Journal: Nutrients

Article Title: Effects of Lingonberry ( Vaccinium vitis-idaea L.) Supplementation on Hepatic Gene Expression in High-Fat Diet Fed Mice

doi: 10.3390/nu13113693

Figure Lengend Snippet: The twenty genes with the largest negative fold change (FC) in the lingonberry supplemented high-fat diet (HF + LGB) group relative to the high-fat diet (HF) group. Mean expression levels are given as DESeq2-normalized counts. p -values are adjusted by false discovery rate (FDR).

Article Snippet: For PCR validation, RNA was transcribed to cDNA (Maxima First Strand cDNA Synthesis Kit, Thermo Fisher Scientific) and subjected to quantitative PCR with TaqMan Universal Master Mix (Thermo Fisher Scientific) and ABI Prism 7500 sequence detection system (Applied Biosystems, Foster City, CA, USA) using the following TaqMan Gene Expression assays (Thermo Fisher Scientific); Mm00432403_m1 ( Cd36 ), Mm03047343_m1 ( Cd68 ), Mm00617672_m1 ( Cidec ), Mm00444699_m1 ( Cxcl14 ), Mm00725580_s1 ( Cyp2c29 ), Mm00472168_m1 ( Cyp2c55 ), Mm00731567_m1 ( Cyp3a11 ), Mm01607174_mH ( Cyp3a59 ), Mm00487306_m1 ( Cyp46a1 ), Mm00492632_m1 ( Igfbp2 ), Mm00434228_m1 ( IL1b ), Mm00440181_m1 ( Lepr ), Mm00503358_m1 ( Mogat1 ), Mm01184322_m1 ( Pparg ), Mm04208126_mH ( Saa2 ), Mm00446229_m1 ( Slc2a2 ), Mm00443260_g1 ( Tnfa ).

Techniques: Expressing, Activity Assay, Antioxidant Activity Assay, Migration, Binding Assay, Sequencing

Journal: EMBO Molecular Medicine

Article Title: Combined mutation of Vhl and Trp53 causes renal cysts and tumours in mice

doi: 10.1002/emmm.201202231

Figure Lengend Snippet: A–O. Serial sections of a simple cyst (A,D,G,J,M) and two neoplasms (B,E,H,K,N and C,F,I,L,O) stained with H&E (A–C) or stained immunohistochemically for Ki67 (D–F), phospho-Thr37/46-4E-BP1 (G–I), phospho-Ser240/244-ribosomal S6 protein (J–L) or Myc (M–O). Dotted lines indicate the boundary of normal tissue and neoplasms. P. Quantification of the percentage of simple cysts ( n = 68–185) or atypical cysts and neoplasms ( n = 34–51) that display higher levels (strong) of staining than adjacent normal tissue in the same section (negative/weak). Q. Model summarising the proposed sequence of morphological and molecular alterations involved in formation of ccRCC. For details see the Discussion Section.

Article Snippet: Western blotting, immunohistochemistry or immunofluorescence were conducted using previously described methods (Frew et al, ) and the antibodies against the following epitopes: Acetylated tubulin (Sigma, #T6793), Actin (Sigma-Aldrich, A2228), AQP2 (Wagner et al, ), Aurora A (Abcam, ab13824), BubR1 (BD Biosciences, 612502), CDK-2 (Santa Cruz, sc-163-g), Cenp-E (Meraldi et al, ), E-cadherin (Abcam, ab11512), phospho-Thr37/46-4E-BP1 (Cell Signaling Technology, #2855), HIF1α (Novus Biologicals, NB100-105), HIF2α (Pollard et al, , PM8), Ki67 (DakoCytomation, TEC-3), Mad2 (Bethyl Laboratories, A300301A), Myc (Epitomics, Y69), p53 (Novocastra, NCL-p53-CM5p), NaPi2 (Custer et al, ), NCC (Millipore, AB3553), phospho-Ser240/244-ribosomal S6 protein (Cell Signaling Technology, #2215), THP (Santa Cruz Biotechnology, sc-20631), pVHL(m) CT antibody (Hergovich et al, ), pVHL (Santa Cruz, sc-5575), Vimentin (Cell Signaling Technology, #5741).

Techniques: Staining, Sequencing

Journal: Frontiers in Aging Neuroscience

Article Title: Pentazocine Protects SN4741 Cells Against MPP + -Induced Cell Damage via Up-Regulation of the Canonical Wnt/β-Catenin Signaling Pathway

doi: 10.3389/fnagi.2017.00196

Figure Lengend Snippet: The primers for real time PCR.

Article Snippet: The membranes were blocked with 5% BSA in TBST at room temperature for 2 h and incubated with Antibodies to β-catenin (90 kDa), PARP (116 kDa), GAPDH (36 kDa) and TH (56 kDa; Abcam, Cambridge, UK) and Antibodies to GSK-3β (46 kDa), p-GSK-3β (ser9; 46 kDa), cleaved caspase-3 (19 kDa), cleaved caspase-8 (43 kDa) and β-actin (42 kDa; Cell Signaling, Beverly, MA, USA) at 4°C overnight.

Techniques:

Journal: Frontiers in Aging Neuroscience

Article Title: Pentazocine Protects SN4741 Cells Against MPP + -Induced Cell Damage via Up-Regulation of the Canonical Wnt/β-Catenin Signaling Pathway

doi: 10.3389/fnagi.2017.00196

Figure Lengend Snippet: Pentazocine effectively rescued β-catenin from MPP + -induced decline via canonical Wnt pathway. (A) Cells were treated as described in Figure . Western blots was performed for the TH, β-catenin, GSK-3β, and p -GSK-3β (ser9) measurements. (B–D) Relative amounts of TH/actin, β-catenin/actin, p -GSK-3β (ser9)/GSK-3β were quantified (the means ± SEM; n = 3; * p < 0.05; ** p < 0.01). (E–G) RNA was obtained from the SN4741 cells and analyzed with quantitative real-time PCR. The values of TH, β-catenin and GSK-3β were normalized to that of β-actin (the means ± SEM; n = 3; * p < 0.05).

Article Snippet: The membranes were blocked with 5% BSA in TBST at room temperature for 2 h and incubated with Antibodies to β-catenin (90 kDa), PARP (116 kDa), GAPDH (36 kDa) and TH (56 kDa; Abcam, Cambridge, UK) and Antibodies to GSK-3β (46 kDa), p-GSK-3β (ser9; 46 kDa), cleaved caspase-3 (19 kDa), cleaved caspase-8 (43 kDa) and β-actin (42 kDa; Cell Signaling, Beverly, MA, USA) at 4°C overnight.

Techniques: Western Blot, Real-time Polymerase Chain Reaction

Journal: Nature Communications

Article Title: Single cell profiling of female breast fibroadenoma reveals distinct epithelial cell compositions and therapeutic targets

doi: 10.1038/s41467-023-39059-3

Figure Lengend Snippet: a Patient-derived fibroadenoma organoid experimental setup. b HE staining of fibroadenoma tissue and organoids. Scale bars: 100 μm and 25 μm. Experiment was performed with three independent replicates. c Whole-exome sequencing of organoids and patient samples. d Heatmap of hormone-sensitive and hormone resistance gene signatures in fibroadenoma tissues (Tt), fibroadenoma organoids (To), and normal organoids (No) by limited RNA sequencing. e GSEA of the estrogen signaling pathway and endocrine resistance in fibroadenoma versus normal organoids. f FACS plot of epithelial cell subtypes in fibroadenoma tissue (Tt) and organoids (To) (left); quantification of epithelial cell subtypes in Tt and CD45-CD31- cells (right). g Drug response curves of tamoxifen in different fibroadenoma organoid lines. CellTiter-Glo® 3D Cell Viability Assay was used to measure cell viability. n = 3/group from three independent experiments. Data are shown as mean +/− s.e.m. h Heatmap of the drug sensitivity of tamoxifen in fibroadenoma organoid lines (F111T, F70T). i IHC of resistance pathway markers in F111T tissues (left). Scale bar: 50 μm. The drug combination test showed that F111T organoids with high ERBB2 expression were more sensitive to tamoxifen (Tam) combined with lapatinib (Lap) treatment (right). n = 3/group from three independent experiments. Data are expressed as the mean +/− s.e.m. **** p = 0.0000034 (DMSO vs Tam [10 μM] + Lap [10 nM]), ** p = 0.00033 (DMSO vs Tam [10 μM] + Ven [5 μM]), * p = 0.022 (DMSO vs Tam [10 μM] + Pal [10 nM]), one-way ANOVA. j IHC of resistance pathway markers (ERBB2, BCL2, CCND1) in F70T tissues (left). Scale bar: 50 μm. The drug combination test showed that F70T organoids with high expression of CCND1 and BCL2 were more sensitive to tamoxifen (Tam) combined with palbociclib (Pal) or tamoxifen plus venetoclax (Ven) (right). n = 3/group from three independent experiments. Data are expressed as the mean +/− s.e.m. *** p = 0.000019 (DMSO vs Tam [10 μM] + Ven [5 μM]), ** p = 0.0020 (DMSO vs Tam [10 μM] + Pal [10 nM]), one-way ANOVA. Source data are provided as a Source data file.

Article Snippet: Groups were (1) DMSO control; (2) Tamoxifen (used at 10 μM); (3) Tamoxifen (10 μM) + Lapatinib (Selleckchem, Cat.# S2111, stock 10 mM in DMSO, used at 10 nM); (4) Tamoxifen (10 μM) + Venetoclax (Aladdin, Cat.# A124869, stock 10 mM in DMSO, used at 5 μM); (5) Tamoxifen (10 μM) + Palbociclib (Selleckchem, Cat.# S1579, stock 10 mM in DMSO, used at 10 nM).

Techniques: Derivative Assay, Staining, Sequencing, RNA Sequencing, Viability Assay, Expressing

Journal: International Journal of Molecular Sciences

Article Title: Potential Use of Biotherapeutic Bacteria to Target Colorectal Cancer-Associated Taxa

doi: 10.3390/ijms21030924

Figure Lengend Snippet: Examples of microbial patterns observed in colorectal cancer (CRC) patients.

Article Snippet: Faecal , 46 , 56 , 16S rRNA gene (V3) pyrosequencing , , No antibiotic exposure within 3 months , Fusobacterium , Enterococcus , Escherichia/Shigella , Klebsiella , Streptococcus , and Peptostreptococcus , Roseburia , [ ] .

Techniques: Amplification, Sequencing, Probiotics, Terminal Restriction Fragment Length Polymorphism

Journal: Scientific Data

Article Title: RNA sequencing analysis of the human retina and associated ocular tissues

doi: 10.1038/s41597-020-0541-4

Figure Lengend Snippet: Associated RNA-seq sample metadata.

Article Snippet: Human Donor Eye 8 , 46 hours , Homo sapiens , macular retina , Qiagen AllPrep Mini Kit , Illumina stranded TruSeq cDNA libraries with poly dT enrichment; Illumina HiSeq sequencer , 78 years , male , macula_8.

Techniques: Isolation, Sequencing, Staining