Journal: Cell Metabolism

Article Title: Nutrient-sensing AgRP neurons relay control of liver autophagy during energy deprivation

doi: 10.1016/j.cmet.2023.03.019

Figure Lengend Snippet:

Article Snippet: Sections were then mounted with DAPI using Vectashield Antifade Mounting Medium (Vector Laboratories), covered using a coverslip and stored at 4°C in the dark.

Techniques: Virus, Plasmid Preparation, Recombinant, Protease Inhibitor, Western Blot, Blocking Assay, In Vitro, In Vivo, Enzyme-linked Immunosorbent Assay, Isolation, Bicinchoninic Acid Protein Assay, Reverse Transcription, RNAscope, Multiplex Assay, Software, Microscopy, Mass Spectrometry, Liquid Chromatography, Chromatography

Journal: Neuron

Article Title: Motor neurons use push-pull signals to direct vascular remodeling critical for their connectivity

doi: 10.1016/j.neuron.2022.09.021

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: When indicated, neutralizing anti-Plexin-D1 antibody (5μg/ml) (R&D Systems Cat# AF4160) was added to the co-cultures at the time of HUVEC seeding.

Techniques: Recombinant, Protease Inhibitor, Transfection, Plasmid Preparation, Cloning, Mutagenesis, Reverse Transcription, Sample Prep, RNA Library Preparation, Knock-Out, Control, Quantitative RT-PCR, In Situ, Software, Expressing, CRISPR, RNAscope

Journal: Neuron

Article Title: Motor neurons use push-pull signals to direct vascular remodeling critical for their connectivity

doi: 10.1016/j.neuron.2022.09.021

Figure Lengend Snippet: (A) Immunohistochemistry for Plexin-D1 reveals restricted vascular expression at E11.5.

Article Snippet: When indicated, neutralizing anti-Plexin-D1 antibody (5μg/ml) (R&D Systems Cat# AF4160) was added to the co-cultures at the time of HUVEC seeding.

Techniques: Immunohistochemistry, Expressing

Journal: Neuron

Article Title: Motor neurons use push-pull signals to direct vascular remodeling critical for their connectivity

doi: 10.1016/j.neuron.2022.09.021

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: When indicated, neutralizing anti-Plexin-D1 antibody (5μg/ml) (R&D Systems Cat# AF4160) was added to the co-cultures at the time of HUVEC seeding.

Techniques: Recombinant, Protease Inhibitor, Transfection, Plasmid Preparation, Cloning, Mutagenesis, Reverse Transcription, Sample Prep, RNA Library Preparation, Knock-Out, Control, Quantitative RT-PCR, In Situ, Software, Expressing, CRISPR, RNAscope

Journal: Cell reports

Article Title: Unique molecular features and cellular responses differentiate two populations of motor cortical layer 5b neurons in a preclinical model of ALS

doi: 10.1016/j.celrep.2022.110556

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Donkey polyclonal anti-Chicken, Alexa 488-conjugated , Jackson Immunoresearch , Cat# 703-545-155; RRID: AB_2340375.

Techniques: Recombinant, RNAscope, Protease Inhibitor, Plasmid Preparation, Multiplex Assay, Positive Control, Software

Journal: Neuron

Article Title: m 6 A mRNA methylation is essential for oligodendrocyte maturation and CNS myelination

doi: 10.1016/j.neuron.2019.12.013

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Goat anti-mouse IgG+IgM , Jackson ImmunoResearch , Cat# 115-055-044, RRID:AB_2338532.

Techniques: Recombinant, RNAscope, Derivative Assay, Protease Inhibitor, Electron Microscopy, Bicinchoninic Acid Protein Assay, Western Blot, Reverse Transcription, Multiplex Assay, Plasmid Preparation, Software

Journal: The Journal of Neuroscience

Article Title: Neuregulin1 Nuclear Signaling Influences Adult Neurogenesis and Regulates a Schizophrenia Susceptibility Gene Network within the Mouse Dentate Gyrus

doi: 10.1523/JNEUROSCI.0063-24.2024

Figure Lengend Snippet: Key resources table

Article Snippet: Recombinant mouse ErbB4/Her4 Fc chimera protein, CF , R&D Systems , Catalog #4387-ER-050.

Techniques: Affinity Purification, Virus, Recombinant, Protease Inhibitor, Sequencing, RNAscope, Variant Assay, Plasmid Preparation, Software

Journal: The Journal of Neuroscience

Article Title: Neuregulin1 Nuclear Signaling Influences Adult Neurogenesis and Regulates a Schizophrenia Susceptibility Gene Network within the Mouse Dentate Gyrus

doi: 10.1523/JNEUROSCI.0063-24.2024

Figure Lengend Snippet: The V 321 L substitution decreases nuclear back signaling. A , Immunoblot of triplicate nuclear fractions isolated from pooled cortical and hippocampal lysates. Nrg1 ICD was detected using Santa Cruz Biotechnology antibody sc-348. Histone H3 served as a nuclear loading control and Na+/K+ ATPase as a marker for the membrane fraction ( N = 3 mice/genotype). B , Immunoblot of two replicates of membrane fractions isolated from pooled cortical and hippocampal lysates. NRG1 ICD was detected using Santa Cruz Biotechnology antibody sc-348. Na+/K+ ATPase served as a marker for the membrane fraction; note the lack of the nuclear marker Histone H3 or cytoplasmic marker CyclophilinA indicating clean membrane preps. FL Nrg1 is indicated with a yellow arrowhead as “Nrg1-FL,” and the membrane-bound C-terminal fragment not cleaved by γ-secretase is indicated as “Nrg1 TM-CTF.” A positive control consisting of total lysate from N2A cells transfected with a Type III Nrg1 plasmid is shown in the lane labeled “C.” ( N = 2 mice/genotype.) C , Left, Hippocampal neurons from WT (dark blue) and V 321 L (light blue) neonatal pups (P4) were cultured for 17 d in vitro and were stimulated with either vehicle (Veh), 20 nM sERBB4 (sB4), or 20 nM sErbB4 after a 24 h pretreatment with 20 µM of the γ-secretase inhibitor DAPT (DAPT). Neurons were fixed and stained using an antibody directed against the Nrg1 ICD and counterstained with DAPI. Scale bar, 10 µm. Right, Quantification of nuclear clusters of Nrg1-ICD. Neurons from WT mice show increased nuclear ICD clusters in response to sB4 stimulation, which is counteracted by pretreatment with DAPT (DAPT). Neurons from V 321 L mice do not respond to sB4 stimulation ( N = 6–13 neurons, 3 platings/mouse, 3 mice/genotype; one-way ANOVA p values corrected for multiple comparisons using Tukey’s post hoc test; WT Veh vs WT sB4, p < 0.0001 (****); WT sB4 vs WT sB4 + DAPT, **** p < 0.0001; WT sB4 vs V 321 L Veh, **** p < 0.0001; WT sB4 vs V 321 L B4, **** p < 0.0001). All other comparisons are statistically not statistically significant. D , Cortical neurons from embryonic WT (dark blue) and V 321 L mice (light blue; E18.5) were cultured for DIV3 and were stimulated with soluble ErbB4 (sB4), PI3K inhibitor WM, γ-secretase inhibitor L-685,458 (L6), WM + B4, or L6 + B4. Neurons that underwent no drug treatments/sB4 stimulation are indicated as the control group (C). Neurons were fixed and axonal length was quantified. (Two-way ANOVA with Tukey’s post hoc correction, WT C vs WT B4, **** p = 0.0002; WT L6 vs WT L6 + B4, ** p = 0.0047; V 321 L C vs V 321 L B4, *** p = 0.001; V 321 L WM vs V 321 L WM + B4, p = 0.1; V 321 L L6 vs V 321 L L6 + B4, * p = 0.03.) N = 20–37 neurons per genotype per condition. ns, not significant. E , Treatment and conditions same as in D . Quantification is for dendritic length. (two-way ANOVA w/ Tukey’s post hoc correction: WT C vs WT B4, ** p = 0.002; WT WM vs WT WM + B4, **** p < 0.0001). N = 20–37 neurons per genotype per condition. ns, not significant.

Article Snippet: Recombinant mouse ErbB4/Her4 Fc chimera protein, CF , R&D Systems , Catalog #4387-ER-050.

Techniques: Western Blot, Isolation, Control, Marker, Membrane, Positive Control, Transfection, Plasmid Preparation, Labeling, Cell Culture, In Vitro, Staining

Journal: Cell

Article Title: Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration

doi: 10.1016/j.cell.2024.07.041

Figure Lengend Snippet:

Article Snippet: Gapdh (ThermoFisher, Mm99999915_g1) served as a normalization factor for all gene probes.

Techniques: Virus, Plasmid Preparation, Recombinant, Control, Protease Inhibitor, RNAscope, Multiplex Assay, Negative Control, Software, Modification

Journal: Current biology : CB

Article Title: RNA degradation is required for the germ-cell to maternal transition in Drosophila

doi: 10.1016/j.cub.2021.04.052

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Anti-mouse HRP , Jackson ImmunoResearch Labs , Code:115–035-003.

Techniques: Virus, Recombinant, Plasmid Preparation, Protease Inhibitor, SYBR Green Assay, RNAscope, Western Blot, Mutagenesis, Control, Cloning, Labeling, Transformation Assay, Sequencing, Software

Journal: Cell reports

Article Title: Runx2+ Niche Cells Maintain Incisor Mesenchymal Tissue Homeostasis through IGF Signaling

doi: 10.1016/j.celrep.2020.108007

Figure Lengend Snippet: (A) Heatmap hierarchical clustering showing the gene expression profiles of Runx2 fl / fl (control) and Gli1 - Cre ERT2 ; Runx2 fl / fl (mutant) mice one week after induction at one month of age. (B) Volcano plot revealing that 299 genes were upregulated and 212 genes were downregulated (>2-fold, p < 0.05) in Gli1 - Cre ERT2 ; Runx2 fl / fl mice. (C) IPA based on RNA-seq data. (D) Immunostaining of Igf2 (a and c), p-Igf1r (e and g), p-Irs1 (i and k), and p-Akt (m and o) in incisors from Runx2 fl / fl mice (a, e, i, and m) and Gli1 - Cre ERT2 ; Runx2 fl / fl mice (c, g, k, and o) 1 week after induction at 1 month of age. (b, d, f, h, j, l, n, and p) High-magnification images of the insets in (a), (c), (e), (g), (i), (k), (m), and (o), respectively. Arrows indicate a positive signal, and asterisks indicate the absence of a signal. (E) Western blot of Igf2, p-Igf1r, Igf1r, p-Irs1, Irs1, p-Akt, and Akt in the incisor mesenchyme from Runx2 fl / fl (control) and Gli1 - Cre ERT2 ; Runx2 fl / fl (mutant) mice one week after induction. (F) Igfbp3 RNAscope and Runx2 immunostaining of incisor from Runx2 fl / fl mice (a) and Gli1 - Cre ERT2 ; Runx2 fl / fl mice (c) 1 week after induction at 1 month of age. (b and d) High-magnification images of the insets in (a) and (c), respectively. (e) Real-time PCR analysis of Igfbp3 in the incisor mesenchyme from Runx2 fl / fl and Gli1 - Cre ERT2 ; Runx2 fl / fl mice 1 week after induction at 1 month of age. n = 3/group, *p < 0.05. Arrows indicate coexpression of the Igfbp3 mRNA and Runx2 protein, and asterisks indicate the absence of a signal. (G) ELISA showing the secreted Igf2 in the culture medium supernatant from the MSCs of Runx2 fl / fl (control) and Gli1 - Cre ERT2 ; Runx2 fl / fl (mutant) mice with or without Igfbp3 protein. n = 3, ***p < 0.001. (H) ATAC-seq analysis of the incisor mesenchyme from 1-month-old wild-type mice. The black box indicates the Runx2 binding motif located at the promoter of Igfbp3 . (I) ChIP with Runx2 antibody (or immunoglobulin G [IgG]), followed by qPCR to compare levels of Runx2 the near transcription start site of Igfbp3 , in the incisor mesenchyme from 1-month-old wild-type mice. n = 4, **p < 0.01. The schematic at the bottom of each group of subpanels shows tamoxifen induction protocols. The white dotted line in (D) and (F) shows the cervical loop. All data are represented as mean ± SEM. Scale bars, (D) 50 μm, (F) 100 μm.

Article Snippet: After 80% confluency, the culture plate was washed with Phosphate-buffered saline (PBS) for three times and then added 200 μL serum-free media, i.e., α-MEM with or without 50nM mouse recombinant Igfbp3 protein (R&D Systems, 775-B3).

Techniques: Gene Expression, Control, Mutagenesis, RNA Sequencing, Immunostaining, Western Blot, RNAscope, Real-time Polymerase Chain Reaction, Enzyme-linked Immunosorbent Assay, Binding Assay

Journal: Cell reports

Article Title: Runx2+ Niche Cells Maintain Incisor Mesenchymal Tissue Homeostasis through IGF Signaling

doi: 10.1016/j.celrep.2020.108007

Figure Lengend Snippet:

Article Snippet: After 80% confluency, the culture plate was washed with Phosphate-buffered saline (PBS) for three times and then added 200 μL serum-free media, i.e., α-MEM with or without 50nM mouse recombinant Igfbp3 protein (R&D Systems, 775-B3).

Techniques: Recombinant, Protease Inhibitor, TUNEL Assay, In Situ, Imaging, RNAscope, Multiplex Assay, cDNA Synthesis, Enzyme-linked Immunosorbent Assay, Software

Journal: Cell

Article Title: Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration

doi: 10.1016/j.cell.2024.07.041

Figure Lengend Snippet:

Article Snippet: Quantitative PCR was performed with TaqMan probes for target genes Hr (ThermoFisher, Mm00498963_m1), Dio1 (ThermoFisher, Mm00839358_m1), Cyp11a1 (ThermoFisher, Mm00490735_m1), and Ier5 (ThermoFisher, Mm01295615_s1) using a standard protocol on a QuantStudio 3 (ThermoFisher, A28567).

Techniques: Virus, Plasmid Preparation, Recombinant, Control, Protease Inhibitor, RNAscope, Multiplex Assay, Negative Control, Software, Modification