Journal: BMC Immunology

Article Title: Establishment and validation of a recurrent prediction model for glioma: extrinsic apoptotic molecules FADD and CASP8 are closely associated with glioma recurrence

doi: 10.1186/s12865-025-00746-z

Figure Lengend Snippet: Biological functions associated with the recurrent scores. (A-B) The recurrent score related biological process revealed by Gene ontology analysis in the CGGA 693 and CGGA 325 database . (C-D) The heatmap showed the recurrent score and the enrichment scores of apoptosis-related functions of each patient in the CGGA 693 and CGGA 325 database. The samples were arranged in ascending order of the recurrent score. The column graph and line graph on the right showed the R -value and P -value of the correlation analysis. (E) Flow chart for recurrent score correlation analysis. (F-G) Using Pearson correlation analysis, the top 18 apoptosis-related genes mostly correlated with recurrent score were selected in CGGA 693 and CGGA 325 database. (H-I) The relationship between recurrent score and 6 apoptosis-related genes in glioma. The correlation coefficients were demonstrated as the proportion of the pie charts. The bottom right showed the correlation coefficient. The red parts represented a positive correlation. The correlation was tested by Pearson correlation analysis. (J) Correlation between the expression of the 6 genes in CGGA 693 and CGGA 325 database. ( K ) Expression levels of the 6 genes in primary glioma and recurrent glioma in CGGA 325 database and CGGA 693 database. (L) Survival analyses of the 6 genes by Kaplan-Meier curves and log-rank tests based on CCGA 693 database and CGGA 325 database. ( M ) Protein levels of SH3GLB1, NEK6, CASP8 and ITGB1 in normal tissues and GBM from The Human Protein Atlas database

Article Snippet: Characterizing the differential expression patterns of CASP8 and FADD in gliomas and normal tissues will play a crucial role in the further development of targeted therapeutic strategies for gliomas Fig. 9 RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Techniques: Expressing

Journal: BMC Immunology

Article Title: Establishment and validation of a recurrent prediction model for glioma: extrinsic apoptotic molecules FADD and CASP8 are closely associated with glioma recurrence

doi: 10.1186/s12865-025-00746-z

Figure Lengend Snippet: The association between recurrent score and classical apoptotic genes. (A) The relationship between the 6 genes and recurrent score in CGGA and TCGA database . (B) PPI network of CASP3, CASP9, FADD, CASP7, CASP8, BCL2，and the 9-gene signature from the STRING. (C-D) The expression levels of the 6 apoptotic genes in low- and high-risk levels . (E-J) Correlation between recurrent score and expression levels of apoptotic genes. *P<0.05; ***P<0.001; ns, not significant

Article Snippet: Characterizing the differential expression patterns of CASP8 and FADD in gliomas and normal tissues will play a crucial role in the further development of targeted therapeutic strategies for gliomas Fig. 9 RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Techniques: Expressing

Journal: BMC Immunology

Article Title: Establishment and validation of a recurrent prediction model for glioma: extrinsic apoptotic molecules FADD and CASP8 are closely associated with glioma recurrence

doi: 10.1186/s12865-025-00746-z

Figure Lengend Snippet: RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Article Snippet: Characterizing the differential expression patterns of CASP8 and FADD in gliomas and normal tissues will play a crucial role in the further development of targeted therapeutic strategies for gliomas Fig. 9 RNA and protein levels of CASP8 and FADD in normal tissues and tumors. (A-B) RNA expression of CASP8 and FADD in normal tissues from the NCBI database (https://www.ncbi.nlm.nih.gov/). (C-D) RNA expression of CASP8 and FADD in normal tissues from the Human Protein Atlas database (https://www.proteinatlas.org/). (E) Protein levels of CASP8 and FADD in normal brain tissues from The Human Protein Atlas database. (F) Protein levels of CASP8 and FADD in normal tissues from The Human Protein Atlas database. (G) Protein levels of CASP8 and FADD in tumors from The Human Protein Atlas database

Techniques: RNA Expression

Journal: Human Molecular Genetics

Article Title: PD-linked CHCHD2 mutations impair CHCHD10 and MICOS complex leading to mitochondria dysfunction

doi: 10.1093/hmg/ddy413

Figure Lengend Snippet: PD-linked CHCHD2 mutants showed reduced binding to CHCHD10. ( A ) Co-immunoprecipitation of endogenous CHCHD2 by antibody against CHCHD2 in SK-N-SH cells. WCL: whole cell lysate, 5% total protein used in co-IP experiment. ( B ) Co-immunoprecipitation of endogenous CHCHD10 by antibody against CHCHD10 in SK-N-SH cells. WCL: whole cell lysate, 5% total protein used in co-IP experiment. ( C ) Co-immunoprecipitation of endogenous CHCHD2 by antibody against CHCHD2 in human brain tissue lysates. ( D ) Co-immunoprecipitation of CHCHD2 by a CHCHD2 antibody against middle region of CHCHD2 (labeled as CHCHD2-TF) in SK-N-SH cells transfected with non-tagged CHCHD2 WT/T61I/R145Q/Q126X. WCL: whole cell lysate, 5% total protein used in co-IP experiment. Lower arrow pointed to CHCHD2 Q126X and higher arrow pointed to full length CHCHD2. ( E ) Co-immunoprecipitation of CHCHD2 by a CHCHD2 antibody against middle region of CHCHD2 (labeled as CHCHD2-TF) in hESCs of H9 and isogenic lines harboring homozygous R145Q (−/−).WCL: whole cell lysate, 5% total protein used in co-IP experiment. Arrow pointed to CHCHD10. Representative results from R10 and R17 (R145Q−/−) were shown. ( F ) Quantification of protein abundance of CHCHD10 normalized with CHCHD2 on the co-immunoprecipitation complex from isogenic hESC lysates.

Article Snippet: Human brain tissue lysates were from Novus Centennial, CO. Elamipretide was from MedChemExpress Monmouth Junction, NJ.

Techniques: Binding Assay, Immunoprecipitation, Co-Immunoprecipitation Assay, Labeling, Transfection, Quantitative Proteomics

Journal: The European journal of neuroscience

Article Title: Cholesterol-recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: The case of TRKB.

doi: 10.1111/ejn.15218

Figure Lengend Snippet: FIGURE 1 (a) Workflow of data mining. The TMR (transmembrane sequence +5 amino acid residues from each N- and C-terminal sides) of curated entries found in UniProt using the code for tyrosine-kinase receptor family (2.7.10.1) were screened for the presence of cholesterol recognition and alignment consensus (CRAC and CARC). The incidence of CRAC and CARC motifs in (b) human, (c) mouse, (d) zebrafish, (e) fruit fly, and (f) C. elegans TMR of RTK family members. (g) Library of CRAC and CARC sequences (all combinations used can be found in the stored data). Residue sequence predicted to be embedded into the cell membrane shown in yellow

Article Snippet: The plates were washed 3× with PBS buffer, and a mixture of biotinylated BDNF (bBDNF: 0, 0.05, 0.1, 0.5, 1, 5, or 10 ng/ml, Alomone Labs, #B- 250- B) and cholesterol (0, 20, 50 or 100 μM) was added for 1h at room temperature, followed by washing with PBS.

Techniques: Sequencing, Residue, Membrane

Journal: The European journal of neuroscience

Article Title: Cholesterol-recognition motifs in the transmembrane domain of the tyrosine kinase receptor family: The case of TRKB.

doi: 10.1111/ejn.15218

Figure Lengend Snippet: FIGURE 3 TRKB interaction with cholesterol. (a,b) Snapshots of the interaction between TRKB and cholesterol at the TMR (see supplement video) indicating that cholesterol (orange) interacts with the OH- group (red) in Y433 (cyan) of the TRKB.TMR (green). The TRKB.TMR helix is shown in the cartoon, the lipids and Y433 sidechain in van der Waals representations. (c) Molecular dynamics simulations show that cholesterol predominantly resides close to the C-alpha atom of Y433 but not C-alpha atom of R427, highlighting the significance of the aromatic Y in the TRKB CARC domain. (d) The binding of biotinylated BDNF (bBDNF) to TRKB is modulated by added cholesterol in a bell-shaped fashion [from Scatchard analysis Kd for bBDNF ctrl: 2.77 pM; chol 20 μM: 2.27pM; chol 50 μM: 2.61 pM; chol 100 μM: 1.93 pM; Bmax for bBDNF ctrl: 96.18; chol 20 μM: 108.9; chol 50 μM: 80.81; chol 100 μM: 65.35]. Curves from the Scatchard transformation of the TRKB:BDNF binding are depicted in the insert. Data expressed as mean/SEM of binding normalized by bBDNF10 ng/ml ctrl (no added cholesterol). (e) Expansion of the binding of bBDNF 1 ng/ml (black circles) and bBDNF 0 (ctrl, open circles), depicting the bell-shaped effect of different concentrations of cholesterol on bBDNF:TRKB interaction. Data expressed as mean/SEM of binding normalized by bBDNF 1 ng/ml ctrl. (f) Unlabeled BDNF (0-20 ng/ ml) dislocates bBDNF (1 ng/ml) binding to immobilized TRKB assayed at no supplemented cholesterol (0 μM). Data expressed as mean/SEM normalized by bBDNF 1 ng/ml at BDNF 0 ng/ml. *p < .05 from control (BDNF 1 ng/ml–cholesterol ctrl, R427)

Article Snippet: The plates were washed 3× with PBS buffer, and a mixture of biotinylated BDNF (bBDNF: 0, 0.05, 0.1, 0.5, 1, 5, or 10 ng/ml, Alomone Labs, #B- 250- B) and cholesterol (0, 20, 50 or 100 μM) was added for 1h at room temperature, followed by washing with PBS.

Techniques: Binding Assay, Transformation Assay, Control

Journal: Brain Sciences

Article Title: Neonatal Handling Positively Modulates Anxiety, Sensorimotor Gating, Working Memory, and Cortico-Hippocampal Neuroplastic Adaptations in Two Genetically Selected Rat Strains Differing in Emotional and Cognitive Traits

doi: 10.3390/brainsci15080776

Figure Lengend Snippet: Western blot analysis of the BDNF ( A , B ), trkB ( C , D ), and the PSA-NCAM ( E , F ), in the prefrontal (prelimbic/infralimbic) cortex of the RHA and the RLA rats, either untreated controls (CTRL) or treated with neonatal handling (NH). The values represent the densitometric analysis of the BDNF/GAPDH ( B ), trkB/GAPDH ( D ), and the PSA-NCAM/GAPDH ( F ) band grey optical density (O.D.) ratios. The bars denote the mean ± S.E.M. of 9–10 rats, in each experimental group. ***: p < 0.001 (post hoc Duncan’s multiple range test).

Article Snippet: Molecular weight (mw) standards (Precision Plus Protein Western C Standards, Cat# 161–0376, Bio-Rad, Hercules, CA, USA) and recombinant human BDNF protein (rhBDNF) (Cat# B-257, Alomone Labs, Jerusalem, Israel) were run in parallel.

Techniques: Western Blot

Journal: Brain Sciences

Article Title: Neonatal Handling Positively Modulates Anxiety, Sensorimotor Gating, Working Memory, and Cortico-Hippocampal Neuroplastic Adaptations in Two Genetically Selected Rat Strains Differing in Emotional and Cognitive Traits

doi: 10.3390/brainsci15080776

Figure Lengend Snippet: Western blot analysis of the BDNF ( A , B ), trkB ( C , D ), and the PSA-NCAM ( E , F ), in the anterior cingulate cortex of the RHA and the RLA rats, either untreated controls (CTRL) or treated with neonatal handling (NH). The values represent the densitometric analysis of the BDNF/GAPDH ( B ), trkB/GAPDH ( D ), and the PSA-NCAM/GAPDH ( F ) band grey optical density (O.D.) ratios. The bars denote the mean ± S.E.M. of 9–10 rats, in each experimental group. **: p < 0.01 (post hoc Duncan’s multiple range test).

Article Snippet: Molecular weight (mw) standards (Precision Plus Protein Western C Standards, Cat# 161–0376, Bio-Rad, Hercules, CA, USA) and recombinant human BDNF protein (rhBDNF) (Cat# B-257, Alomone Labs, Jerusalem, Israel) were run in parallel.

Techniques: Western Blot

Journal: Brain Sciences

Article Title: Neonatal Handling Positively Modulates Anxiety, Sensorimotor Gating, Working Memory, and Cortico-Hippocampal Neuroplastic Adaptations in Two Genetically Selected Rat Strains Differing in Emotional and Cognitive Traits

doi: 10.3390/brainsci15080776

Figure Lengend Snippet: Western blot analysis of the BDNF ( A , B ), trkB ( C , D ), and the PSA-NCAM ( E , F ), in the ventral hippocampus of the RHA and the RLA rats, either untreated controls (CTRL) or treated with neonatal handling (NH). The values represent the densitometric analysis of the BDNF/GAPDH ( B ), trkB/GAPDH ( D ), and the PSA-NCAM/GAPDH ( F ) band grey optical density (O.D.) ratios. The bars denote the mean ± S.E.M. of 9–10 rats, in each experimental group. *: p < 0.05; **: p < 0.02 (post hoc Duncan’s multiple range test).

Article Snippet: Molecular weight (mw) standards (Precision Plus Protein Western C Standards, Cat# 161–0376, Bio-Rad, Hercules, CA, USA) and recombinant human BDNF protein (rhBDNF) (Cat# B-257, Alomone Labs, Jerusalem, Israel) were run in parallel.

Techniques: Western Blot

Journal: Brain Sciences

Article Title: Neonatal Handling Positively Modulates Anxiety, Sensorimotor Gating, Working Memory, and Cortico-Hippocampal Neuroplastic Adaptations in Two Genetically Selected Rat Strains Differing in Emotional and Cognitive Traits

doi: 10.3390/brainsci15080776

Figure Lengend Snippet: Western blot analysis of the BDNF ( A , B ), trkB ( C , D ), and the PSA-NCAM ( E , F ), in the dorsal hippocampus of the RHA and the RLA rats, either untreated controls (CTRL) or treated with neonatal handling (NH). The values represent the densitometric analysis of the BDNF/GAPDH ( B ), trkB/GAPDH ( D ), and the PSA-NCAM/GAPDH ( F ) band grey optical density (O.D.) ratios. The bars denote the mean ± S.E.M. of 9–10 rats, in each experimental group.

Article Snippet: Molecular weight (mw) standards (Precision Plus Protein Western C Standards, Cat# 161–0376, Bio-Rad, Hercules, CA, USA) and recombinant human BDNF protein (rhBDNF) (Cat# B-257, Alomone Labs, Jerusalem, Israel) were run in parallel.

Techniques: Western Blot

Journal: FEBS letters

Article Title: miR-190a inhibits epithelial-mesenchymal transition of hepatoma cells via targeting the long non-coding RNA treRNA.

doi: 10.1016/j.febslet.2015.11.024

Figure Lengend Snippet: Fig. 3. Suppression of treRNA by miR-190a inhibits EMT in HCC. (A) 20 nM miR-190a, 20 nM siRNA duplexes against treRNA (si-treRNA1 or sitreRNA2), 20 nM miR-190a, or NC RNA was transfected into Huh-7 or HepG2 cells. EMT related genes were quantified 72 h post-transfection as indicated. (B) Cells were treated with antagomiR (anti-miR- 190a) or NC RNA as in (A). The mRNA level of different EMT genes was quantified and normalized to b-actin. (C) Cell lysates were blotting with EMT marker E-cadherin (E-cad), Claudin-1 (Claud), Vimentin (Vimen), N-cadherin (N-cad), SNAI1 (Snail). b-Actin was used as endogenous control. The EMT marker expression level in was calculated using Image J and presented as histogram (right panel). (D) Cells were treated with TGF-b for 12 h and transfected with 20 nM miR-190a, 20 nM siRNA duplexes against treRNA (si-treRNA1 or si-treRNA2) or NC RNA subsequently. The morphological change was captured 24 h after transfection.

Article Snippet: Membranes were blocked by 5% BSA or 5% non-fat milk for 3 h at 25 C and incubated with primary antibody against Ago2 (#2897, Cell Signaling, US), Dicer (#5362, Cell Signaling), E-Cadherin (#3195, Cell Signaling), Claudin-1 (#13255, Cell Signaling), Vimentin (#5741, Cell Signaling), N-Cadherin (#13116, Cell Signaling), SNAI1 (#3897, Cell Signaling), or b-actin (C-4, Santa cruz, US) for 12 h at 4 C. Membranes were incubated with secondary antibody diluted in Tris-buffered saline supplemented with 0.5% Tween-20 and 5% BSA or 5% non-fat milk for 1 h at 25 C. The signal was detected with the enhanced chemiluminescence system (Pierce, US) and exposed to X-ray film (Kodak, US).

Techniques: Transfection, Marker, Control, Expressing