Journal: Neuron

Article Title: Gating of hippocampal rhythms and memory by synaptic plasticity in inhibitory interneurons

doi: 10.1016/j.neuron.2021.01.014

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: HEK293 cells expressing GluR1 WT or GluR1 S831A were stimulated with 200 nM phorbol 12-myristate 13-acetate (PMA, HY-18739, Med ChemExpress) for 15 min at room temperature.

Techniques: Virus, shRNA, Recombinant, Protease Inhibitor, Bicinchoninic Acid Protein Assay, RNAscope, Multiplex Assay, Transfection, Sequencing, Plasmid Preparation, Software

Journal: bioRxiv

Article Title: Age-associated sleep-wake patterns are altered with Prdm13 signaling in the dorsomedial hypothalamus and dietary restriction in mice

doi: 10.1101/2022.09.26.509442

Figure Lengend Snippet: a , Numbers of cFos+ cells in the DMH during SD, RS and sleeping-control (SD-Cont, RS-Cont) detected by cFos immunohistochemistry. The total number of cFos+ cells in the DMH was counted at bregma -1.67 mm to, -1.79 mm and -1.91 mm and summed up (total three sections) each mouse (n=3). The third ventricle (3V) is shown. Values are shown as means ± S.E., *p<0.05, ***p<0.001, and non-significant (ns) by one-way ANOVA with Bonferroni’s post hoc test. b , c , Representative images of DMH sections at bregma -1.67 mm from mice under SD-Cont (left) and SD (right) with cFos. Boxed areas were shown at high magnification in c. d , Images of the ZsGreen signal including the DMH, amygdala (Amg) and tuberal nucleus (TN) at bregma -1.54, -1.79, -1.91 and -2.13 mm of Prdm13 -ZsGreen mice. e , Ratios of cFos + cells within Prdm13 + cells in young mice during SD and SD-Cont detected by RNAscope in situ hybridization (n=7-8). Values are shown as means ± S.E., *p<0.05 and **p<0.01 by two-way ANOVA with Bonferroni’s post hoc test. f , g , Representative images of DMH sections from young mice under SD-Cont (left) and SD (right) with Prdm13 (yellow) and cFos (red) visualized by RNAscope. Boxed areas were shown at high magnification in g . Cells were counterstained with DAPI (blue). Scale bars indicate 100 and 10 μm ( f and g , respectively).

Article Snippet: The 8% equivalent of each fraction by volume was run on a 4-15% TGX gel (Bio-Rad) for Western blotting using affinity-purified polyclonal rabbit anti-mouse Prdm13.

Techniques: Control, Immunohistochemistry, RNAscope, In Situ Hybridization

Journal: bioRxiv

Article Title: Age-associated sleep-wake patterns are altered with Prdm13 signaling in the dorsomedial hypothalamus and dietary restriction in mice

doi: 10.1101/2022.09.26.509442

Figure Lengend Snippet: a , Breeding strategy to generate DMH-specific Prdm13 -knockout (Prdm13-KO) mice. After crossing Prdm13 fl/f ;Rosa26R ZsGreen/ZsGreen mice and Nkx2-1 CreERT2/+ ;Prdm13 fl/fl mice, Prdm13 fl/fl ;Nkx2-1 CreERT2/+ ;Rosa26R ZsGreen/+ mice were used as Prdm13-KO mice and Prdm13 fl/fl ;Nkx2-1 +/+ ;Rosa26R ZsGreen/+ mice were used as control (Cont) mice. b , Expression of Prdm13 in the DMH, tuberal nucleus (TN) and amygdala (Amg) of Prdm13-KO and Cont mice (n=5). Values are shown as means ± S.E., **p<0.01, ***p<0.001 and non-significant (ns) by two-way ANOVA with Bonferroni’s post hoc test. c , d , Number of episodes ( c ) or duration ( d ) of wakefulness (top), NREM sleep (middle) and REM sleep (bottom) every 3 hours through a day (left) and during the light (L) and dark (D) periods (right) in Prdm13-KO and Cont mice. Shading indicates dark period (n=6). Values are shown as means ± S.E., #p<0.05 by repeated measures ANOVA, listed p-values and *p<0.05 by repeated measures ANOVA with Bonferroni’s post hoc test (left) or unpaired t-test (right). e , Number of sleep attempts during SD from 6am to 8am (6-8), 8am to 9am (8-9), 9am to 10am (9-10), 10am to 11am (10-11) and 11am to 12pm (11-12) in Prdm13-KO and Cont mice (n=13-14). Values are shown as means ± S.E., *p<0.05, ***p<0.001 by repeated measures ANOVA with Bonferroni’s post hoc test. f , SWA during NREM sleep after SD. Normalized power is relative to the average of the 24-hour baseline day each group (n=6). Values are shown as means ± S.E. g , Total amount of wakefulness, NREM sleep and REM sleep during a 24-hour period (24h total), 12-hour light period (12h light) or 12-hour dark period (12h dark) (n=6). Values are shown as means ± S.E. h , EEG spectra of wakefulness (left), NREM sleep (middle) and REM sleep (right) during the light period (n=5-6). Values are shown as means ± S.E.

Article Snippet: The 8% equivalent of each fraction by volume was run on a 4-15% TGX gel (Bio-Rad) for Western blotting using affinity-purified polyclonal rabbit anti-mouse Prdm13.

Techniques: Knock-Out, Control, Expressing

Journal: bioRxiv

Article Title: Age-associated sleep-wake patterns are altered with Prdm13 signaling in the dorsomedial hypothalamus and dietary restriction in mice

doi: 10.1101/2022.09.26.509442

Figure Lengend Snippet: a , b , Numbers of episodes ( a ) and duration ( b ) of wakefulness (top), NREM sleep (middle) and REM sleep (bottom) every 3 hours through a day (left) and during the light (L) and dark (D) periods (right) in old DMH-specific Prdm13 -knockout (Prdm13-KO) and control (Cont) mice (n=5-6). Values are shown as means ± S.E., #p<0.05 and ##p<0.01 by repeated measures ANOVA, *p<0.05 and **p<0.01 by repeated measures ANOVA with Bonferroni’s post hoc test (left) or unpaired t-test (right). c , EEG spectra of wakefulness (left), NREM sleep (middle) and REM sleep (right) during the light period (n=4-6). Values are shown as means ± S.E. d , Number of sleep attempts during SD from 6am to 8am (6-8), 8am to 9am (8-9), 9am to 10am (9-10), 10am to 11am (10-11) and 11am to 12pm (11-12) in old Prdm13-KO and Cont mice (n=5-6). Values are shown as means ± S.E., **p<0.01 by repeated measures ANOVA with Bonferroni’s post hoc test. e , SWA after SD of Prdm13-KO and Cont mice at 20 months of age. Normalized power is relative to the average of the 24-hour baseline day (n=5-6). Values are shown as means ± S.E., **p<0.01 by Bonferroni’s post hoc test. f , Body weight of old Prdm13-KO and Cont mice (n=5-7). Values are shown as means ± S.E., *p<0.05 by unpaired t-test. g , The level of wheel-running activity in old Prdm13-KO and Cont mice for six consecutive days (n=5-7). Values are shown as means ± S.E., #p<0.05 by repeated measures ANOVA. h , Kaplan-Meier curves of Prdm13-KO and Cont mice (n=13-18). Listed p-value was calculated by log-rank test.

Article Snippet: The 8% equivalent of each fraction by volume was run on a 4-15% TGX gel (Bio-Rad) for Western blotting using affinity-purified polyclonal rabbit anti-mouse Prdm13.

Techniques: Knock-Out, Control, Activity Assay

Journal: bioRxiv

Article Title: Age-associated sleep-wake patterns are altered with Prdm13 signaling in the dorsomedial hypothalamus and dietary restriction in mice

doi: 10.1101/2022.09.26.509442

Figure Lengend Snippet: a , DR paradigm in C57BL/6J at 20 months of age. Mice at 20-months-old were fed under 60% diet or AL-diet for 14 to 28 days. b , c , Number of episodes ( b ) and duration ( c ) of wakefulness (top), NREM sleep (middle) and REM sleep (bottom) during the light (L) and dark (D) periods in AL and DR mice at 20 months of age (n=5). Values are shown as means ± S.E., listed p-value, *p<0.05 and **p<0.01 by unpaired t-test. d , EEG spectra of wakefulness (upper left), NREM sleep (upper right) and REM sleep (lower) during the light period (n=5). Values are shown as means ± S.E. e , Number of sleep attempts during SD from 6am to 8am (6-8), 8am to 9am (8-9), 9am to 10am (9-10), 10am to 11am (10-11) and 11am to 12pm (11-12) in AL and DR mice at 20 months of age (n=5-6). Values are shown as means ± S.E., **p<0.01 by repeated measures ANOVA with Bonferroni’s post hoc test. f , SWA after SD of AL and DR mice at 20 months of age. Normalized power is relative to the average of the 24-hour baseline day (n=5). Values are shown as means ± S.E., *p<0.05 by Bonferroni’s post hoc test. g , Number of sleep attempts during SD from 6am to 8am (6-8), 8am to 9am (8-9), 9am to 10am (9-10), 10am to 11am (10-11) and 11am to 12pm (11-12) in Prdm13-KO-AL and Prdm13-KO-DR mice (n=8). Values are shown as means ± S.E. h , Expression of Prdm13 in the hypothalamus of Prdm13 -overexpressing (Prdm13-OE) and control (Cont) mice (n=4-5). Values are shown as means ± S.E., *p<0.05 by unpaired t-test. i , j , Number of episodes ( i ) and duration ( j ) of wakefulness (top), NREM sleep (middle) and REM sleep (bottom) during the light (L) and dark (D) periods in Prdm13-OE and Cont mice (n=5). Values are shown as means ± S.E., *p<0.05 by unpaired t-test. k , Number of sleep attempts during SD from 6am to 8am (6-8), 8am to 9am (8-9), 9am to 10am (9-10), 10am to 11am (10-11) and 11am to 12pm (11-12) in Prdm13-OE and Cont mice (n=4). Values are shown as means ± S.E., *p<0.05 by repeated measures ANOVA with Bonferroni’s post hoc test. l , SWA after SD of Prdm13-OE and Cont mice. Normalized power is relative to the average of the 24-hour baseline day (n=4). Values are shown as means ± S.E.

Article Snippet: The 8% equivalent of each fraction by volume was run on a 4-15% TGX gel (Bio-Rad) for Western blotting using affinity-purified polyclonal rabbit anti-mouse Prdm13.

Techniques: Expressing, Control

Journal: bioRxiv

Article Title: Age-associated sleep-wake patterns are altered with Prdm13 signaling in the dorsomedial hypothalamus and dietary restriction in mice

doi: 10.1101/2022.09.26.509442

Figure Lengend Snippet: a , Western blot of Prdm13 in DMH collected by laser microdissection from DMH-specific Prdm13-KO and Cont mice (n=4 mice/lane). The arrow indicates the band for Prdm13; asterisks (*) indicate non-specific bands. b , Schematic of fractionation protocol from mouse hypothalami (left). Western blot of Prdm13 in hypothalamic fractions of C57BL/6J mice (right). Hypothalami from two C57BL/6J female mice were combined for each lane, and 8% equivalent of each fraction was run on the gel. Cytoplasmic supernatant (S1), RNase-extractable supernatant (S2), DNase-extractable supernatant (S3), and insoluble pellet (P) were run each lane. The arrow indicates the band for Prdm13; asterisks (*) indicate non-specific bands. c , Western blot of Prdm13 in hypothalamic fractions of Prdm13 -PA-Tag (KI) and wild-type (WT) mice. Cytosolic and nuclear fractions were run each lane as indicated. d , Expression of Cck, Grp and Pmch mRNA in the DMH of DMH- Prdm13 -KO (Prdm13-KO) and control (Cont) mice (n=3-5). Values are shown as means ± S.E., listed p-value, **p<0.01 and ***p<0.001 by unpaired t-test. e , Transcriptional activity of Prdm13-202 and Prdm13-mutants for the luciferase reporter vector containing the promoter region of Cck, Grp and Pmch . Schematic representation of Prdm13-202 and Prdm13-mutants are shown above. NIH3T3 cells were co-transfected with 250 ng of luciferase reporter plasmid and plasmid expressing Prdm13-202 (Prdm13), Prdm13-Zif mutant (mutZif) or Prdm13-deltaPR mutant (deltaPR). Obtained luminescence was normalized to total protein concentration (n=3, four individual experiments). Values are shown as means ± S.E., listed p-value, *p<0.05, **p<0.01 and ***p<0.001 by one-way ANOVA with Bonferroni’s post hoc test, # p<0.05 and ## p<0.01 and ### p<0.001 by unpaired t-test. f , Transcriptional activity of hypothalamic Prdm13 (htPrdm13) for the luciferase reporter plasmid containing the promoter region of Cck . NIH3T3 cells were co-transfected with 250 ng of reporter plasmid and 10, 50 or 250 ng of htPrdm13 -expressing plasmid. Obtained luminescence was normalized to total protein concentrations (n=3, three individual experiments). Values are shown as means ± S.E., *p<0.05 by one-way ANOVA with Bonferroni’s post hoc test.

Article Snippet: The 8% equivalent of each fraction by volume was run on a 4-15% TGX gel (Bio-Rad) for Western blotting using affinity-purified polyclonal rabbit anti-mouse Prdm13.

Techniques: Western Blot, Laser Capture Microdissection, Fractionation, Expressing, Control, Activity Assay, Luciferase, Plasmid Preparation, Transfection, Mutagenesis, Protein Concentration

Journal: bioRxiv

Article Title: Age-associated sleep-wake patterns are altered with Prdm13 signaling in the dorsomedial hypothalamus and dietary restriction in mice

doi: 10.1101/2022.09.26.509442

Figure Lengend Snippet: a , Representative images of the DMH with Prdm13 (yellow) and one of the two genes, Cck or Grp (green) visualized by RNAscope. Cells were counterstained with DAPI (blue). White boxes show the DMH, which is divided into medial and lateral areas by dashed lines. White arrows show yellow+green+ cells. Scale bar indicates 100 μm. b , Ratios of Cck + or Grp + cells within Prdm13 + cells in medial, lateral or total (medial and lateral) DMH (n=3-5). Values are shown as means ± S.E., ***p<0.001 by unpaired t-test. c , Distribution of cFos + Prdm13 + cells (n=5). d , Representative images of the DMH from young mice under SD-Cont and SD with Prdm13 (yellow), Cck (green) and cFos (red) visualized by RNAscope. Cells were counterstained with DAPI (blue). White arrows show Prdm13+Cck+cFos+ cells. Scale bar indicates 100 μm. e , f , Ratios of cFos + cells within Prdm13 + Cck -(left) or Prdm13 + Cck + (right) cells in young ( e ) or old ( f ) mice during SD-Cont and SD (n=7-8). Values are shown as means ± S.E., *p<0.05, ***p<0.001 by two-way ANOVA with Bonferroni’s post hoc test.

Article Snippet: The 8% equivalent of each fraction by volume was run on a 4-15% TGX gel (Bio-Rad) for Western blotting using affinity-purified polyclonal rabbit anti-mouse Prdm13.

Techniques: RNAscope

Journal: Translational Neurodegeneration

Article Title: Abnormal α-synuclein binds to synaptotagmin 13, impairing extracellular vesicle release in synucleinopathies

doi: 10.1186/s40035-025-00493-6

Figure Lengend Snippet: Incorporation of SYT13 into Lewy bodies and glial cytoplasmic inclusions (GCIs). a – f Immunohistochemical analysis of the human brain tissues of patients with Parkinson’s disease (PD) ( n = 7), dementia with Lewy bodies (DLB) ( n = 7), and multiple system atrophy (MSA) ( n = 7), and controls ( n = 7). Lewy bodies and GCIs were immunopositive for α-Syn (syn211). Immunohistochemistry shows the incorporation of SYT13 into both Lewy bodies ( b , d , arrows) and GCIs ( f , arrowhead). g – o Double immunofluorescence staining confirmed the presence of SYT13 in Lewy bodies ( g – l , white arrows) and GCIs ( m – o , white arrowheads). Scale bars, 10 μm

Article Snippet: Out of the three rabbit anti-SYT13 antibodies (NBP2-93419, Novus Biologicals, Centennial, CO; MBS9606007, MyBioSource, San Diego, CA; ABIN2840354, Antibodies-online.com, Limerick, PA) (Fig. 2), MBS9606007 was selected for IP using human brain tissues.

Techniques: Immunohistochemical staining, Immunohistochemistry, Double Immunofluorescence Staining

Journal: Translational Neurodegeneration

Article Title: Abnormal α-synuclein binds to synaptotagmin 13, impairing extracellular vesicle release in synucleinopathies

doi: 10.1186/s40035-025-00493-6

Figure Lengend Snippet: Alterations of 10 vesicular transport proteins in Lewy body diseases and multiple system atrophy (MSA). a – r Immunohistochemical analysis of human brain sections using antibodies for 9 vesicle transport proteins identified by the transcriptome analysis in the mouse model of MSA. Brain tissues of patients with Parkinson’s disease ( n = 7), dementia with Lewy bodies (DLB) ( n = 7) and MSA ( n = 7), and controls ( n = 7) were used for this analysis. SNAP25 was incorporated into glial cytoplasmic inclusions (GCIs) but not into Lewy bodies ( a , j ). Lewy bodies were immunopositive for Piccolo ( b ), Rab11b ( c ), Rab7( d ), RIMS3 ( e ) and RIMS4 ( f ) but not GCIs ( k – o ). Rab23, VTI1A and Exophilin5 were not incorporated into both Lewy bodies and GCIs ( g – i , p – r ). s Immunoblotting using temporal lobe tissues of human cases (control: n = 6 and DLB: n = 6; control: n = 6 and MSA: n = 6) for the 10 vesicle transport proteins. t – w Elevated SYT13 protein levels were observed in patients with DLB ( t ) and MSA ( u ), compared with the control groups, whereas RIMS3 protein level was elevated only in patients with DLB ( v , w ). Scale bars, 10 μm

Article Snippet: Out of the three rabbit anti-SYT13 antibodies (NBP2-93419, Novus Biologicals, Centennial, CO; MBS9606007, MyBioSource, San Diego, CA; ABIN2840354, Antibodies-online.com, Limerick, PA) (Fig. 2), MBS9606007 was selected for IP using human brain tissues.

Techniques: Immunohistochemical staining, Western Blot, Control

Journal: Translational Neurodegeneration

Article Title: Abnormal α-synuclein binds to synaptotagmin 13, impairing extracellular vesicle release in synucleinopathies

doi: 10.1186/s40035-025-00493-6

Figure Lengend Snippet: SYT13 interacts more with phosphorylated α-Syn than with endogenous α-Syn. A proximity ligation assay (PLA) was performed to visualise protein–protein interactions between SYT13 and α-Syn in the affected regions. a , b No signals were observed in Lewy bodies and glial cytoplasmic inclusions (GCIs) in the absence of primary antibodies. c - f The presence of strings of PLA signals indicates an interaction between SYT13 and both endogenous α-Syn in Lewy bodies ( c , arrows) and a GCI ( d , white arrow) and phosphorylated α-Syn in a Lewy body ( e , black arrowhead) and in GCIs ( f , white arrowheads). g – r The semi-quantification of PLA signals indicated that SYT13 interacts with phosphorylated α-Syn to a greater extent than with endogenous α-Syn in the substantia nigra ( g, h, i ) and the temporal lobe ( j, k, l ) of Parkinson’s disease (PD) cases ( n = 4), and the pons ( m, n, o ) and the temporal lobe ( p, q, r ) of multiple system atrophy (MSA) cases ( n = 4) compared with that observed in control cases ( n = 4). Data in ( i, r ) are presented as a box-and-whisker plot and were analysed via a Mann–Whitney U test. Data in ( l, o ) display the mean ± SD and were analysed with two-sample t -test. Scale bars, 10 μm. * P < 0.05; ** P < 0.01

Article Snippet: Out of the three rabbit anti-SYT13 antibodies (NBP2-93419, Novus Biologicals, Centennial, CO; MBS9606007, MyBioSource, San Diego, CA; ABIN2840354, Antibodies-online.com, Limerick, PA) (Fig. 2), MBS9606007 was selected for IP using human brain tissues.

Techniques: Proximity Ligation Assay, Protein-Protein interactions, Control, Whisker Assay, MANN-WHITNEY

Journal: Translational Neurodegeneration

Article Title: Abnormal α-synuclein binds to synaptotagmin 13, impairing extracellular vesicle release in synucleinopathies

doi: 10.1186/s40035-025-00493-6

Figure Lengend Snippet: SYT13 binds to abnormal α-Syn. a FLAG-tagged SYT13 was immunoprecipitated from the cell lysates of HEK293 cells, as a negative control (lane 1), and HEK293 cells co-transfected with one of the SYT13 constructs (lane 2, full-length; lane 3, Δ1-159; lane 4, C2A; or lane 5, C2B) and S129E α-Syn, a phosphorylation-mimic mutant in which serine residue (S) at position 129 was substituted with glutamic acid (E). Anti-FLAG antibody was used for this analysis. The expression levels of α-Syn and SYT13 were analysed via immunoblotting. In addition to full-length SYT13, the co-immunoprecipitation of α-Syn with the C2B domain of SYT13 was detected (arrowhead). b, c To compare the interaction between SYT13 and endogenous versus phosphorylated α-Syn, temporal lobe homogenates of dementia with Lewy bodies (DLB) ( n = 5) and control cases ( n = 5) as well as multiple system atrophy (MSA) ( n = 3) and control cases ( n = 3) were immunoprecipitated using an antibody against SYT13 (arrows). No bands indicating the binding of endogenous α-Syn and SYT13 were observed in the controls and samples from the DLB and MSA cases, whereas SYT13 was found to bind phosphorylated α-Syn in all DLB and MSA cases (asterisks). d, e In patients with DLB and MSA, the higher interaction between phosphorylated α-Syn and SYT13 was observed compared with endogenous α-Syn and SYT13. The Y-axis indicates the extent of binding of SYT13 to endogenous or phosphorylated α-Syn.

Article Snippet: Out of the three rabbit anti-SYT13 antibodies (NBP2-93419, Novus Biologicals, Centennial, CO; MBS9606007, MyBioSource, San Diego, CA; ABIN2840354, Antibodies-online.com, Limerick, PA) (Fig. 2), MBS9606007 was selected for IP using human brain tissues.

Techniques: Immunoprecipitation, Negative Control, Transfection, Construct, Phospho-proteomics, Mutagenesis, Residue, Expressing, Western Blot, Control, Binding Assay

Journal: Translational Neurodegeneration

Article Title: Abnormal α-synuclein binds to synaptotagmin 13, impairing extracellular vesicle release in synucleinopathies

doi: 10.1186/s40035-025-00493-6

Figure Lengend Snippet: SYT13 interacts with toxic β-sheet-richα-Syn oligomers in synucleinopathies. a , b To qualitatively investigate the changes in SYT13 in synucleinopathies, we performed fraction analysis (DLB, n = 3 and control n = 3; MSA, n = 3 and control n = 3) using the human temporal lobe homogenates. Representative data demonstrate the presence of SYT13 smear bands in the urea-insoluble fraction (f5) of DLB ( a ) and MSA ( b ) samples (black asterisks), but not in controls. In addition, the SYT13 bands were observed in the Tris-buffered saline (TBS) (f1)-soluble fraction of DLB ( a , white asterisk) as well as the TBS (f1)- and Triton (f2)-soluble fractions of MSA samples ( b , white asterisk). The immunoblotting patterns observed in the other DLB and MSA cases were comparable. F3, 1% sarkosyl fraction; f4, CHAPS fraction. c – e To ascertain whether the abnormal α-Syn that binds to SYT13 is predominantly composed of soluble toxic α-Syn oligomers or insoluble α-Syn fibrils, a filter trap assay was performed based on the same cases used for immunoblotting (MSA n = 6 and control n = 6) in Fig. s, with corresponding case numbers. The 26F1 antibody detects toxic β-sheet-rich α-Syn oligomers and fibrils. ( c ) There was a strong correlation between the protein level of SYT13 determined via immunoblotting (Fig. u), and the level of aggregated α-Syn in TBS ( R = 0.720, P = 0.008). ( d ) A weak but significant correlation was also observed between SYT13 and aggregated α-Syn levels in the insoluble sarkosyl fraction ( R = 0.594, P = 0.042). ( e ) No such correlation was observed in the insoluble urea fraction ( R = − 0.203, P = 0.527). Correlation was analysed based on Spearman’s rank correlation coefficient ( c , d ) or Pearson’s correlation coefficient ( e ), based on normality examined via the Shapiro–Wilk test. The protein levels of 26F1-positive α-Syn were normalised to the Coomassie Brilliant Blue (CBB) staining

Article Snippet: Out of the three rabbit anti-SYT13 antibodies (NBP2-93419, Novus Biologicals, Centennial, CO; MBS9606007, MyBioSource, San Diego, CA; ABIN2840354, Antibodies-online.com, Limerick, PA) (Fig. 2), MBS9606007 was selected for IP using human brain tissues.

Techniques: Control, Saline, Western Blot, TRAP Assay, Staining

Journal: Translational Neurodegeneration

Article Title: Abnormal α-synuclein binds to synaptotagmin 13, impairing extracellular vesicle release in synucleinopathies

doi: 10.1186/s40035-025-00493-6

Figure Lengend Snippet: SYT13 binds to the SNARE complex and regulates extracellular vesicle release. a Human temporal lobes ( n = 3) were fractionated to identify the location of SYT13 in cells. SYT13 was detected in the synaptosome fraction, but not in the cytosol fraction. b The temporal lobes of patients with multiple system atrophy (MSA) ( n = 3) and controls ( n = 3) were immunoprecipitated with an anti-SYT13 antibody. SYT13 bound SYT1, SNAP25 (arrowhead), VAMP2, Syntaxin, and CPLX1. c – g SYT13 expression was suppressed in SH-SY5Y cells to examine the interactions between SYT13 and α-Syn, SYT1, or the SNARE complexes. A significant decrease in the protein levels of SYT1 and Munc18-1 was observed in SH-SY5Y cells treated with SYT13 siRNA compared to cells treated with control siRNA. There were no discernible differences in the protein levels of α-Syn, SNAP25, Syntaxin, VAMP2, and CPLX1 between the groups. h – l Extracellular vesicles were isolated from the culture supernatant of SH-SY5Y cells with SYT13 knockdown or overexpression. Extracellular vesicle-free 10% foetal bovine serum was used for this analysis. Both knockdown ( j ) and overexpression ( l ) of SYT13 resulted in impaired extracellular vesicle release. No difference was observed in α-Syn protein levels in extracellular vesicles isolated from cells treated with or without SYT13 siRNA. Mean ± SD, two-sample t -test. * P < 0.05; ** P < 0.01

Article Snippet: Out of the three rabbit anti-SYT13 antibodies (NBP2-93419, Novus Biologicals, Centennial, CO; MBS9606007, MyBioSource, San Diego, CA; ABIN2840354, Antibodies-online.com, Limerick, PA) (Fig. 2), MBS9606007 was selected for IP using human brain tissues.

Techniques: Immunoprecipitation, Expressing, Control, Isolation, Knockdown, Over Expression

Journal: Translational Neurodegeneration

Article Title: Abnormal α-synuclein binds to synaptotagmin 13, impairing extracellular vesicle release in synucleinopathies

doi: 10.1186/s40035-025-00493-6

Figure Lengend Snippet: SYT13 interacts with abnormal α-Syn and disrupts extracellular vesicle release in synucleinopathies. a – e , g – k Interaction between SYT13 and α-synuclein (α-Syn) in the synaptosome fraction of human temporal lobes (DLB n = 5 and control n = 4; MSA n = 3 and control n = 3). Immunoblotting revealed a significant elevation in the SYT13 protein levels and aggregated α-Syn levels (arrowheads) in the synaptosome fraction of the brains of DLB ( b ) and MSA ( h ) cases, compared to controls. Moreover, there was a significant correlation between the protein levels of 5G4-positive aggregated α-Syn and SYT13 in DLB ( R = 0.86, P = 0.003, d ) and MSA ( R = 0.91, P = 0.013, j ). No such correlation was found between SYT13 and α-Syn monomer levels in DLB ( R = 0.25, P = 0.52, e ) and MSA ( R = 0.73, P = 0.10, k ). f , l The number of extracellular vesicles, measured using anti-CD81 antibodies, decreased significantly in the temporal lobe homogenates from patients with DLB ( f ) and MSA ( l ) compared to the controls. Data presented in ( b , c , f , h , i , and l ) are mean ± SD and were analysed with two-sample t -test. Pearson’s correlation coefficient was analysed ( d , e , j , k ), based on normality examined via the Shapiro–Wilk test. * P < 0.05; ** P < 0.01

Article Snippet: Out of the three rabbit anti-SYT13 antibodies (NBP2-93419, Novus Biologicals, Centennial, CO; MBS9606007, MyBioSource, San Diego, CA; ABIN2840354, Antibodies-online.com, Limerick, PA) (Fig. 2), MBS9606007 was selected for IP using human brain tissues.

Techniques: Control, Western Blot

Journal: Translational Neurodegeneration

Article Title: Abnormal α-synuclein binds to synaptotagmin 13, impairing extracellular vesicle release in synucleinopathies

doi: 10.1186/s40035-025-00493-6

Figure Lengend Snippet: Alterations of SYT13 mRNA expression in multiple brain regions of advanced-stage patients with synucleinopathies. RNAscope ® was performed to visualise SYT13 mRNA. a No signals were observed when a negative control probe was employed. b A positive control probe showed signals of mRNA encoding a housekeeping protein Cyclophilin B. c – i mRNA expression levels of SYT13 in advanced stages of synucleinopathies, comprising PD ( n = 4) and control ( n = 4) cases as well as MSA ( n = 4) and control ( n = 4) cases. j SYT13 mRNA expression was reduced in the substantia nigra of PD cases compared to control cases. k SYT13 mRNA expression was reduced in the pons of MSA cases compared to control cases. l Lower mRNA expression of SYT13 in the temporal lobe of PD and MSA cases compared to controls. Mean ± SD, two-sample t -test ( j, k ) and one-way analysis of variance followed by the Tukey test ( l ). Scale bars, 10 μm. *P < 0.05

Article Snippet: Out of the three rabbit anti-SYT13 antibodies (NBP2-93419, Novus Biologicals, Centennial, CO; MBS9606007, MyBioSource, San Diego, CA; ABIN2840354, Antibodies-online.com, Limerick, PA) (Fig. 2), MBS9606007 was selected for IP using human brain tissues.

Techniques: Expressing, RNAscope, Negative Control, Positive Control, Control

Journal: bioRxiv

Article Title: Sustained Yap/Taz activation promotes aberrant alveolar epithelial cell differentiation and drives persistent fibrotic remodeling

doi: 10.1101/2025.07.16.665213

Figure Lengend Snippet: A ) Timeline of YT active mouse bleomycin injury model with Yap/Taz inhibition with Verteporfin (60mg/kg) at 14-days post-injury. B ) Masson’s trichrome staining of WT and YT active mice with and without Verteporfin following saline or bleomycin. C ) Ashcroft scoring of fibrosis and ( D ) total collagen analysis of wild-type and YT active mice with and without Verteporfin following saline or bleomycin. WT saline (n=9). and YT active saline (n=9), WT (n=9) and YT active (n=8) saline and Verteporfin, WT (n=16) and YT active (n=14) bleomycin, WT (n=11) and YT active (n=16) bleomycin and Verteporfin-treated mice. E ) Immunofluorescence analysis of Sp-C + (red), Hopx + (white), and lineage-traced AT2 (green) cells. Quantification of ( F ) lineage traced AT2 cells expressing Hopx, ( G ) Sp-C + /Hopx + cells, and ( I ) total Sp-C + cells per frame. H ) Scgb1a1 + cells (green), AT2 lineage-labeled cells (red), and Sp-C + cells (white) in wild-type and YT active mice given saline, bleomycin, or bleomycin and Verteporfin. J ) Quantification of Scgb1a1 + cells outside of airways in the alveolar region. WT and YT active saline (n=6), WT and YT active saline/Verteporfin (n=6), WT (n=14) and YT active (n=16) bleomycin, WT (n=8) and YT active (n=9) bleomycin/Verteporfin-treated mice. To determine significance an ordinary one-way ANOVA with Sidak’s multiple comparisons test with a single pooled variance was used. Immunofluorescent analysis scale bars represent 50μm. Trichrome staining scale bars are 100μm.

Article Snippet: For Yap/Taz inhibition experiments, Verteporfin (Cell Signaling 64260) dissolved in DMSO was administered via i.p. injection at 60mg/kg 2-weeks after injury.

Techniques: Inhibition, Staining, Saline, Immunofluorescence, Expressing, Labeling

Journal: bioRxiv

Article Title: Sustained Yap/Taz activation promotes aberrant alveolar epithelial cell differentiation and drives persistent fibrotic remodeling

doi: 10.1101/2025.07.16.665213

Figure Lengend Snippet: A ) Immunofluorescence and RNAscope analysis of Krt19 (white) and lineage traced AT2 cells (green). B) Quantification of Krt19 + /Lineage traced cells in each treatment group. WT and YT active saline (n=4), WT and YT active saline/Verteporfin (n=4), WT and YT active bleomycin (n=6), and WT and YT active bleomycin/Verteporfin-treated (n=6) mice. C ) Immunofluorescence analysis of AT2 lineage-labeled cells (green), Cebpa (red), and Hopx + AT1 cells (white) in wild-type and YT active mice given saline, bleomycin, or bleomycin and Verteporfin. D ) Quantification of Cebpa + nuclei in AT2 lineage-labeled cells. Ordinary one-way ANOVA with Sidak’s multiple comparisons test with a single pooled variance was used to determine significance. Scale bars are 50μm.

Article Snippet: For Yap/Taz inhibition experiments, Verteporfin (Cell Signaling 64260) dissolved in DMSO was administered via i.p. injection at 60mg/kg 2-weeks after injury.

Techniques: Immunofluorescence, RNAscope, Saline, Labeling

Journal: eLife

Article Title: The long noncoding RNA lnc-FANCI-2 intrinsically restricts RAS signaling in human papillomavirus type 16-infected cervical cancer cells

doi: 10.7554/eLife.102681

Figure Lengend Snippet: ( A ) RT-qPCR detection of lnc-FANCI-2 in HPV16 + cervical cancer cell lines SiHa, CaSki, and W12 20861 (integrated HPV16) and 20863 (episomal HPV16), HPV18 + cervical cancer cell lines HeLa and C4II, and HPV - cell lines C33A (cervical cancer cells with mutations of p53 and pRb), HCT116 (colorectal cancer cells), BCBL-1 (body cavity B lymphoma cells), HEK293 (Ad5 E1/E2-immortalized human kidney cells), and HaCaT (spontaneously immortalized human epidermal cells) in triplicates. ( B ) HeLa cells express no lnc-FANCI-2 when compared with C33A cells by northern blot. ( C ) lnc-FANCI-2 is mainly cytoplasmic in CaSki but nuclear in SiHa and C33A cells. Cytoplasmic and nuclear fractionation efficiency was blotted for nuclear SRSF3 (serine- and arginine-rich splicing factor 3) and cytoplasmic GAPDH. Total fractionated cytoplasmic and nuclear RNAs were quantified for lnc-FANCI-2 by RT-qPCR in triplicates, with GAPDH RNA serving as an internal control for RNA fractionation efficiency. ( D ) Subcellular lnc-FANCI-2 (red) localization in CaSki, SiHa, and C33A cells determined by RNAscope RNA in situ hybridization (RNA-ISH) analysis. Nuclei were stained with DAPI (blue). Scale bars: 25 μm in the top and 10 μm in the zoom. Figure 2—source data 1. Northern blot and western blot data for . Figure 2—source data 2. Northern blot and western blot data for .

Article Snippet: Antibody , Anti-p53 (Rabbit polyclonal) , ProteinTech , Cat# 10442-1-AP , Rabbit polyclonal; WB (1:1000).

Techniques: Quantitative RT-PCR, Northern Blot, Fractionation, Control, RNAscope, RNA In Situ Hybridization, Staining, Western Blot

Journal: eLife

Article Title: The long noncoding RNA lnc-FANCI-2 intrinsically restricts RAS signaling in human papillomavirus type 16-infected cervical cancer cells

doi: 10.7554/eLife.102681

Figure Lengend Snippet: ( A ) Effect of lnc-FANCI-2 KO in CaSki cells on the expression of HPV16 E6 and E7 and their downstream targets. Total cell extracts from parental CaSki, ΔPr-A9, and ΔPr-B3 cells were immunoblotted with the corresponding antibodies. Tubulin or GAPDH served as a protein loading control. The relative protein levels of E6, E7, p53, and E2F1 were calculated after normalizing to tubulin or GAPDH in the corresponding experiment. Expt I or II = experiment I or II. ( B ) KO of lnc-FANCI-2 expression enhances cell senescence in β-gal analysis. Figure 3—figure supplement 2—source data 1. lnc-FANCI-2 KO in CaSki cells and the expression of HPV16 E6 and E7 and their downstream targets. Figure 3—figure supplement 2—source data 2. lnc-FANCI-2 KO in CaSki cells and the expression of HPV16 E6 and E7 and their downstream targets.

Article Snippet: Antibody , Anti-p53 (Rabbit polyclonal) , ProteinTech , Cat# 10442-1-AP , Rabbit polyclonal; WB (1:1000).

Techniques: Expressing, Control