Preparation, characterization and use of Aβ oligomers
Oligomers were prepared from Aβ1-42 peptide (American Peptide) as previously described64. Briefly, solid Ab1-42 was dissolved in cold hexafluoro-2-propanol (HFIP; Sigma). The peptide was incubated at room temperature for at least 1 hour to establish monomerization and randomization of structure. The HFIP was aliquoted and allowed to evaporate overnight, followed by 10 minutes in a Savant Speed Vac. The resulting peptide was stored as a film at -80 °C. The film was dissolved in anhydrous dimethylsulfoxide (Sigma) to 5 mM, diluted to 100 mM with Ham’s F12 (without phenol red, with glutamine; Caisson Laboratories) and briefly vortexed. The solution was incubated at 4 °C for 22-24 hours and soluble oligomers obtained by centrifugation at 14,000 g for 10 minutes at 4 °C. Protein concentration was estimated using Coomassie Plus Protein Assay (Thermo Scientific) and a bovine serum albumin (BSA) standard. For shipping purposes, small aliquots of the soluble oligomers were dried using a Savant Speed Vac and reconstituted with cold sterile water and gentle pipetting immediately prior to use. Tetramethyl rhodamine (TAMRA)-conjugated Aβ1-42 (Cambridge Bioscience/AnaSpec) was subjected to the same protocol to prepare fluorescently-tagged oligomers.
Hippocampal cell culture, adenoviral infection and plasmid transfections
Dissociated hippocampal cultures were prepared from E18 Wistar rat embryos (Charles River Laboratory) as already described15. SypHy (kind gift of Prof. L. Lagnado) was cloned into an adenoviral expression vector using the Ad-HQ system (Vector Biolabs, Philadelphia, PA, USA), and packaged to produce an active human Adenovirus Type 5 (dE1/E3). This was used to infect cultured hippocampal neurons 8 days after plating at a multiplicity of infection (MOI) of 0.2. Other plasmids were introduced into neurons 8 days after plating using Lipofectamine 2000. For each well, DNA and Lipofectamine were added to 200 mL Neurobasal at a ratio of 3 mg:3 mL and incubated for 20 minutes before transfection, which was carried out in 2 mL of medium per well. Transfection mix was incubated with the cultures for 1 hour before being removed and replaced with a 2:1 ratio of conditioned to fresh medium. The SypH 2x plasmid was a gift of Dr. Y. Zhu, the GAD67pro-vGAT-pH plasmid was a gift of Prof. S. H. Kim and SyGCamP5 was a gift of Prof. L. Lagnado. The CRISPR/Cas9 plasmids were generated by the Weatherall Institute of Molecular Medicine Genome Engineering Facility (University of Oxford) and based on the vector px458 into which sequences coding for sgRNA directed against either the firefly luciferase gene (control) or mouse Chrna7 (g13)65 were cloned.
Patch-clamp electrophysiology in cultured hippocampal neurons
Whole-cell patch recordings were made using either an Axoclamp 900A or an Axoscope 2B amplifier (both Axon Instruments). Data was low-pass filtered at 3k Hz, sampled at >10kHz. Data was acquired using WinWCP and analyzed using Clampfit software. Patch electrodes (4-8 MΩ) contained (in mM): 120 CsMeSO4, 10 KCl, 10 NaPhosphocreatine, 10 HEPES, 4 MgATP and 0.4 Na3GTP. Spontaneous activity was recorded in Tyrode’s solution containing (in mM): 120 NaCl, 30 Glucose, 25 HEPES, 5.4 KCl, 1.5 CaCl2 and 0.5 MgCl2. Miniature excitatory postsynaptic currents (mEPSC) comprising of mixed AMPAR and NMDAR currents were recorded at -70 mV in Mg2+-free conditions using Tyrodes solution containing (in mM): 120 NaCl, 30 Glucose, 25 HEPES, 5.4 KCl, 4 CaCl2, 0 MgCl2, to which 1 µM of TTX and 100 µM of picrotoxin was added. For each cell recorded, 30 isolated mEPSCs were chosen for analysis. As previously described36, AMPAR currents were measured at the peak of the mEPSC trace and NMDAR currents were measured by averaging the peak current across a 5 ms window, 15 ms following the mEPSC peak.
Live cell imaging and analysis
Experiments were performed 14-21 days after plating (6-13 days after transfection) when synapses are mature. Coverslips were mounted in a Chamlide EC-B18 stimulation chamber (Live Cell Instrument) on the stage of an Olympus IX-71 inverted microscope fitted with a 100X, NA 1.40 UPlanSApo objective and an Andor iXon EM CCD camera, and imaging of live neurons was carried out as described15. Phluorin imaging was carried out at 1 Hz for 100 AP stimulation and 5 Hz for 1 AP stimulation; Ca2+ imaging was carried out at 10 Hz. All time series images were acquired with 2 X 2 pixel binning. Unless otherwise specified, Aβo were applied at 200 nM (monomer equivalent) in culture medium in the incubator for 2 hours. Where cells had been incubated with Aβo or vehicle, these were present throughout the experiment. Where the following were used they were added 10 minutes before Aβo or vehicle treatment and were present throughout the incubation and experiment: w-Agatoxin IVA (100 nM, Alomone); w-conotoxin GVIA (250 nM, Alomone); amiloride (100 μM, Sigma); BAPTA (5 mM tetrapotassium salt, Molecular Probes); SNX-482 (500 nM, Alomone); SIB-1757 (3 μM, Tocris); Go 6976 (100 nM, Abcam); α-bungarotoxin (100 nM, Life Technologies). In experiments measuring basal Ca2+ concentration, ionomycin (Calbiochem) was used at 10 μM following initial image acquisition to elicit maximal Ca2+ entry; the maximal signal value obtained is used to normalize the basal Ca2+ signal measurements to account for differences in SyGCamP5 expression. In experiments imaging binding of either α-bungarotoxin CF594 (100 nM, Cambridge Bioscience/Biotium) or TAMRA-conjugated Aβo (200 nM), which were applied in the incubator for 10 minutes or 2 hours respectively, the image acquisition system described above was used but with a 900 ms exposure time and no pixel binning.
Time series images were analyzed in ImageJ (http://rsb.info.nih.gov/ij) using the Time Series Analyzer plugin (http://rsb.info.nih.gov/ij/plugins/time-series.html). All visible varicosities were selected for analysis with a 2 mm diameter ROI. Terminals were excluded from analysis in pHluorin experiments if their maximum response to 40 AP or 100 AP was less than 2 SD of baseline noise; for Ca2+ experiments, terminals were excluded if their peak response to 1 AP averaged over 5 trials was less than 2 SD of baseline noise, or of they did not show a response to ionomycin application. Data exported from ImageJ were background adjusted and pHluorin data were normalized to the peak signal obtained following NH4Cl application (mean value of plateau over 5 seconds). Ca2+ indicator data were normalized to either the basal, unstimulated signal or to the signal elicited by ionomycin. Peak fluorescence in all experiments was taken at the end of the stimulation period. For analysis of single images generated during Aβo binding experiments, segmentation was first carried out using inbuilt ImageJ functionality to generate a mask from a 50 μm section of axon in the GFP channel, and this was then used to measure mean fluorescence in the red fluorophore channel with additional background adjustment. All analysis was performed using custom-written macros or scripts in Microsoft Excel or MatLab.
Optical fluctuation analysis
Optical fluctuation analysis analyses trial-to-trial variation in Ca2+ transients through VGCC to determine whether changes in Ca2+ influx are due to changes in the number (N), open probability (p) or unitary channel currents (q) of functional channels11. We used the experimentally derived inverse squared coefficient of variation (CV-2) of boutonal Ca2+ transients along with a published value for p at cultured hippocampal terminals61 to calculate the mean N at each terminal under control conditions (N = 19.5). We then extrapolated both N and p to values expected if the experimentally observed increase in mean Ca2+ transient size following Aβo treatment were solely a result of an increase in either of these parameters alone, and used these to calculate the CV-2 that would be expected after Aβo treatment in each instance. Note that in optical fluctuation analysis, changes in N or p (or some combination of these) are associated with a change in CV-2, while changes in q are not.
Immunofluorescence and quantification
Cultured neurons were subjected to relevant treatments before being washed twice with PBS; where used, Aβo were applied at 200 nM for 2 hours. For all experiments except surface ENaC staining, coverslips were then treated with 0.1% saponin on ice for 15 minutes, before incubation in 10% FCS in PBS at room temperature for 30 minutes. Cells were then incubated with guinea pig anti-synaptophysin (1:1000; Synaptic Systems) together with either anti-GSK-3β (CST 9832, 1:1000; Cell Signaling Technology) and anti-phospho-GSK-3β (S9) (ab131097 1:500; Abcam), or anti-ENaC α-subunit (SPC-403, 1:1000, StressMarq). For surface ENaC staining, the procedure was identical except that the primary antibody incubations were carried out in succession, anti-ENaC antibody first, and the permeabilization step was carried between the two. Following primary antibody incubation, coverslips were washed, incubated for 1 hour at room temperature with various AlexaFluor-conjugated secondary antibodies (Abcam), all used at 1 in 400 dilution, washed again and mounted using ProLong Gold antifade (Thermo Fisher). For double immunostaining of surface GluR1 receptors and synaptophysin, live neurons were incubated with rabbit anti-GluR1 (pc246, Calbiochem) diluted with well medium for 1 hour in a 5% CO2 incubator at 37 °C, followed by 1 hour with 2 ml of medium to wash out unbound and nonspecifically bound antibodies. The cells were then fixed in 4% paraformaldehyde for 15 minutes on ice before incubating with an anti-rabbit Cy-3 conjugated IgG (Jackson Immunoresearch) for 1 hour at room temperature. This was followed by block/permeabilisation in 10% foetal calf serum/0.1% Triton X-100 for 60 minutes at room temperature and incubation with guinea pig anti-synaptophysin (Synaptic Systems) at 4 C overnight. Alexa 488-conjugated anti-guinea pig IgG (Jackson Immunoresearch) was then applied at room temperature for 1 hour, and coverslips were mounted using ProLong Gold antifade.
Images were collected using an Olympus Fluoview FV1000 confocal system with an Olympus IX-81 inverted microscope, and either a 100X, NA 1.40 UPlanSApo or a 60X, NA 1.35 UPlanSApo oil immersion objective. Images were acquired in Olympus Fluoview software and analyzed using ImageJ as described in the main text or caption. Image segmentation was carried out using inbuilt ImageJ functionality to generate a mask from the synaptophysin (green) channel, and this was then used to measure mean fluorescence in the red fluorophore channel. For GluR1 labelling experiments, 50 μm sections of dendrite were examined. For all experiments, image acquisition parameters, as well as any image thresholding applied, were fixed within an experiment to allow for comparison between conditions.
Protein kinase C activity assay
Synaptosomes were prepared 14 days after plating from individual 35 mm culture wells of hippocampal neurons cultured as described above. Syn-PER reagent (Thermo Fisher) was used according to the manufacturer’s instructions, and each pellet representing synaptosomes from a single well was resuspended in 100 μl Syn-PER, before this was then divided into three parts that were exposed to either a vehicle, Aβo (200 nM) or Aβo + SNX-482 (500 nM) treatment for 2 hours before immediate freezing at -80 °C. Protein concentration in each sample was assessed with a BCA assay, and PKC activity in the samples was then assessed with an ELISA-based kit (ADI-EKS-420A, Enzo Life Sciences) used according to manufacturer’s instructions. Based on preliminary experiments with a purified PKC standard included with the kit, a 0.1 μg total protein equivalent of each sample was loaded per assay well, as this amount gave results within the dynamic range of the assay, and all samples were assayed in duplicate.
Preparation of acute hippocampal slices and slice electrophysiology
Field excitatory postsynaptic potentials (fEPSPs) were recorded in 300 μm thick acute hippocampal slices prepared as described66 from 7 - 8 week old C57BL/6J mice, or from aged, genotyped mice as specified. Slices were placed in an interface recording chamber perfused with oxygenated ACSF at 1 - 2 mL/min, and a bipolar stimulating electrode (FHC Inc., Bowdoin, ME, USA) was placed in Schaffer collaterals to deliver test and conditioning stimuli. For most experiments, a borosilicate glass recording electrode filled with artificial cerebrospinal fluid was positioned in stratum radiatum of CA1; for the fEPSP–population spike coupling experiment, the recording electrode was placed in stratum pyramidale to better capture population spike firing. Test responses, to stimuli delivered at 0.067 Hz, were recorded for at least 10 minutes prior to beginning experiments to ensure stable responses. Field potentials were amplified using a Digitimer NeuroLog amplifier, filtered below 3 Hz and above 3 KHz and digitized with a BNC-2090A converter (National Instruments). Recording was carried out on WinWCP software and and analyzed using the Clampfit program. LTP was induced using a 20X theta-burst protocol comprising a block of 4 stimuli at 100 Hz repeated 20 times over 20 seconds. For drug treatments, slices were incubated for > 2 hours prior to the experiment and drugs were maintained in the perfusing ACSF for the duration of the recording. Concentrations used were as follows: w-agatoxin IVA (Alomone Labs) 400 nM, or 50 nM for LTP experiments only; Ab oligomers 10 nM; cyclothiazide (Abcam) 100 μm; amiloride (Sigma) 100 μM. Other than these, drugs were not included in the experiments in order to preserve intact neuronal circuits. The magnitude of fEPSPs was determined as the gradient of the rising slope to avoid population spike contamination. Paired-pulse ratios were obtained by delivering two stimuli at intervals as specified and expressed as fEPSP2/fEPSP1.
Organotypic hippocampal slice preparation, adeno-associated virus infection and dendritic spine quantification
Organotypic hippocampal slices were prepared from day 7 postnatal male Wistar rats as previously described67 and used at 21-28 DIV. We took advantage of the Cre-lox expression system, which gives sparse but strong expression of eGFP, for spine counting. Accordingly, a mixture of two adeno-associated viruses was used: AAV1.CAG.Flex.eGFP.WPRE.bGH (2.35 x 1013 GC/mL) and AAV1.hSyn.Cre.WPRE.hGH (1.47 x 108 GC/mL). Both were obtained from the University of Pennsylvania Vector Core. Slices were infected at 14 DIV using a patch pipette to deliver ~1 μl aliquots into CA1 directly, and left for 7-10 days to allow strong expression. Aβo were applied at 200 nM for chronic incubation. Slices were imaged on an Olympus BX50WI microscope fitted with a BioRad Radiance 2000 confocal scanhead. For each dendrite, a z stack of 21 images at 512 x 512 pixels was acquired at 1 μm intervals using Zeiss LaserSharp software, and 50 μm sections were analyzed with ImageJ.
Mouse lines
All mouse work was carried out in accordance with the Animals (Scientific Procedures) Act, 1986 (UK) and under project and personal licenses approved by the Home Office (UK). Both the Cacna1a knockout (from Prof. A. van den Maagdenberg, Leiden University Medical Centre) and J20 hAPP (kind gift of Prof. D. Anthony, University of Oxford) transgenic mouse lines were on a C57BL/6J background, and the lines were maintained by crossing heterozygotes or hemizygotes with wild-type C57BL/6J mice. Crossing hAPP hemizygote with Cacna1a+/- mice yielded all four of the genotypes used in in vivo assays, and animals used in these experiments were therefore littermates. For co-immunoprecipitation experiments only, another mouse line carrying, like J20, an APP transgene with Swedish and Indiana mutations, was used. Line B6.Cg-Tg(tetO-APPSwInd)102Dbo/Mmjax was crossed with a CamKIIα-tTA line to activate hAPP expression68, and 20 month old double transgenic (tTA/hAPP) individuals along with accompanying non-transgenic littermate controls, a kind gift of Dr. Mariana Vargas-Caballero, were sacrificed for removal of the cortex and hippocampus. All genotyping was carried out by Transnetyx Inc.
FM dye loading and unloading in acute hippocampal slices
Slices of 300 μm thickness were transferred to a custom-made recording chamber mounted on an Olympus BX50WI microscope fitted with a BioRad Radiance 2000 confocal scanhead (BioRad/Zeiss) and were superfused at 35°C with oxygenated aCSF supplemented with 10 μM NBQX and 50 μM APV (both Tocris) to block recurrent activity. A patch pipette was filled with a 20 μM solution of the styryl dye FM1-43 (Molecular Probes) in aCSF and placed in stratum radiatum of CA1 at a depth of approximately 100 μm. The dye was pressure applied for 3 minutes using a custom-made picospritzer before a 10 Hz train of 1200 stimuli (100 μA) was delivered to Schaffer collaterals using a glass stimulating electrode (4-8 MΩ) filled with 150 mM NaCl placed within 70 μm of the dye-filled pipette; the stimulating electrode was under the control of WIN WCP software (Strathclyde Electrophysiology Software) and a DS3 stimulation box (Digitimer). Pressure application of dye was maintained throughout the loading stimulus and for 2 minutes afterwards to ensure completion of endocytosis. Slices were then perfused continuously in fresh aCSF containing 0.2 mM ADVASEP-7 (Cambridge Bioscience) for 15-20 minutes to wash residual FM dye from extracellular membranes. Imaging of labeled terminals was performed using a 60X, NA 1.1 LUMFL N objective (Olympus), a 488 nm Argon laser for excitation and a 500 nm long-pass emission filter. Image stacks were acquired every 15 seconds throughout the unloading stimulus (3000 stimuli at 10 Hz). Each image stack comprised 6 images of 512 x 512 pixels acquired at 1 μm intervals in the z-axis, and a digital zoom of 3X and 2X Kalman averaging were applied. Images were acquired using Zeiss LaserSharp software and analyzed using ImageJ and custom-written scripts in MatLab.
Human tissue
Samples of human frontal cortex were obtained from the MRC London Neurodegenerative Diseases Brain Bank, King’s College, London (part of the Brains for Dementia Research initiative) with full ethical approval; 5 AD cases, all BrainNet Europe stage or modified Braak stage VI, and 5 age-matched controls, all BrainNet Europe or Braak stage I or II, were used (see Table S1).
Co-immunoprecipitation
For co-immunoprecipitations, approximately 500 mg of either human or mouse brain tissue was homogenized using a Dounce tissue grinder into 2 mL buffer A containing (in mM): 320 sucrose, 5 Tris base, pH 7.4, 2 EDTA, on ice; note that all buffers used throughout the immunoprecipitations included HALT protease and phosphatase inhibitor cocktail (Thermo Scientific) at 1:100. After a 10 minute centrifugation at 750 rpm, the supernatant was removed and centrifuged at 17,000 rpm for 1 hour. This yielded a membrane pellet which was resuspended in 1 mL buffer A + 1% CHAPS, and 300 μL of this was rotated for 3 hours at 4°C with Novex magnetic Protein G Dynabeads (Life Technologies) to which anti-CaV2.1 or antibody had previously been bound (see below). After incubation, the beads were retrieved by magnetic separation and washed twice in buffer B containing (in mM): 150 NaCl, 25 Tris base, pH 7.4, 2 EDTA, to which 0.5% BSA and 0.4% CHAPS had also been added. Beads were then washed once in buffer B alone before being resuspended in 100 μL 2X Laemmli sample buffer with 5% β–mercaptoethanol for Western blotting. For binding of antibodies to Protein G Dynabeads, the supplied buffer was removed from 50 μL of bead suspension, and beads were washed once in buffer A + 0.5% BSA + 0.4% CHAPS. 5μL of anti-CaV2.1 antibody (as used for Western blotting) was then added, and the bead/antibody mixture was rotated for 10 minutes at room temperature before beads were washed twice in buffer A + 0.5% BSA.
Western blotting
Samples were dissolved in 2X Laemmli sample buffer with 5% β–mercaptoethanol, heated to 60°C for 3 minutes and run on a precast 4-20% gradient SDS-PAGE gel (Thermo Scientific). The separated samples were transferred to a nitrocellulose membrane (Bio-Rad) before blocking with 5% milk and 1% horse serum in TBS with 0.05% Tween-20 (TBST) and subsequent probing with a mixture of anti-CaV2.1 (ACC-001, 1:200; Alomone Labs) and anti-stx1 (110 011, 1:1000; Synaptic Systems) antibodies. After three TBST washes, bound antibodies were detected with IRDye 680LT donkey anti rabbit IgG (Li-Cor, 1:20,000) and IRDye 800CW goat anti-mouse IgG (Li-Cor, 1:15,000) fluorescent secondary antibodies, washed three times in TBST and imaged on a Li-Cor Odyssey system. Image analysis was performed in Li-Cor Image Studio Lite software.
Mouse behavioral testing
Locomotor activity in a novel environment was assessed in clear plastic cages (26 x 16 x 17 cm), containing clean sawdust. Mice were allocated a different cage each day. Activity levels were assessed by an array of infrared photobeam sensors that covered the x- and y-axes of the cages (San Diego Instruments). Beam breaks were recorded in 12 bins of 5 minutes over a one hour session to assess total ambulatory activity and this was repeated over three days. Results for each animal over the three days were averaged.
To assess hippocampus-dependent spatial novelty preference, a perspex Y-maze with arms of 30 x 8 x 20 cm was placed into a room containing a variety of extramaze cues. Mice were assigned two arms (the ‘start’ and the ‘other’ arm) to which they were exposed during the first phase (the exposure phase), for 5 minutes. This selection of arms was counterbalanced with respect to genotype. Timing of the 5 minute period began only once the mouse had left the start arm. The mouse was then removed from the maze and returned to its home cage for a one minute interval between the exposure and test phases. During the test phase, mice were allowed free access to all three arms. Mice were placed at the end of the start arm and allowed to explore all three arms for 2 minutes beginning once they had left the start arm. An entry into an arm was defined as a mouse placing all four paws inside the arm. Similarly, a mouse was considered to have left an arm if all four paws were placed outside the arm. The times that mice spent in each arm were recorded manually and a novelty preference ratio was calculated for the time spent in arms [novel arm/(novel + other arm)].
To assess hippocampus-dependent spatial reference memory, mice were trained on an aversively motivated, Y-maze swim-escape task. Like the well-known Morris water maze (MWM), performance in this task relies on the ability to associate a particular spatial location with the hidden escape platform. However, we have shown previously that it is more sensitive to disruption of hippocampal CA1 synaptic plasticity than the classical open-field MWM69, and it is also less susceptible to a variety of confounds. Performance is unlikely to be influenced by innate differences in preferred swimming distance from the side walls (thigmotaxis)51, which have been reported in mouse models of AD70, or by apathy or floating behavior, which we observed in some of our mouse lines in preliminary experiments in the MWM. As it uses a fractional choice-accuracy measure, it is also insensitive to confounds associated with locomotor activity differences. The apparatus was a transparent acrylic Y-maze, with each arm measuring 30 cm in length and 8 cm in width. The maze was surrounded by a 20 cm high wall. The maze was filled with water, rendered opaque with white paint, to a depth of 12 cm. The water temperature was 20 ± 2°C. A variety of distal extramaze cues were positioned around the laboratory, which remained constant across all sessions. Mice could escape from the water by climbing onto a hidden platform positioned 1.5 cm beneath the water surface. The platform was consistently positioned at the end of one of the three arms, with the allocation of target arm counterbalanced across genotype groups. In all trials, mice were released at the end of one of the two non-target arms, facing towards the wall. The release arm was varied pseudo-randomly across trials and test sessions. Training trials were 90 seconds in duration and mice that did not locate the platform within this time were guided towards the platform by the experimenter. All mice completed a single training session each day for six consecutive days. Each session consisted of five consecutive trials, with an inter-trial interval of 45 seconds (30 seconds spent on the platform and 15 seconds drying time). During each training trial, first choice accuracy (i.e. whether the first arm entered was the target arm) was recorded. A probe trial was performed on day 7, during which mice were able to swim freely for 60 seconds with the platform removed, and the percentage of total time spent in each of the three maze arms was recorded.
Golgi-Cox staining
We used the FD Rapid Golgi Stain Kit (FD Neurotechnologies, Inc.) to label neurons in the CA1 region of hippocampus. Animals were sacrificed by cervical dislocation and brains were immediately removed and rinsed in distilled water. Brains were then sagittally bisected and one half of each was treated according to kit instructions before embedding in agarose and cutting. Brains were sectioned in the coronal plane at 100 μm thickness on a Leica VT 1000M vibratome. Sliced tissues were transferred onto gelatin-coated slides and were air dried at room temperature in the dark. After drying, sections were rinsed with distilled water, stained in the developing solution and dehydrated with 50%, 75%, 95%, and 100% ethanol. Finally, the sections were defatted in xylene substitute and coverslipped with Permount (Fisher Scientific). All images were collected using an Olympus Fluoview FV1000 confocal system with an Olympus IX-81 inverted microscope and a 100X, NA 1.40 UPlanSApo oil immersion objective was used. For each dendrite, a 7 μm pseudostack comprising 11 differential interference contrast (DIC) images was acquired using Olympus Fluoview software and 50 μm sections were analyzed using NeuronStudio (http://research.mssm.edu/cnic/tools-ns.html).
Statistical analysis
Statistical analysis was performed using GraphPad Prism software. Data were assessed for normality using the Shapiro-Wilk test, and analyzed using parametric or non-parametric tests accordingly. Unless otherwise stated, the two-tailed unpaired Student’s t-test was used to determine the statistical significance of observed differences between various conditions. Where other tests were used, this is clearly stated in the caption of the appropriate figure. P values greater than 0.05 were regarded as non-significant. For optical fluctuation analysis, we determined whether changes in N, p or q best described our data using the Bayesian Information Criterion (BIC), with a BIC difference of 10 or more providing strong evidence in favor of the model with the lowest BIC score71.
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