Confirm the specificity. The secondary antibodies were conjugated with horseradish peroxidase

Confirm the specificity. The secondary antibodies were conjugated with horseradish peroxidase (Thermo scientific). We used ECL (Millipore) to detect the signals, which were quantified in Image J (National Institutes of Health). Each experiment was repeated three times to obtain an average value for each sample.Table 1. Clinical and pathological features of ET cases and controls.Cerebellar cortex Western Blot Analysis ET N Age at death (years) Female Gender Brain Weight (grams) Postmortem Interval (hours) Braak AD Stage CERAD Plaque Score 0 A B C Purkinje cell counts Axonal Torpedoes* 5 (50.0 ) 3 (30.0 ) 2 (20.0 ) 0 (0.0 ) 7.362.6 23.9624.8 5 (45.5 ) 3 (27.3 ) 3 (27.3 ) 0 (0.0 ) 8.562.2 4.462.2 7 (58.3 ) 3 (25.0 ) 2 (16.7 ) 0 (8.3 ) 6.260.8 29.8628.1 7 (53.8 ) 4 (30.8 ) 2 (15.3 ) 0 (0.0 ) 9.062.6 3.662.1 10 85.766.1 5 (50.0 ) 12116126 3.162.3 2.061.2 Controls 11 84.566.4 6 (54.5 ) 11746145 1326631 4.762.3 2.061.1 Immunohistochemistry ET 12 86.566.4 8 (75 ) 11876123 2.661.8 2.561.2 Controls 13 83.067.6 7 (58.3 ) 12316140 8.9610.5A 1.761.Occipital cortex Western Blot Analysis ET 7 84.368.8 3 (42.9 ) 12076140 4.463.8 1.661.0 Controls 9 84.866.3 5 (55.6 ) 11756157 4.161.7 2.061.4 (57.1 ) 1 (14.2 ) 2 (28.6 ) 0 (0.0 ) 7.562.6 14.961.5 (55.6 ) 1 (11.1 ) 3 (33.3 ) 0 (0.0 ) 10.263.4 2.661.*p,0.05. A Two controls had PMI .15 hours. Median PMI in controls = 5.3 hours. doi:10.1371/journal.pone.0053040.tAutophagy in Essential Tremorthe 40 points above the average background value as the threshold for AV quantification. All the pixels above the threshold and within PC cell bodies were quantified. The usual size of AVs is 0.1?0 mm in diameter, but many AVs in PCs are either fused with or close to each other. Therefore, it is difficult to quantify the actual numbers of AVs. Instead, we summed the pixels above the threshold 23977191 value and divided by the cell body area, excluding the nucleus, to obtain the percentage of cell body area occupied by AVs. We also used a second analytic method, in which we used a set threshold value for all the images, and calculated the percentage of cell body area occupied by AVs; this analysis showed similar results.Data AnalysesAnalyses were performed in SPSS (Epigenetic Reader Domain version 18.0) and GraphPad Prism (version 5.0). Demographic and clinical characteristics of ET cases and controls were compared using Student’s t tests and chi square tests. The mean LC3-II protein levels, mitochondrial membrane protein levels, and Epigenetic Reader Domain beclin-1 levels (Western blot) and the percentage of cell bodies occupied by AVs (immunohistochemistry) were normally distributed; hence, parametric tests (Student’s t test, Pearson’s correlation coefficient [r]) were used when assessing these variables. Based on the presence in our sample of a clear bimodal distribution in disease duration among ET cases (#40 years vs. .40 years), study subjects were stratified into 3 diagnosis-duration groups: controls, ET cases with shorter duration disease, and ET cases with longer duration disease. In linear regression models, we examined the association between LC3-II protein level or the percentage of cell bodies occupied by AVs (dependent variables in different models) and the diagnosisduration group (controls, ET of shorter duration, ET of longer duration).ResultsCerebellar tissue was available for Western blot analysis on 10 ET cases and 11 age-matched controls who were similar with respect to age, gender, brain weight and other variables of interest (Table 1). The mean LC3-II protein level.Confirm the specificity. The secondary antibodies were conjugated with horseradish peroxidase (Thermo scientific). We used ECL (Millipore) to detect the signals, which were quantified in Image J (National Institutes of Health). Each experiment was repeated three times to obtain an average value for each sample.Table 1. Clinical and pathological features of ET cases and controls.Cerebellar cortex Western Blot Analysis ET N Age at death (years) Female Gender Brain Weight (grams) Postmortem Interval (hours) Braak AD Stage CERAD Plaque Score 0 A B C Purkinje cell counts Axonal Torpedoes* 5 (50.0 ) 3 (30.0 ) 2 (20.0 ) 0 (0.0 ) 7.362.6 23.9624.8 5 (45.5 ) 3 (27.3 ) 3 (27.3 ) 0 (0.0 ) 8.562.2 4.462.2 7 (58.3 ) 3 (25.0 ) 2 (16.7 ) 0 (8.3 ) 6.260.8 29.8628.1 7 (53.8 ) 4 (30.8 ) 2 (15.3 ) 0 (0.0 ) 9.062.6 3.662.1 10 85.766.1 5 (50.0 ) 12116126 3.162.3 2.061.2 Controls 11 84.566.4 6 (54.5 ) 11746145 1326631 4.762.3 2.061.1 Immunohistochemistry ET 12 86.566.4 8 (75 ) 11876123 2.661.8 2.561.2 Controls 13 83.067.6 7 (58.3 ) 12316140 8.9610.5A 1.761.Occipital cortex Western Blot Analysis ET 7 84.368.8 3 (42.9 ) 12076140 4.463.8 1.661.0 Controls 9 84.866.3 5 (55.6 ) 11756157 4.161.7 2.061.4 (57.1 ) 1 (14.2 ) 2 (28.6 ) 0 (0.0 ) 7.562.6 14.961.5 (55.6 ) 1 (11.1 ) 3 (33.3 ) 0 (0.0 ) 10.263.4 2.661.*p,0.05. A Two controls had PMI .15 hours. Median PMI in controls = 5.3 hours. doi:10.1371/journal.pone.0053040.tAutophagy in Essential Tremorthe 40 points above the average background value as the threshold for AV quantification. All the pixels above the threshold and within PC cell bodies were quantified. The usual size of AVs is 0.1?0 mm in diameter, but many AVs in PCs are either fused with or close to each other. Therefore, it is difficult to quantify the actual numbers of AVs. Instead, we summed the pixels above the threshold 23977191 value and divided by the cell body area, excluding the nucleus, to obtain the percentage of cell body area occupied by AVs. We also used a second analytic method, in which we used a set threshold value for all the images, and calculated the percentage of cell body area occupied by AVs; this analysis showed similar results.Data AnalysesAnalyses were performed in SPSS (version 18.0) and GraphPad Prism (version 5.0). Demographic and clinical characteristics of ET cases and controls were compared using Student’s t tests and chi square tests. The mean LC3-II protein levels, mitochondrial membrane protein levels, and beclin-1 levels (Western blot) and the percentage of cell bodies occupied by AVs (immunohistochemistry) were normally distributed; hence, parametric tests (Student’s t test, Pearson’s correlation coefficient [r]) were used when assessing these variables. Based on the presence in our sample of a clear bimodal distribution in disease duration among ET cases (#40 years vs. .40 years), study subjects were stratified into 3 diagnosis-duration groups: controls, ET cases with shorter duration disease, and ET cases with longer duration disease. In linear regression models, we examined the association between LC3-II protein level or the percentage of cell bodies occupied by AVs (dependent variables in different models) and the diagnosisduration group (controls, ET of shorter duration, ET of longer duration).ResultsCerebellar tissue was available for Western blot analysis on 10 ET cases and 11 age-matched controls who were similar with respect to age, gender, brain weight and other variables of interest (Table 1). The mean LC3-II protein level.