Sample preparation

In contrast to many previous studies based on the analysis of aldehyde-fixed tissue, my thesis work was almost entirely founded upon the ultrastructural analysis of tissue that had been rapidly cryo-fixed by HPF in a living, unfixed state. To assess the potential benefits of this approach in the context of synaptic vesicle docking analyses, I compared the effects of aldehyde fixation on synaptic vesicle docking in hippocampal mossy fiber synapses prepared for ultrastructural analysis by i) transcardial perfusion of aldehyde fixative cocktails, ii)

100 immersion of organotypic slice cultures in aldehyde fixative cocktails, and by iii) HPF of organotypic slice cultures.

I found that in comparison to high-pressure frozen organotypic slices, the abundance of membrane proximal and docked vesicles was severely reduced in perfusion fixed tissue.

Moreover, I observed that the extent of perturbation correlated with the fixative osmolarity, perhaps reflecting the sensitivity of the synaptic RRP, and presumably of the vesicle fusion apparatus, to osmotic pressure (Bekkers and Stevens, 1995; Rosenmund and Stevens, 1996;

Stevens and Tsujimoto, 1995). The osmolarity of aldehyde fixative cocktails typically exceeds that of physiological buffers (Hayat, 1981). In my study, two different fixative cocktails were used: PF1 [4% PFA, 2.5% GA in 0.1 M PB, pH 7.4, 4°C; approximately 1900 mOsm (Hayat, 1981)] and PF2 [2% PFA, 2.5% GA, 2 mM CaCl2 in 0.1 M cacodylate buffer, 37°C; approximately 1200 mOsm (Hayat, 1981)]. Another consideration concerns the speed with which the synaptic ultrastructure is immobilized. Aldehyde fixation via transcardial perfusion occurs relatively slowly because the fixative must diffuse through tissue while cross-linking proteins in an outside-in direction (Hopwood, 1969).

My observation that membrane proximal vesicles are depleted in perfusion-fixed mossy fiber synapses is in line with a previous study comparing the ultrastructural organization of synapses in the somatosensory cortex prepared by transcardial aldehyde perfusion fixation and by HPF of acutely dissected tissue (Korogod et al., 2015). Korogod and colleagues used serial section transmission EM, electron tomography, and focused ion-beam scanning electron microscopy (FIB-SEM) to compare the effects of perfusion fixation of aldehyde cocktails to high-pressure frozen acute slice preparations (Korogod et al., 2015). Using electron tomography, they found a reduction in membrane-proximal synaptic vesicles in reconstructed tomograms of synaptic profiles from perfusion-fixed compared to cryo-fixed tissue (Korogod et al., 2015). I interpret the loss of membrane proximal vesicles in my study as a consequence of aldehyde-triggered vesicle fusion rather than a rapid redistribution from the active zone membrane. This hypothesis is supported by my frequent observation of omega-shaped membrane profiles at active zones in the perfusion-fixed mossy fiber synapses, which is indicative of full-collapse synaptic vesicle fusion. The notion that aldehyde exposure can trigger vesicle fusion was initially proposed by Smith and Reese (Smith and Reese, 1980), who observed that perfusion of different aldehydes: GA, formaldehyde, or

101 crotonaldehyde, caused an increase in post-synaptic endplate potentials recorded from the frog neuromuscular junction, as well as an increase in pits in proximity to the active zone attributed to fusing vesicles (Smith and Reese, 1980). A contrasting view was presented by Rosenmund and Stevens, who recorded EPSCs in dissociated hippocampal neurons and found minimal synaptic vesicle fusion upon fast perfusion of 2% GA (Rosenmund and Stevens, 1997).

They found that fixation was rapid and caused a 10% depletion of the functional RRP (Rosenmund and Stevens, 1997), indicating that the speed at which synaptic ultrastructure is immobilized is likely an important factor involved in the effect of aldehydes on docked vesicle pools.

Consistent with this view, the number of docked vesicles at synapses in immersion-fixed and high-pressure frozen slices was comparable at the surface of the tissue (5-11 µm from the tissue surface; Table 30, Figure 21 A-E), whereas the depletion of docked vesicle pools became apparent in synapses located deeper in the tissue (20-22 µm from tissue surface; Table 31;

Figure 21 F-I). Since identical aldehyde-based fixative cocktails were used for perfusion and immersion fixation experiments, these data imply that synaptic ultrastructure in surface-exposed synapses is immobilized before the osmotic pressure exerted by the fixatives can manifest and trigger vesicle fusion. However, additional analysis is required to assess whether docked vesicle pools are maintained only at the expense of membrane-proximal, putatively tethered vesicles in surface-exposed and immersion fixed synapses. Regardless, my observations, which appear consistent with the aforementioned study by Rosenmund and Stevens (Rosenmund and Stevens, 1997), identify synapse location and accessibility as important variables affecting the impact of immersion fixation on synaptic ultrastructure.

Taken together, the results of my study emphasize that caution must be exercised when interpreting synaptic ultrastructure in aldehyde-fixed samples and that rapid cryo-fixation is more reliable for the analysis of synaptic vesicle organization at presynaptic active zones. I cannot, however, exclude the possibility that more refined fixative compositions or perfusion protocols may limit the artifactual effects of aldehydes on vesicle organization at individual active zones. Aldehyde fixation will remain an extremely useful means of preserving synaptic ultrastructure for light and electron microscopic analysis, since many brain structures are incompatible with rapid dissection for cryo-fixation (i.e. HPF), and the dissection process itself risks mechanical trauma and anoxia (Korogod et al., 2015; Sosinsky et al., 2008). Protocols

102 involving sequential aldehyde perfusion, dissection, and HPF have therefore been proposed (Sosinsky et al., 2008), the effects of aldehydes on membrane-proximal vesicle pools notwithstanding.

Future work based on my study would be to investigate the spatial distribution of synaptic vesicles within 100 nm of the active zone in mossy fiber synapses from immersion-fixed hippocampal slices to test whether the membrane-proximal, or tethered synaptic vesicle pools change in mossy fiber synapses after immersion fixation. It is possible that in the superficial mossy fiber synapses, the RRP was depleted by 10%, as was observed in the Rosenmund and Stevens study (Rosenmund and Stevens, 1997), however, the loosely docked (LS) or tethered synaptic vesicles observed in mossy fiber synapses at rest may rapidly dock and prime during immersion fixation. To better study the effects of aldehydes on membrane-proximal pools of synaptic vesicles, a full 3D study of synaptic vesicles within 100 nm is necessary. Furthermore, a more thorough study of the diffusion distance of aldehydes is necessary to test whether the distance of fixatives is proportional to the deficits of membrane-proximal synaptic vesicles observed in this study. This could be accomplished by comparing the change in the spatial distribution of synaptic vesicles at mossy fiber synapses closer to blood vessels with those farther away in perfusion-fixed mice.

4.2.2. Limitations of 2D electron microscopy and advantages of 3D electron tomography

Although conceptually simple, the accurate assessment of synaptic vesicle docking is non-trivial. Multiple factors contribute to this: (i) Synaptic vesicles are small and the defining structural feature of a docked synaptic vesicle, i.e. the point of contact between the outer lipid bilayer of a synaptic vesicle and the inner lipid bilayer of the presynaptic membrane, is considerably smaller. (ii) Synaptic membranes are inherently curved. (iii) Electron microscopic images, even from ultrathin sections (20-100 nm thick), represent 2D projections through a volume. (iv) Due to mechanical limitations, plastic sections are difficult to cut thinner than the approximate diameter of a synaptic vesicle (~40 nm). In addition to the sample preparation considerations outlined in the previous section, the accuracy with which vesicle docking is assessed in electron micrographs is dependent on z-resolution. Since z-resolution is defined by plastic section thickness in 2D imaging approaches, including serial section-based 3D EM techniques, certain ambiguities are introduced and it is not possible to determine whether

103 the midline of a synaptic vesicle is contained within the imaged volume. This limitation also excludes the possibility of accurate vesicle volume measurements. Nevertheless, 3D serial section EM analyses offer a larger field-of-view than electron tomography, are compatible for the reconstruction of large tissue volumes, and provide access to important quantitative information, including volume measurements of pre- and postsynaptic compartments and total numbers of active zone release sites (Chicurel and Harris, 1992; Harris and Sultan, 1995;

Rollenhagen et al., 2007; Sätzler et al., 2002; Spacek and Harris, 1998; Xu-Friedman et al., 2001).

Electron tomography circumvents this limitation by achieving a higher z-resolution, which is inversely related to the number of images in the tilt-series, the tilt increment separating them, and the pixel spacing used for image acquisition (Koster et al., 1997). The final voxel dimensions achieved in tomographic slices are therefore dependent on the magnification used to acquire the tilt-series and the extent of binning used for weighted back-projection to convert the tilt series into a volume (Koster et al., 1997). Since functionally critical, but morphologically subtle, changes in vesicle organization can manifest within the range of several nanometers (Imig et al., 2014; Siksou et al., 2009a), it is important to resolve the spatial organization of synaptic vesicles as accurately as possible. For example, electron tomographic reconstructions generated in my comparative analyses revealed that mossy fiber synapses not only harbor a lower spatial density of docked vesicles at individual active zones compared to Schaffer collateral synapses, but that they are distinguished by the presence of a prominent membrane-proximal, possibly tethered, pool of synaptic vesicles.

The novelty of these observations implies that the combination of good ultrastructural preservation and high resolution imaging is required to dissect functionally relevant structural features of vesicle organization at active zone release sites. Consistent with this view, previously reported differences in the numbers of docked vesicles at facilitating and depressing synapses were generated using electron tomography (Eltes et al., 2017).

In conclusion, I used electron tomography to reconstruct synaptic subvolumes in 3D with an isotropic voxel dimension of about 1.6 nm. In comparison to conventional 2D transmission EM analysis, electron tomography provides a better z-resolution and reveals fine structural changes in the spatial distribution of synaptic vesicles at active zone release sites that have otherwise been elusive.

104