Journal: BMC Pediatrics

Article Title: Predicting neuroblastoma prognosis using machine learning analysis of metabolism-related gene network perturbation

doi: 10.1186/s12887-026-06512-3

Figure Lengend Snippet: Validation of UCK2 in clinical tissues. Immunohistochemistry staining was used to evaluate the UCK2 expression in NB and ganglioneuroma tissues

Article Snippet: The slides were then treated with a nonspecific sodium citrate antigen repair solution (pH 6.0), 3% bovine serum albumin before undergoing sequential incubation with an anti-UCK2 antibody (10511-1-AP, Proteintech) and HRP-conjugated secondary antibodies (SA00001-2, Proteintech).

Techniques: Biomarker Discovery, Immunohistochemistry, Staining, Expressing

Journal: PLoS ONE

Article Title: Tissue-Specific Differences in DNA Modifications (5-Hydroxymethylcytosine, 5-Formylcytosine, 5-Carboxylcytosine and 5-Hydroxymethyluracil) and Their Interrelationships

doi: 10.1371/journal.pone.0144859

Figure Lengend Snippet: Transition patterns and specific detector settings for all analyzed compounds.

Article Snippet: Stable-isotope-labelled internal standards of [ 15 N-U, 13 C-U]-2′-deoxythymidine were purchased from Cambridge Isotope Laboratories, [D 3 ]-5-hydroxymethyl-2'-deoxycytidine from Toronto Research Chemicals (Toronto, Canada).

Techniques: Formulation

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 1. Structure and activity of APOBEC3B constructs. (A) Align- ment between parts of A3G and A3B sequences is shown. The sec- ondary structural elements within A3G [21] are shown as boxes above the sequences. The amino-terminal ends of 193-CTD, 195-CTD and 187-CTD are indicated by arrows. (B) Results of KanR reversion assay for 195-CTDintheabsenceofIPTG in the host BH214. The horizontal lines within the data points represent the median values. (C) KanR revertants due to 195-CTD following induction of its transcription using 50 μM or 100 μM IPTG. ** represents P value of b0.01. (D) The results of KanR

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Activity Assay, Construct

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 2. KanR reversion and RifR mutation assay for APOBEC3B mutants. (A) Effect of D194A mutation on KanR

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Mutagenesis

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 4. Preliminary characterization of purified APOBEC3B 193-CTD. (A) Stability of 193-CTD during reaction incubations. The ability of 193-CTD protein to convert cytosine into uracil is quantified following pre-incubations for different lengths of time. (B) Ability of 193-CTD to turn over. The amount of product generated by the enzyme is shown under two different ratios of substrate to enzyme.

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Purification, Generated

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 5. Inability of APOBEC3B NTD to deaminate cytosines. (A) KanR reversion assay for A3B NTD. The revertant frequencies due to the NTD are compared to full-length A3B and the empty vector. (B) Lack of cytosine deamination activity for partially purified NTD. The TCGA-40 substrate (2 pmol) was incubated with different amounts of the NTD alone (lanes 4, 6 and 8, respectively) or together with 10 pmol of 193-CTD (lanes 5, 7 and 9).

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Plasmid Preparation, Activity Assay, Purification, Incubation

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 6. Ability of APOBEC3B to deaminate 5mCs. (A) Comparison of KanR revertant frequencies due to conversion of 5mC into T. The abilities of 193-CTD, 187-CTD and full-length A3B to deaminate 5mC are compared with empty vector and A3A. ** represents P value of b0.01 and *** represents P value of b0.001. (B) Comparison of kinetics of cytosine and 5mC deamination by 193-CTD. DNA oligomers containing a single C or 5mC in the indicated sequence context were treated with increasing concentrations of purified 193-CTD and the products were quantified. (C) Kinetics of cytosine and 5mC deamination by partially purified A3A.

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Comparison, Plasmid Preparation, Sequencing, Purification

Journal: Journal of molecular biology

Article Title: Characterization of the Catalytic Domain of Human APOBEC3B and the Critical Structural Role for a Conserved Methionine.

doi: 10.1016/j.jmb.2015.08.006

Figure Lengend Snippet: Fig. 7. Sequence alignment of APOBEC3B CTD and APOBEC3 proteins with known structures. Clustal Omega alignment of APOBEC3 single-domain proteins (A3A and A3C) and CTD of two-domain proteins (A3F and A3G) with A3B CTD are shown. The structural motifs are shown according the structure of A3G CTD [21]. The conserved methionine at the junction of NTD and CTD is marked with a green arrow. All the conserved residues between the five proteins are shown in blue and marked by asterisks. The residues that line the hydrophobic pocket in which the conserved methionine resides are shown in red and are marked with a dot.

Article Snippet: The full length of APOBEC3B was amplified from the human APOBEC3B cDNA purchased from OriGene Technologies (Rockville, MD) and cloned into vector plasmid pSU24 as HindIII-KpnI fragments.

Techniques: Sequencing

Journal: Biological & pharmaceutical bulletin

Article Title: Z-360, a novel cholecystokinin-2/gastrin receptor antagonist, inhibits gemcitabine-induced expression of the vascular endothelial growth factor gene in human pancreatic cancer cells.

doi: 10.1248/bpb.33.216

Figure Lengend Snippet: Fig. 1. Changes of Genes Expression in Human Pancreatic Carcinoma Cells Treated with Gemcitabine

Article Snippet: Gemcitabine hydrochloride (for in vitro analysis) was purchased from Toronto Research Chemicals Inc. (North York, Canada).

Techniques: Expressing

Journal: Biological & pharmaceutical bulletin

Article Title: Z-360, a novel cholecystokinin-2/gastrin receptor antagonist, inhibits gemcitabine-induced expression of the vascular endothelial growth factor gene in human pancreatic cancer cells.

doi: 10.1248/bpb.33.216

Figure Lengend Snippet: Fig. 2. Effect of Z-360 on Gemcitabine-Induced Genes Expression in PANC-1 Cells

Article Snippet: Gemcitabine hydrochloride (for in vitro analysis) was purchased from Toronto Research Chemicals Inc. (North York, Canada).

Techniques: Expressing

Journal: Biological & pharmaceutical bulletin

Article Title: Z-360, a novel cholecystokinin-2/gastrin receptor antagonist, inhibits gemcitabine-induced expression of the vascular endothelial growth factor gene in human pancreatic cancer cells.

doi: 10.1248/bpb.33.216

Figure Lengend Snippet: Fig. 3. Effect of CCK-2/Gastrin Antagonists on Gemcitabine-Induced VEGF Expression in PANC-1 Cells

Article Snippet: Gemcitabine hydrochloride (for in vitro analysis) was purchased from Toronto Research Chemicals Inc. (North York, Canada).

Techniques: Expressing

Journal: Biological & pharmaceutical bulletin

Article Title: Z-360, a novel cholecystokinin-2/gastrin receptor antagonist, inhibits gemcitabine-induced expression of the vascular endothelial growth factor gene in human pancreatic cancer cells.

doi: 10.1248/bpb.33.216

Figure Lengend Snippet: Fig. 4. Effect of Z-360 on Gemcitabine-Induced VEGF Protein Expres- sion Levels in Conditioned Media from PANC-1 Cells

Article Snippet: Gemcitabine hydrochloride (for in vitro analysis) was purchased from Toronto Research Chemicals Inc. (North York, Canada).

Techniques:

Journal: Biological & pharmaceutical bulletin

Article Title: Z-360, a novel cholecystokinin-2/gastrin receptor antagonist, inhibits gemcitabine-induced expression of the vascular endothelial growth factor gene in human pancreatic cancer cells.

doi: 10.1248/bpb.33.216

Figure Lengend Snippet: Fig. 5. Effects of Z-360 on Gemcitabine-Induced Gene Expression in Orthotopic Xenografts

Article Snippet: Gemcitabine hydrochloride (for in vitro analysis) was purchased from Toronto Research Chemicals Inc. (North York, Canada).

Techniques: Gene Expression

Journal: Biological & pharmaceutical bulletin

Article Title: Z-360, a novel cholecystokinin-2/gastrin receptor antagonist, inhibits gemcitabine-induced expression of the vascular endothelial growth factor gene in human pancreatic cancer cells.

doi: 10.1248/bpb.33.216

Figure Lengend Snippet: Fig. 6. Effect of Z-360 and Gemcitabine on VEGFA Protein Expression Levels in Orthotopically Implanted PANC-1 Xenograft

Article Snippet: Gemcitabine hydrochloride (for in vitro analysis) was purchased from Toronto Research Chemicals Inc. (North York, Canada).

Techniques: Expressing

Journal: PLoS Pathogens

Article Title: Reassessing the Role of APOBEC3G in Human Immunodeficiency Virus Type 1 Infection of Quiescent CD4+ T-Cells

doi: 10.1371/journal.ppat.1000342

Figure Lengend Snippet: (A) Quiescent CD4+ T-cells were purified from freshly isolated PBMCs of two independent donors with CD4 magnetic beads and nucleofected with siRNA targeting APOBEC3G (siA3G 883 ), conjugated with (FITC) or without FITC (None). Cells were analyzed by flow cytometry 3 hr after nucleofection. (B) To monitor the integrity of the RNAi machinery, quiescent CD4+ T-cells derived from PBMCs were nucleofected with siRNA targeting CD4 (siCD4), control siRNA (siControl), or no siRNA (None). The levels of cell surface CD4 expression were monitored by flow cytometry using PE-conjugated anti-CD4 antibody or isotype-matched control 48 hr after nucleofection and represented by mean fluorescent intensity (MFI) in each panel. The solid line represents PE-CD4 antibody stained cells, whereas the shaded area represents isotype control staining.

Article Snippet: After blocking with 5% skim milk in PBS with 0.05% Tween-20 (PBS-T), membranes were reacted with either polyclonal anti-APOBEC3G antibody (Cat. No. 10201, NIH AIDS Research and Reference Reagent Program) or polyclonal anti-β-Actin (Rockland Immunochemicals Inc., Gilbertsville, PA).

Techniques: Purification, Isolation, Magnetic Beads, Flow Cytometry, Derivative Assay, Control, Expressing, Staining

Journal: PLoS Pathogens

Article Title: Reassessing the Role of APOBEC3G in Human Immunodeficiency Virus Type 1 Infection of Quiescent CD4+ T-Cells

doi: 10.1371/journal.ppat.1000342

Figure Lengend Snippet: (A) Quiescent CD4+ T-cells derived from PBMCs were nucleofected with siRNAs and cultured for two days. Total RNA was isolated, and the levels of APOBEC3G mRNA were monitored by quantitative real time RT-PCR using β-actin as an internal control . P values (asterisks) versus control siRNA were 0.00022 (siA3G 240 WT ), 0.00013 (siA3G 726 ), 0.00005 (siA3G 883 ), respectively. (B) Quiescent CD4+ T-cells derived from PBMCs were nucleofected with siRNAs and cultured for two days. Cells were lysed in 0.5% SDS, and the levels of APOBEC3G protein were monitored by Western blotting. β-actin was used as a loading control.

Article Snippet: After blocking with 5% skim milk in PBS with 0.05% Tween-20 (PBS-T), membranes were reacted with either polyclonal anti-APOBEC3G antibody (Cat. No. 10201, NIH AIDS Research and Reference Reagent Program) or polyclonal anti-β-Actin (Rockland Immunochemicals Inc., Gilbertsville, PA).

Techniques: Derivative Assay, Cell Culture, Isolation, Quantitative RT-PCR, Control, Western Blot