cluster can be analysed to report on the lateral separations between the molecules in the cluster. FLImP can measure separations between identical fluorophores in the 0–60 nm range, and can achieve sub-5 nm resolution
[85]. Combined with atomic molecular dynamics (MD) simulations, it can report on the dimer and oligomer structure
[85][86].