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: bioRxiv

Article Title: XIST Drives X-Chromosome Inactivation and Safeguards Female Extraembryonic Cells in Humans

doi: 10.1101/2025.11.19.689206

Figure Lengend Snippet: A. Schematic illustration showing wild type (WT) and XIST inducible knock down (iKD) H9 naive hESCs under trophoblast differentiation medium with or without Doxycycline (Dox) and assaying cell identity and X-chromosome inactivation using microscopy, scRNA-seq, bulk RNA-seq and flow cytometry. B. Representative bright-field microscopy images showing the morphology of H9 XIST iKD clone-1 hESCs at Day 15 of culture in trophoblast differentiation medium with or without Dox. Note: Feeders only are seen in the +Dox conditions. Scale bar, 200 µm. The experiment was performed in 3 independent XIST iKD clones of H9 hESCs. Out of which one is shown here and the other two are shown in figure S5E (total n=3 independent clones). C. Representative IF of GATA3 (Green) of cells mentioned in 4B. DAPI is shown in blue. Scale bar, 20 µm. The experiment was performed in 3 independent XIST iKD clones of H9 hESCs. Out of which one is shown here and the other two are shown in figure S5F (total n=3 independent clones). D. The proportion of GATA3 positive nuclei in both WT and XIST iKD H9 hESCs at Day 15 of trophoblast differentiation with or without Dox. The number of nuclei counted is indicated above each bar. Each dot represents one of three independent XIST iKD clones (n=3) or WT clones (n=3). Statistical significance was assessed using a t-test. A p-value <0.05 was considered statistically significant. The number of nuclei counted is indicated in supplemental table S1. E. Flow cytometry quantification of the proportion of ENPEP positive cells at day 15 of trophoblast differentiation of XIST iKD hESCs with or without Dox. Statistical significance was tested using a Chi² test, resulting in p<0,0001. Each dot represents one of three independent XIST iKD clones (n=3). F. UMAP of scRNA-seq time course during differentiation of H9 WT and XIST iKD hESCs with or without Dox under trophoblast culture conditions, 13 clusters are shown using different colors. The scRNA-seq data was generated using one of the above 3 clones both for the WT and the XIST iKD hESCs with or without Dox (n=1). G. As in 4F but colored by cell types. Lineage information where Naive = Naive epiblast, Differ Naive = Differentiated naive epiblast, Epi interim 1 = Epiblast intermediate type 1, Epi interim 2 = Epiblast intermediate type 2, Epi interim 3 = Epiblast intermediate type 3, Epi interim 4 = Epiblast intermediate type 4, TSC = Trohpblast stem cells, and EXMC = Extraembryonic mesoderm cells. H. UMAPs from showing the expression of KLF4 and DNMT3L (naive hESC markers), GATA3 and GATA2 (TSC markers), LUM and NID2 (EXMC markers) in time course scRNA-seq data. I. Dot plot showing the expression of marker genes for core pluripotency, naive pluripotency, trophoblast and embryo extraembryonic mesoderm (EXM) in time course scRNA-seq data from this study. J. The proportion of each cell type at different time points during differentiation of naive hESCs into TSCs and EXMCs. Colored by cell types. K. Differential gene expression as detected by scRNA-seq between Day 8 XIST iKD (Top) and WT cells (Bottom) with Dox vs without Dox. Dashed lines indicate -log10 adjusted p-Value <0.05 and log2 fold change < -0.5 or > 0.5. L. GO enrichment analysis of differentially expressed genes as a result of XIST depletion comparing Day 8 XIST iKD cells with and without Dox.

Article Snippet: In summary, starting from day 1 or day 2 after seeding primed hESCs in E8 onto Geltrex, cells were lipofected daily with KLF4 mRNA (Miltenyi, 130-101-115) for 9 days .

Techniques: Knockdown, Microscopy, RNA Sequencing, Flow Cytometry, Clone Assay, Generated, Expressing, Marker, Gene Expression

Journal: Evidence-based Complementary and Alternative Medicine : eCAM

Article Title: Vascular Protective Effects of Malus toringoides (Rehd.) Hughes Extracts and their Mechanism in Diabetic Rats and HUVECs

doi: 10.1155/2022/4348435

Figure Lengend Snippet: Effects of EMT on CX3CL1 expression in rat aortic histological sections and HUVECs. (a) Immunohistochemical detection of CX3CL1 expression in aortic sections from a diabetic rat model established for 6 weeks and administered treatment for 8 weeks. (b, c) HUVECs were pretreated for 12 h with the indicated concentrations of EMT and stimulated for 48 h with high glucose (25 mM). Western blot and ELISA analysis of CX3CL1 and CX3CR1 were performed as described in the materials and methods section. (d) After high glucose treatment, intense immunoreactions were observed in CX3CL1-positive cells (green), and blue staining of the nuclei was observed by DAPI. The values are mean ± SD of 3 independent experiments with triplicate samples. # P < 0.05 or ## P < 0.01 compared to the group treated with high glucose.

Article Snippet: ELISA kits for C-reactive protein (CRP, EK0978) tumor necrosis factor alpha (TNF- α , EK0526), interleukin 1 β (IL-1 β , EK0393), IL-6 (EK0412), VCAM-1 (EK0537), ICAM-1 (EK0370), E-selectin (EK0501) and CX3CL1 (EK0356) were obtained from BOSTER Biological Technology (Wuhan, China).

Techniques: Expressing, Immunohistochemical staining, Western Blot, Enzyme-linked Immunosorbent Assay, Staining

Journal: Frontiers in Endocrinology

Article Title: Positive Effects of Extra-Virgin Olive Oil Supplementation and DietBra on Inflammation and Glycemic Profiles in Adults With Type 2 Diabetes and Class II/III Obesity: A Randomized Clinical Trial

doi: 10.3389/fendo.2022.841971

Figure Lengend Snippet: Baseline sample characteristics, the DietBra Trial.

Article Snippet: Enzyme-linked immunosorbent assays were used to measure adiponectin (Human Adiponectin PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA), leptin (Human Leptin PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA), IL-1β, and IL-6 (Human IL-1β PicoKineTM ELISA Kit and Human IL-6 PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA, respectively) per manufacturer’s instructions.

Techniques:

Journal: Frontiers in Endocrinology

Article Title: Positive Effects of Extra-Virgin Olive Oil Supplementation and DietBra on Inflammation and Glycemic Profiles in Adults With Type 2 Diabetes and Class II/III Obesity: A Randomized Clinical Trial

doi: 10.3389/fendo.2022.841971

Figure Lengend Snippet: Comparisons of inflammatory biomarkers at the end of the intervention between two intervention groups. (A) TNF-α; (B) IL-1α; (C) MCP-1; (D) adiponectin; (E) IL-6; (F) leptin. Differences in TNF-α, MCP-1 adiponectin IL-6 and leptin were analyzed by the Mann-Whitney test and the difference in IL-lα was analyzed by the independent t-test. * p <0.05.

Article Snippet: Enzyme-linked immunosorbent assays were used to measure adiponectin (Human Adiponectin PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA), leptin (Human Leptin PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA), IL-1β, and IL-6 (Human IL-1β PicoKineTM ELISA Kit and Human IL-6 PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA, respectively) per manufacturer’s instructions.

Techniques: MANN-WHITNEY

Journal: Frontiers in Endocrinology

Article Title: Positive Effects of Extra-Virgin Olive Oil Supplementation and DietBra on Inflammation and Glycemic Profiles in Adults With Type 2 Diabetes and Class II/III Obesity: A Randomized Clinical Trial

doi: 10.3389/fendo.2022.841971

Figure Lengend Snippet: Comparison between baseline and final follow-up variables in two intervention groups with class II/III obesity, Brazil, 2016 (n = 40).

Article Snippet: Enzyme-linked immunosorbent assays were used to measure adiponectin (Human Adiponectin PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA), leptin (Human Leptin PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA), IL-1β, and IL-6 (Human IL-1β PicoKineTM ELISA Kit and Human IL-6 PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA, respectively) per manufacturer’s instructions.

Techniques: Comparison, Fat, Marker, Synthesized

Journal: Frontiers in Endocrinology

Article Title: Positive Effects of Extra-Virgin Olive Oil Supplementation and DietBra on Inflammation and Glycemic Profiles in Adults With Type 2 Diabetes and Class II/III Obesity: A Randomized Clinical Trial

doi: 10.3389/fendo.2022.841971

Figure Lengend Snippet: Comparison of changes (delta) in outcome variables between two intervention groups with class II/III obesity, Brazil (n = 34).

Article Snippet: Enzyme-linked immunosorbent assays were used to measure adiponectin (Human Adiponectin PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA), leptin (Human Leptin PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA), IL-1β, and IL-6 (Human IL-1β PicoKineTM ELISA Kit and Human IL-6 PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA, respectively) per manufacturer’s instructions.

Techniques: Comparison, Marker, Synthesized

Journal: Frontiers in Endocrinology

Article Title: Positive Effects of Extra-Virgin Olive Oil Supplementation and DietBra on Inflammation and Glycemic Profiles in Adults With Type 2 Diabetes and Class II/III Obesity: A Randomized Clinical Trial

doi: 10.3389/fendo.2022.841971

Figure Lengend Snippet: Comparison of outcome variables at the end of intervention between two intervention groups with class II/III obesity, Brazil, 2016 (n = 34).

Article Snippet: Enzyme-linked immunosorbent assays were used to measure adiponectin (Human Adiponectin PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA), leptin (Human Leptin PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA), IL-1β, and IL-6 (Human IL-1β PicoKineTM ELISA Kit and Human IL-6 PicoKineTM ELISA Kit, Boster Bio, Pleasanton, CA, respectively) per manufacturer’s instructions.

Techniques: Comparison, Marker, Synthesized