Key Resources Table
Reagent or Resource
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Source
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Identifier
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Antibodies
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anti-Aβ-oligomer (A11)
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Invitrogen
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#AHB0052
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anti-6E10 (Aβ1-16)
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Covance
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#SIG-39300
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anti-D54D2 (Aβ1-40, Aβ1-42)
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Cell signaling
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#8243
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anti-BrdU
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Thermo
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#MA3-071
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anti-OMP
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WAKO
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#019-22291
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anti-synaptophysin
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Dako
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#M0776
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anti-TH
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Santa Cruz
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#sc-14007
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anti-Ki67
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Cell signaling
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#12202
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Chemicals
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Fura-2
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Promo Cell
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PK-CA707-50034
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BrdU
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Sigma-Aldrich
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#59-14-3
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Acetophenone
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Sigma-Aldrich
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#42163
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Allyl phenylacetate
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Sigma-Aldrich
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#W203904
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Eugenol
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Sigma-Aldrich
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#E51791
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Geraniol
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Sigma-Aldrich
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#163333
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Heptanal
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Sigma-Aldrich
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#W254002
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Heptanoic acid
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Sigma-Aldrich
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#75190
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Lyral
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Sigma-Aldrich
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#95594
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Mineral oil
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Sigma-Aldrich
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#M5904
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Experimental models: Organisms/Strains
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5xFAD (Tg6799)
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K.A. Chang’s Lab
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C57BL/6J
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KOATECH
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http://www.koatech.co.kr/
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Software and Algorithms
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ImageJ
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NIH
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https://imagej.nih.gov/ij/
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Fiji
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NIH
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https://imagej.nih.gov/ij/
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Prism Software
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GraphPad Software,Inc, La Jolla, USA
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https://www.graphpad.com/scientific-software/prism/
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Method details
Animals
All experimental protocols were approved by the Institutional Animal Care and Use Committees of DGIST(DGIST-IACUC_0104). All applicable guidelines for the care and use of laboratory animals from the National Institutes of Health Guide were followed. Only male animals were used in this study. Adult mice (C57/BL6, two-months-old) were obtained from KOATECH (Daegu, Korea). 5xFAD transgenic mice harboring the mutated human APP (695 amino acids) and human PS1 genes (Tg6799, 3–4 months old) were obtained from Prof. K.A. Chang (Gachon Medical School, Incheon, Korea). All behavioral, physiological and histological analyses using animals in this study were blind tested.
Behaviors
We conducted behavioral experiments with the isolated preparation.
1) Y-maze test
The test was performed to evaluate the ability of the mice to act in a sequence and to measure short-term memory. Each branch (A, B, and C) of the maze was 40 cm long, 5 cm wide, and 10 cm high at an angle of 120°. The maze was constructed of white polyvinyl plastic. The animal was placed in the maze for 8 min, and the frequency with which the tail entered each branch was counted for each branch. The number of times the animal entered the branches (in the A, B, C sequence) was also counted and awarded 1 point (real change, actual alternation). Ability to take action to change (%) = Actual change (actual alternation)/maximum change (maximum alternation) × 100 (maximum change: the total entrance number − 2)
2) Morris water maze (MWM) test
The test was conducted in a circular pool (diameter 90 cm, height 45 cm, outer height [from the ground] 61.5 cm) using the EthoVision Maze task system (Noldus Information Technology, Wageningen, the Netherlands). The time required to find the platform and the latency to escape (escape latency) was measured. The animals underwent four training trials per day (one time per quadrant) over 4 consecutive days with a 30 min interval. If the animal could not find the platform within 60 s, they were placed on the platform for 20 s. The platform was removed on the last day, the animals were placed in the water to swim for 60 s, and memory was compared by measuring swimming around the area where the platform was installed. The C57/BL6 mouse was used for verifying the background feature of the adult olfactory system. The two months old mouse was considered as an adult. In our experimental condition, we compared all values from wild-type mice with age-matched.
3) Food-seeking test
The test was performed in three-month-old 5xFAD mice (WT, n=6; 5xFAD, n=6) and as described previously (11). Prior to the food-seeking tests, food restriction was applied for over 35 h to motivate animals to search for food, either hidden underneath a layer of bedding or not. Therefore, this test was used to assess latency in finding food as the buried pellet-seeking test. Mice were habituated in a clean home cage for one day prior to testing. A food pellet was buried 5 cm under the bedding in a middle region of the edge of the cage and a mouse was placed at the opposite edge. The time to the first bite of the food pellet was measured using an installed digital camera (maximum recording time was 10 min based on the assumption that food-restricted mice that fail to use odor cues to locate the food within a 10-min period are likely to have deficits in olfactory abilities). In data analysis and figure, we normalized the data by an average of wildtype’s time latency to evaluate effectively how time latency would be changed in a transgenic mouse.
4) Odor detection (nose poke) tests
The test was performed at three months of age for the Tg6799 and wild-type (WT) groups (n = 6 per group) and by modifying the odor-preference test described previously (19, 23). Instead of filter paper, a cotton tip scented with odorant was used to allow for the nose poke of mice to more accurately direct them to the odor (Fig. 1c). The following commonly used odor preference test odorants were used and presented for 2 min: acetophenone (8.6 M), allyl phenylacetate (5.9 M), eugenol (6.5 M), geraniol (5.7 M), heptanal (7.2 M), heptanoic acid (7.1 M), and lyral (4.7 M). Mineral oil (MO) was used as a control odorant. After 5 min habituation, mice were transferred to a new cage and the tip scented with a test odorant carefully set so that the mouse could not directly reach it. Investigation times were measured for 2 min. The performance index (PI) was determined based on a previously described method (24). PI is the percentage of time to detection of the experimental odorant minus the percentage of time in the control. A PI close to 0 indicates difficulty in detecting an odor and a PI of 100 indicates that a mouse could definitively detect an odor. The mouse behavior was recorded with a digital video camera (rate of 30 frames/s). Four points of interest (POIs) that we tracked in each frame were the nose, ears, and tail (Movie S1). In each group, we first randomly selected 180 frames and manually labeled POIs in those frames and used them to train and test a neural network model implemented in DeepLabCut (25). Evaluation of labeling accuracy was achieved by comparing the labels acquired from the convolutional neural network on the test set with manual labels. The model was then used to evaluate all frames in each group of the 20 videos used for training. The resulting x and y coordinates corresponding to the middle position of four POIs within each frame were used to determine location. The test cage was divided into equally sized three compartments, and the duration that odorant part of mice stayed inside the third that contains a cotton tip was analyzed for odor attraction.
Calcium imaging
We conducted calcium imaging in the in vivo conditions with the isolated preparation of instrument.
1. Mice preparation
Imaging was performed at three months of age for the Tg6799, age matched WT, and C57BL6 mice (n = 5–6 per group). Prior to the operations and administration of a calcium indicator (Fura-dextran), mice were anaesthetized with a mixture of ketamine (90 mg kg−1) and xylazine (10 mg kg−1). Calcium dye was administrated by nasal administration of a calcium indicator (using PE-90 tubes attached to a micropipette). A volume of 5–6 l (8 μl mixture of 8 % / 0.2 % calcium dye/Triton-X) was administered to each nostril. Six hours after the operation, mice were anaesthetized again with a mixture of ketamine (90 mg kg−1) and xylazine (10 mg kg−1) and decapitated. The whole olfactory system (MOE and OB) was dissected and peeled off. The sample fixed on 4% low-melting agarose (Sigma A9414, St. Louis, MO, USA) and transferred into Ringer’s solution (140 mM NaCl, 5 mM KCl, 1 mM CaCl2, 1 mM MgCl2, 10 mM HEPES, 10 mM glucose, 1 mM Na pyruvate, pH 7.4). The perfusion rate was 2 ml/min. The sample was flattened by trimming, transferred to a tissue slice chamber (Warner instruments) with the lateral side facing up.
2. Odor stimulation
Odorants were presented as dilutions from saturated vapor in cleaned air using a custom olfactometer which was designed to provide a constant flow of air blown. The olfactometer was built by using manually controlled valves, Teflon tubing, glass syringes (10 cc), scintillation vials, flowmeter, and air pump (600 ml/min). Odorant with specific concentration identified through behavioral experiments are made with saturated vapor, and they are adding on airflow through the odorant tube and delivered directly to the olfactory system. All the odorants diluted in mineral oil (0.0001%), or mineral oil only (control) were used to generate vapor saturation in the syringes. For the different odorant, different odorant tubes set (Teflon tubing, glass syringes (10 cc), scintillation vials) were used to prevent contamination in the experiment (Fig. S2a).
3. Optical recording
A typical stimulation protocol was a 20 s duration including 2 s stimulation repeated 10 times separated by one min between stimulations. The bulb surface of wide-field optical signals was measured using a Nikon 10×, 0.5 NA (2.3 × 2.3 mm field of view), Nikon 16× 0.8 NA (1.4 × 1.4 mm field of view) with a 150 W Xenon arc lamp (Opti Quip), objectives with a 200 mm focal length lens for single bulb measurements. For fluctuation of calcium monitoring, we used 380/10 nm (Chroma, ET380x) excitation light and a 510/84 nm emission filter (Semrock FF01-510/84). Fluorescence emission was recorded with a NeuroCCD-SM256 camera with 2 × 2 binning between 25–125 Hz using NIS-Elements software (Nikon).
4. Data analysis
All target points for analysis were selected on the sagittal view of OB, aligned manually to each mouse, guided by skull features and overall outline connecting OE-OB-brain. In order to confirm the correlation with the IHC results to be followed, we analyzed the (ΔF/F0) change across OB to compare with the IHC analysis. Dorsal to the ventral line for our calcium analysis within OB were aligned to proceed correlation analysis with the coronal sectioned IHC analysis. The entire analysis area of OB is divided equally among 10 sections from the anterior to posterior and 180 sections from dorsal to ventral within a lateral olfactory bulb view, respectively (Fig. S2b).
Activity maps that could reflect the positional variability of glomeruli among individuals for the analysis of calcium activities are adopted. The activity map is defined by the selected target point which is automatically calculated using the LC Pro plugin for ImageJ and an outline with a distance of 200 μm from the selected target point using C57BL6 mice.
The 10 times recordings per each odorant with for the Tg6799, age matched WT were averaged per 1 s and processed for 20 s for further analysis. The individual trials were manually inspected, and occasional trials with obvious artifacts were discarded. Then resting-state (airflow without odorant) data (baseline fluorescence (F0)) was intensity normalized with averaging frames over 3 s for 10 trials before stimulus onset. Activation data with odorant stimulation was calculated with fluorescence signal difference of every time point (ΔF) which was subsequently normalized (ΔF/F0). Calcium measurement (ΔF/F0) of specific activity maps were scaled with the averaged intensity value per each time point.
To perform the correlation, a heat map analysis was also performed on only the subsets of pixels overlaying the ROIs identified in each preparation’s activity map using unfiltered activity maps. All experiments were performed and evaluated by five independent tests.
Tissue preparation
Animals were anesthetized by intraperitoneal injection of 65 mg/kg ketamine with 5 mg/kg xylazine. The mice were then transcardially perfused with prechilled phosphate-buffered saline (PBS, pH 7.6). Heads were removed, skinned, and post-fixed overnight in 4% paraformaldehyde in PBS at 4 °C. The mandibles were discarded, and the trimmed heads were skinned and fixed by immersion in the same fixative for one day at 4°C. The heads were decalcified in Calci-Clear Rapid solution (National diagnostics, GA, USA) for 20 min at room temperature. After decalcification, the specimens were washed, dehydrated in increasing concentrations of ethanol, and transferred into xylene to clear the tissue. The specimens were infiltrated with paraffin and embedded. For cryosectioning, tissue was soaked in sucrose and embedded in Tissue-Tek OCT compound (Sakura Finetek Europe BV, Zoeterwoude, the Netherlands) after post-fixation in 4% paraformaldehyde. Frontal sections (coronal, 5 μm) were cut serially from the tip of the nose to the posterior extension of the OE and OB, and each section was preserved on Matsunami coating slide glass (Matsunami Glass Co., Tokyo, Japan).
Immunohistochemistry (IHC)
For IHC, the tissue was permeabilized in PBS-T (0.1% Triton X-100 in PBS) for 15 min. The endogenous peroxidase in the samples was quenched using 3% hydrogen peroxide in 10% methanol for 30 min. To retrieve antigenicity, the samples were boiled in 0.1 M citrate buffered saline (pH 6.0) for 5 min. The sections were cooled for 30 min and then washed twice in PBS (5 min each). After washing in PBS-T for 30 min, the sections were blocked for 1 h in blocking solution (4% normal donkey serum in PBS-T) and incubated with primary antibodies overnight at 4 °C. Anti-Aβ oligomer (1:100) and anti-bromodeoxyuridine (BrdU; 1:250) antibodies were used. After washing in PBS-T, the sections were incubated with a biotinylated secondary antibody for 1 h at room temperature. Sections were subsequently treated with the avidin-biotin-peroxidase complex (Vectastain Elite ABC kit) for 1 h at room temperature. The sections were developed for 5 min in a 0.05% DAB solution, and counter-stained with hematoxylin. Images were captured with a Nikon digital camera (DS-Ri1) attached to a Nikon-Eclipse-90i microscope (Nikon Corp., Tokyo, Japan).
Immunofluorescence (IF)
For immunofluorescence, tissues were permeabilized in 0.1% PBS-T for 15 min. To retrieve antigens, the samples were boiled in 0.1 M citrate buffered saline (pH 6.0) for 5 min. The sections were cooled for 30 min and then washed twice in PBS (5 min each). After washing in PBS-T for 30 min, the sections were blocked for 1 h in blocking solution (4% normal donkey serum in PBS-T). The sections were incubated with primary antibody overnight at 4 °C. Anti-oligomer A11 (Invitrogen, CA, USA) (1:100), Anti-6E10 (Aβ1-16) (Covance, NJ, USA) (1:500), Anti- D54D2 (Aβ1-40, Aβ1-42) (Cell Signaling, MA, USA) (1:500), anti-synaptophysin (Agilent Dako, CA, USA) (1:250), anti-TH (Santa Cruz Biotech, TX, USA) (1:250), and anti-Ki67 (Cell Signaling, MA, USA) (1:250) antibodies were used. Alexa 488 and Cy3-conjugated secondary antibodies (Jackson Laboratory, Bar Harbor, ME, USA) were used. The sections were counter-stained and mounted using VECTASHIELD mounting medium with 4′,6-diamidino-2-phenylindole (DAPI; Vector Laboratories, CA, USA). The images were visualized and photographed by confocal fluorescence microscopy (Carl Zeiss, Thornwood, NY, USA).
TUNEL staining assay
For TUNEL staining, deparaffinized and rehydrated sections were washed in PBS for 5 min and treated with Proteinase K (10 μg/mL) in PBS at room temperature for 30 min. After they were washed with distilled water for 5 min, the TUNEL incubation solution (Promega, WI, USA), containing the TdT enzyme solution and label solution, was prepared following the manufacturer’s protocol. The sections were incubated in the TdT enzyme and label mixture for 1 h at 37 °C and then washed three times with PBS (5 min each). Fragmented DNA was visualized as green fluorescence inside the nuclei.
BrdU assay
BrdU (Sigma, St. Louis, MO) was injected and detected with an antibody recognizing BrdU. For acute labeling experiments, 100 mg/kg BrdU was injected 1, 3, and 7 day(s) before sacrifice.
Image processing
All images were acquired using a Nikon ECLIPSE 90i microscope and a Nikon DS-Ri 1 digital camera (Nikon Inc., Japan) and LSM700 (+ Zeiss slide scanner). Digital images were processed adjusting only brightness, contrast, and color balance. The numbers of immunoreactive cells were counted manually by two independent investigators blinded to the experimental conditions. Three slides were analyzed for each animal and observed under a microscope (×100–400). To quantify the reciprocal intensity, the intensity per unit area was measured using Image J and the color deconvolution plug-in (http://wiki.imagej.net/Colour_Deconvolution). The target unit area of images was processed using the color deconvolution tool in Image J to separate brown from other colors. The area of brown staining was then quantified and divided by the total area to yield a percentage of staining area. Stereological analyses were conducted using Prism software (GraphPad software, USA).
Spatial analysis
To rate olfactory synapse positions within the sectioned OB (sagittal view), we divided equally among 10 frames from the anterior to posterior within a sagittal olfactory view. The top of the glomeruli in each frame was considered as a “degree of zero” and used to set the relative angle from zero (dorsal to ventral of OB) (Fig. 2c). Spatial correlations of the calcium signal heat maps (Fig. 2d, Fig. S2e) were calculated using the function “cor” in the R software package (version 3.4.2; http://www.r-project.org/), and the correlation coefficient of each calcium signal map evoked by an odor was displayed as a heat map using the function “leverplot” in R (Fig. 2e, g). To rate olfactory synapse positions, the sectioned OB with coronal and rostral migratory stream (RMS) was used as the standard (center of the dorsal-ventral axis). The most pointed/top of the glomeruli are located along the upper RMS track and regarded as “degree of zero” (360° at the same time due to coronal view), and the ROI was measured along with glomeruli; relative angles were then based on this zero point (Fig. 3a). Spatial heat maps (Fig. 3b) representing the Aβ oligomer expression were constructed using the function “leverplot” in R. A heat map matrix represents the intensity distribution of the deconvolution of the DAB signal by the protein expression along the angle. The intensity is presented as a scale bar (0–200 ΔF/F) at the left side of the maps.
Statistical analysis
Statistical analyses for histological ROI evaluation were conducted using Prism software (GraphPad software, USA). Comparisons between WT and experimental mice were conducted using a t-test. Results are presented as mean ± standard error of the mean (SEM). Differences with P-values of ≤0.05 were considered to be statistically significant. Correlations were assessed with a non-parametric Spearman's rank correlation test. Graphs (Fig. 4) show regression lines with a 95% confidence interval.