Journal: PLoS ONE

Article Title: Brain-Derived Neurotrophic Factor-Dependent cdk1 Inhibition Prevents G2/M Progression in Differentiating Tetraploid Neurons

doi: 10.1371/journal.pone.0064890

Figure Lengend Snippet: ( A ) Lysates from DCRNs cultured for 20 h in the presence of different combinations of 100 ng/m NGF and 2 ng/ml BDNF were subjected to western blot with antibodies specific for either cdk1 (upper panel) or β-actin (lower panel). ( B ) Normalized cdk1/β-actin ratio. ( C ) Semiquantitative RT-PCR analysis of mRNA samples obtained from DCRNs cultured for 20 h in the presence of either vehicle (Control) or 2 ng/ml BDNF (BDNF). The levels of Cdk1 expression were normalized to Gapdh . N.S. non-significant; *p<0.05 (Student’s t test; n = 3–4).

Article Snippet: K252a (200 nM) (Alomone Labs) and MK-1775 (300 nM) (Axon MedChem), both prepared in dimethyl sulfoxide, were added to the culture medium 10 min before BDNF treatment (DCRNs).

Techniques: Cell Culture, Western Blot, Reverse Transcription Polymerase Chain Reaction, Expressing

Journal: PLoS ONE

Article Title: Brain-Derived Neurotrophic Factor-Dependent cdk1 Inhibition Prevents G2/M Progression in Differentiating Tetraploid Neurons

doi: 10.1371/journal.pone.0064890

Figure Lengend Snippet: ( A ) General cdk protein kinase activity, based on the phosphorylation of a Rb-derived peptide by the cdk activity present in cell extracts from DCRNs cultured for 20 h in the presence of 100 ng/ml NGF and treated for 30 min with either vehicle (Control) or 2 ng/ml BDNF. Equal amount of cell extracts were used in both cases. ( B ) Left panel, a representative western blot performed with an anti-cdk1 antibody using the cell extracts described above prior to immunoprecipitation (INPUT). Right panel, protein kinase activity immunoprecipitated with an anti cdk1 antibody (i.e. cdk1-specific kinase activity) from the cell extracts described above, normalized to the relative amount of cdk1 present in these extracts (see input in left panel). *p<0.05 (ANOVA; n = 3).

Article Snippet: K252a (200 nM) (Alomone Labs) and MK-1775 (300 nM) (Axon MedChem), both prepared in dimethyl sulfoxide, were added to the culture medium 10 min before BDNF treatment (DCRNs).

Techniques: Activity Assay, Derivative Assay, Cell Culture, Western Blot, Immunoprecipitation

Journal: PLoS ONE

Article Title: Brain-Derived Neurotrophic Factor-Dependent cdk1 Inhibition Prevents G2/M Progression in Differentiating Tetraploid Neurons

doi: 10.1371/journal.pone.0064890

Figure Lengend Snippet: ( A ) Validation of the cdk1 sandwich ELISA assay performed with 10 fg of either GST (GST) or a chimeric protein containing the sequence of human cdk1 bound to GST (Cdk1-GST), and revealed with the anti-cdk1 PSTAIRE antibody. Normalized optical density (O.D.) at 405 nm is shown. ( B ) Validation of the phospho-cdk1 sandwich ELISA assay performed with cell lysates obtained from DCRNs cultured in the presence of 100 ng/ml NGF and 2 ng/ml BDNF, incubated either in the absence (- CIP) or presence (+ CIP) of CIP, and revealed with the anti-cdk1 (pTyr15) antibody. Normalized optical density (O.D.) at 405 nm is shown. ( C ) Cell lysates from DCRNs cultured in the presence (+) or absence (-) of the referred factors were subjected to sandwich ELISA analyses using antibodies specific for either cdk1 phosphorylated at Tyr15 or total cdk1 protein. Colorimetric values for cdk1 phosphorylated at Tyr15 were normalized to the levels of cdk1 protein (Cdk1). ( D ) Cell lysates from DCRNs cultured in the presence of the referred factors and/or K252a were subjected to sandwich ELISA analyses as described above. Colorimetric values for cdk1 phosphorylated at Tyr15 were normalized to the levels of cdk1 protein (Cdk1). *p<0.05; ***p<0.005 (Student’s t test; n = 3).

Article Snippet: K252a (200 nM) (Alomone Labs) and MK-1775 (300 nM) (Axon MedChem), both prepared in dimethyl sulfoxide, were added to the culture medium 10 min before BDNF treatment (DCRNs).

Techniques: Sandwich ELISA, Sequencing, Cell Culture, Incubation

Journal: PLoS ONE

Article Title: Brain-Derived Neurotrophic Factor-Dependent cdk1 Inhibition Prevents G2/M Progression in Differentiating Tetraploid Neurons

doi: 10.1371/journal.pone.0064890

Figure Lengend Snippet: ( A ) Cell lysates from DCRNs cultured in the presence of the referred factors and/or 300 nM MK-1775 were subjected to sandwich ELISA analyses using antibodies specific for either cdk1 phosphorylated at Tyr15 or total cdk1 protein. Colorimetric values for cdk1 phosphorylated at Tyr15 were normalized to the levels of cdk1 protein (Cdk1). ( B ) Cell lysates from CEFs cultured in the presence (+) or absence (-) of 300 nM MK-1775 were subjected to sandwich ELISA analyses as described above. Colorimetric values for cdk1 phosphorylated at Tyr15 were normalized to the levels of cdk1 protein (Cdk1). ***p<0.005 (Student’s t test; n = 3). # p<0.05 (NGF/BDNF/MK-1775 vs NGF/MK-1775; Student’s t test; n = 3).

Article Snippet: K252a (200 nM) (Alomone Labs) and MK-1775 (300 nM) (Axon MedChem), both prepared in dimethyl sulfoxide, were added to the culture medium 10 min before BDNF treatment (DCRNs).

Techniques: Cell Culture, Sandwich ELISA

Journal: PLoS ONE

Article Title: Fine-Tuning Roles of Endogenous Brain-Derived Neurotrophic Factor, TrkB and Sortilin in Colorectal Cancer Cell Survival

doi: 10.1371/journal.pone.0025097

Figure Lengend Snippet: (A) Role of endogenous BDNF and its receptor TrkB on CRC cell proliferation: effects of exogenous BDNF and suppressing endogenous TrkB receptor on cell proliferation. The four cell lines were cultured for 24 h in FCS-free medium (FCS 10%, −) in the presence of exogenous BDNF (+), K252a (+) alone or in combination. Cell proliferation was determined by flow cytometry analysis using EdU Alexa Fluor 488. The data are presented as histograms of proliferating cells in relative units ± SEM of five independent experiments. *, p <0.05; **, p <0.01; ***, p <0.001, when compared with serum-free medium. (B, C) Effects of exogenous BDNF and suppressing endogenous TrkB receptor on cell survival. Apoptotic ratios of soluble nucleosomes were detected by ELISA Cell for WiDr, SW480, SW620, and COLO 205 induced by serum deprivation alone (FCS 10%, −) or in association either with exogenous BDNF (+), or with K252a (+), during 24–72 h of serum deprivation. Histograms, mean ratio of apoptotic cells ± SEM of at least three independent experiments. *, p <0.05; **, p <0.01; ***, p <0.001, when compared with serum-free condition alone. (D, E) apoptotic ratio after 24 h serum deprivation alone (0% FCS) or with combination with a neutralizing anti-BDNF mAb (0% anti-BDNF). Histograms, mean ratio of apoptotic cells ± SEM of three independent experiments. *, p <0.05; **, p <0.01; ***, p <0.001, when compared with serum-free condition alone.

Article Snippet: Recombinant human BDNF (100 ng/ml), recombinant pro-BDNF (4 ng/ml), and K252a (200 nM) were purchased from Alomone labs.

Techniques: Cell Culture, Flow Cytometry, Enzyme-linked Immunosorbent Assay

Journal: PLoS ONE

Article Title: Fine-Tuning Roles of Endogenous Brain-Derived Neurotrophic Factor, TrkB and Sortilin in Colorectal Cancer Cell Survival

doi: 10.1371/journal.pone.0025097

Figure Lengend Snippet: (A, B) Sortilin as a coreceptor of p75 NTR . Double staining (yellow) of sortilin (red) and p75 NTR (green) in SW480 cells (A) and SW620 (B) after 24 h of serum deprivation. (C) Colocalization of pro-BDNF and sortilin. Confocal microscopy study of a WiDr cells stained with an anti-pro-BDNF Ab (green) and an anti-sortilin Ab (red), and double staining (yellow) after 24 h of serum deprivation. (D, E) apoptotic ratios after 24 h serum deprivation alone (0% FCS) or combined with recombinant Pro-BDNF (0% Pro-BDNF). Histograms, mean ratio of apoptotic cells ± SEM of three independent experiments. *, p <0.05; **, p <0.01; ***, p <0.001, when compared with serum-free condition alone (0% FCS).

Article Snippet: Recombinant human BDNF (100 ng/ml), recombinant pro-BDNF (4 ng/ml), and K252a (200 nM) were purchased from Alomone labs.

Techniques: Double Staining, Confocal Microscopy, Staining, Recombinant

Journal: PLoS ONE

Article Title: Fine-Tuning Roles of Endogenous Brain-Derived Neurotrophic Factor, TrkB and Sortilin in Colorectal Cancer Cell Survival

doi: 10.1371/journal.pone.0025097

Figure Lengend Snippet: (A) Role of endogenous BDNF and its receptor TrkB on CRC cell proliferation: effects of exogenous BDNF and suppressing endogenous TrkB receptor on cell proliferation. The four cell lines were cultured for 24 h in FCS-free medium (FCS 10%, −) in the presence of exogenous BDNF (+), K252a (+) alone or in combination. Cell proliferation was determined by flow cytometry analysis using EdU Alexa Fluor 488. The data are presented as histograms of proliferating cells in relative units ± SEM of five independent experiments. *, p <0.05; **, p <0.01; ***, p <0.001, when compared with serum-free medium. (B, C) Effects of exogenous BDNF and suppressing endogenous TrkB receptor on cell survival. Apoptotic ratios of soluble nucleosomes were detected by ELISA Cell for WiDr, SW480, SW620, and COLO 205 induced by serum deprivation alone (FCS 10%, −) or in association either with exogenous BDNF (+), or with K252a (+), during 24–72 h of serum deprivation. Histograms, mean ratio of apoptotic cells ± SEM of at least three independent experiments. *, p <0.05; **, p <0.01; ***, p <0.001, when compared with serum-free condition alone. (D, E) apoptotic ratio after 24 h serum deprivation alone (0% FCS) or with combination with a neutralizing anti-BDNF mAb (0% anti-BDNF). Histograms, mean ratio of apoptotic cells ± SEM of three independent experiments. *, p <0.05; **, p <0.01; ***, p <0.001, when compared with serum-free condition alone.

Article Snippet: Recombinant human BDNF (100 ng/ml), recombinant pro-BDNF (4 ng/ml), and K252a (200 nM) were purchased from Alomone labs.

Techniques: Cell Culture, Flow Cytometry, Enzyme-linked Immunosorbent Assay

Journal: PLoS ONE

Article Title: Fine-Tuning Roles of Endogenous Brain-Derived Neurotrophic Factor, TrkB and Sortilin in Colorectal Cancer Cell Survival

doi: 10.1371/journal.pone.0025097

Figure Lengend Snippet: (A, B) Sortilin as a coreceptor of p75 NTR . Double staining (yellow) of sortilin (red) and p75 NTR (green) in SW480 cells (A) and SW620 (B) after 24 h of serum deprivation. (C) Colocalization of pro-BDNF and sortilin. Confocal microscopy study of a WiDr cells stained with an anti-pro-BDNF Ab (green) and an anti-sortilin Ab (red), and double staining (yellow) after 24 h of serum deprivation. (D, E) apoptotic ratios after 24 h serum deprivation alone (0% FCS) or combined with recombinant Pro-BDNF (0% Pro-BDNF). Histograms, mean ratio of apoptotic cells ± SEM of three independent experiments. *, p <0.05; **, p <0.01; ***, p <0.001, when compared with serum-free condition alone (0% FCS).

Article Snippet: Recombinant human BDNF (100 ng/ml), recombinant pro-BDNF (4 ng/ml), and K252a (200 nM) were purchased from Alomone labs.

Techniques: Double Staining, Confocal Microscopy, Staining, Recombinant

Journal: bioRxiv

Article Title: Axonal ER tubules regulate local translation via P180/RRBP1-mediated ribosome interactions

doi: 10.1101/2022.11.30.518484

Figure Lengend Snippet: (A, D, G) Representative STED (A), TREx (D) and dual-color SMLM (G) images of the ER and ribosomes in axons from neurons expressing GFP-Sec61β and stained for RpS12. (B, E, H) Magnifications and intensity profile lines from merged images for each microscopy method. (C, F, I) Quantification of RpS12 intensity in ER mask, enlarged ER mask, and one-color flipped images, for each microscopy method. (J) Representative STED images and intensity profile line for an axon segment of a neuron transfected as in (A) and co-labeled for puromycilated peptides. (K) Quantification of RpS12 intensity in ER mask and enlarged ER mask with or without high puromycin treatment using dual-color SMLM. (L-N) Schematic representation of split APEX system used to detect ER-ribosome contacts. When the ER protein Sec61β fused to AP module and the ribosomal protein RpL10A fused to EX module interact with each other, APEX is reconstituted and contact sites can be visualized as a biotinylation radius around the interactions (L). Representative images of split APEX assay in distal axons from neurons expressing RpL10A-3xHA-EX and V5-AP-Sec61β (left), or V5-AP-RTN4A as a negative control (right). Expression of constructs are visualized with V5 and HA antibodies, and biotinylation is detected with conjugated Strep-555 (M). Quantification of Strep signal in distal axons from neurons as in (M), and without H2O2 as a negative control for the biotinylation reaction (N). (O) Quantification of axonal ER-bound ribosomes using split APEX assay with RpL10A-3xHA-EX and V5-AP-Sec61β, in neurons stimulated for 30-minutes with BSA (control), BDNF, NT-3 or NGF. Individual data points each represent a neuron in (C, F, I, K, N and O). Boxplots show 25/75-percentiles, the median, and whiskers represent min to max in (C, F, I and K). Data are presented as mean values ± SEM in (N, O). ns = not significant, *p < 0.05, **p < 0.01, ***p<0.001 comparing conditions to control using unpaired t-tests or ordinary one-way ANOVA tests. Scale bars represent 1μm (A, D, G, J) and 5μm (M).

Article Snippet: Other reagents used in this study were: Puromycin dihydrochloride (Sigma-Aldrich, Cat# P8833), Anisomycin (Sigma-Aldrich, Cat#9789), recombinant human Neurotrophin-3 (NT-3) protein (50ng/ml, Alomone labs, Cat#N-260), recombinant human BDNF protein (50ng/ml, Alomone labs, Cat#B-250), recombinant rat beta-NGF Protein (50ng/ml, R&D systems, Cat# 556-NG).

Techniques: Expressing, Staining, Microscopy, Transfection, Labeling, Negative Control, Construct

Journal: bioRxiv

Article Title: Mutation in the TRKB cholesterol recognition site that blocks antidepressant binding does not influence the basal or BDNF-stimulated activation of TRKB

doi: 10.1101/2022.08.26.505413

Figure Lengend Snippet: (A) The sequence of TRKB transmembrane (TM) domain from rat (UniProt: Q63604, residues 430-453) was mutated at Y433 residue (Y433F) or the entire motif was substituted by the rat sequence of TRKA TM (P35739, residues 419-442). (B) The interaction between biotinylated BDNF (bBDNF) and TRKB is not affected by the TRKB.Y433F mutation or in TRKB/TRKA.TM constructs. (C) TRKB.Y433F does not prevent the BDNF-induced dimerization of TRKB. The constructs used allow the formation of TRKB.wt homodimer or TRKB.wt/Y433F heterodimer. (D , E) Analysis of TRKB phosphorylation shows that, cortical cultures from TRKB.Y433F heterozygous mouse embryos respond to BDNF similarly to the the TRKB.wt littermates, regardless of the tyrosine residue tested ( D : Y515, E : Y816).

Article Snippet: The plates were then washed 3x with PBS buffer, and various concentrations of biotinylated BDNF (Alomone Labs, cat#B-250, 0.1 – 100 pM) was added for 1h at RT.

Techniques: Sequencing, Mutagenesis, Construct