Journal: Inflammatory Intestinal Diseases

Article Title: Hypoxia Reduces the Transcription of Fibrotic Markers in the Intestinal Mucosa

doi: 10.1159/000513061

Figure Lengend Snippet: TaqMan gene expression assays

Article Snippet: Relative mRNA expression was determined by the comparative ∆∆Ct method using beta-actin (ACTB) as the reference gene. table ft1 table-wrap mode="anchored" t5 Table 2 caption a7 Gene Full name TaqMan assay ID Human genes TGFβ Transforming growth factor beta Hs00998133_m1 ACTA2 Actin alpha 2, smooth muscle Hs00426835_g1 VIM Vimentin Hs00185584_m1 CDH1 Cadherin 1 Hs01023895_m1 CDH2 Cadherin 2 Hs00983056_m1 COL1A1 Collagen type I alpha 1 chain Hs00164004_m1 COL3A1 Collagen type III alpha 1 chain Hs00943809_m1 COL4A1 Collagen type IV alpha 1 chain Hs00266237_m1 MMP2 Matrix metallopeptidase 2 Hs01548727_m1 MMP3 Matrix metallopeptidase 3 Hs00968305_m1 MMP9 Matrix metallopeptidase 9 Hs00957562_m1 TIMP1 Tissue inhibitor of metalloproteinase 1 Hs01092512_g1 Mouse genes TGFβ Transforming growth factor beta Mm00524541_m1 ACTA2 Actin alpha 2, smooth muscle Mm00725412_s1 VIM Vimentin Mm01333430_m1 CDH1 Cadherin 1 Mm01247357_m1 CDH2 Cadherin 2 Mm01162497_m1 COL1A1 Collagen type I alpha 1 chain Mm00801666_g1 COL3A1 Collagen type III alpha 1 chain Mm00802300_m1 COL4A1 Collagen type IV alpha 1 chain Mm01210125_m1 MMP2 Matrix metallopeptidase 2 Mm00439498_m1 MMP3 Matrix metallopeptidase 3 Mm00440295_m1 MMP9 Matrix metallopeptidase 9 Mm00442991_m1 MMP13 Matrix metallopeptidase 13 Mm00439491_m1 TIMP1 Tissue inhibitor of metalloproteinase 1 Mm01341361_m1 Open in a separate window TaqMan gene expression assays Western Blot Total protein was harvested in M-PER lysis buffer (Thermo Fisher Scientific) supplemented with protease inhibitors (Roche Diagnostics, Mannheim, Germany).

Techniques: Gene Expression, TaqMan Assay

Journal: The Journal of Neuroscience

Article Title: Neural Stem/Progenitor Cells Participate in the Regenerative Response to Perinatal Hypoxia/Ischemia

doi: 10.1523/JNEUROSCI.1898-05.2006

Figure Lengend Snippet: Primer sets used in RT-PCR

Article Snippet: Only those genes that were induced or repressed at least twofold in each replication are listed in supplemental (available at www.jneurosci.org as supplemental material ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Transcript Primers EGFR (TaqMan) Applied Biosystems TaqMan Assay ID Rn00580398_m1 Notch1 (Lux) 5′-CAC GTA CTG CGA GCT GCC CTA CG[FAM]G-3′ 5′-GGC AGG TGC CTC CGT TCT-3′ 18S (TaqMan) Applied Biosystems TaqMan Assay ID Hs99999901_s1 18S (Lux) Invitrogen catalog #115HM-01 Open in a separate window Primer sets used in RT-PCR

Techniques: TaqMan Assay

Journal: The Journal of Neuroscience

Article Title: Neural Stem/Progenitor Cells Participate in the Regenerative Response to Perinatal Hypoxia/Ischemia

doi: 10.1523/JNEUROSCI.1898-05.2006

Figure Lengend Snippet: Signaling pathways involved in control of NSP fate are induced by perinatal H/I. Ipsilateral H/I and control hemispheres were dissected out after 48 h of recovery. A, Total RNA was isolated and amplified by qRT-PCR using primers specific for EGFR and Notch1 and normalized to expression of 18S. Values in parentheses indicate CV for the target gene in the sample groups; n = 10 for ipsilateral and contralateral conditions, and n = 4 for sham condition. *p < 0.05 versus sham; †p < 0.05 versus contralateral by pairwise fixed reallocation randomization. Immunostaining for Notch1 was performed on cryostat sections from H/I (B) and control (C) animals. In situ hybridization was performed on cryostat sections of contralateral (D, G), ipsilateral (E, H), and control (F, I) hemispheres using a digoxigenin-labeled RNA probe for Hes5 (D–F) and Hes1 (G–I). Arrows in E delineate the region of increased Hes5 expression. Inset in E shows high-magnification 100× Nomarski image of the Hes5+ region showing a subependymal Hes5+ cell body (arrowhead) with processes (arrow) projecting through the ependyma. There was no evident change in Hes1 expression. Scale bars: inset in E, 4 μm; F, 10 μm. cp, Choroid plexus; V, ventricle.

Article Snippet: Only those genes that were induced or repressed at least twofold in each replication are listed in supplemental (available at www.jneurosci.org as supplemental material ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Transcript Primers EGFR (TaqMan) Applied Biosystems TaqMan Assay ID Rn00580398_m1 Notch1 (Lux) 5′-CAC GTA CTG CGA GCT GCC CTA CG[FAM]G-3′ 5′-GGC AGG TGC CTC CGT TCT-3′ 18S (TaqMan) Applied Biosystems TaqMan Assay ID Hs99999901_s1 18S (Lux) Invitrogen catalog #115HM-01 Open in a separate window Primer sets used in RT-PCR

Techniques: Protein-Protein interactions, Control, Isolation, Amplification, Quantitative RT-PCR, Expressing, Immunostaining, In Situ Hybridization, Labeling

Journal:

Article Title: CORNEAL ANGIOGENIC PRIVILEGE: ANGIOGENIC AND ANTIANGIOGENIC FACTORS IN CORNEAL AVASCULARITY, VASCULOGENESIS, AND WOUND HEALING (AN AMERICAN OPHTHALMOLOGICAL SOCIETY THESIS)

doi:

Figure Lengend Snippet: VEGF INHIBITORS

Article Snippet: Karumanchi and associates 205 demonstrated that endostatin binds to glypicans. table ft1 table-wrap mode="anchored" t5 TABLE 8 caption a7 VEGF INHIBITOR MECHANISM ADVANTAGES SUBJECTS REFERENCES Macugen (pegaptanib, Eyetech) VEGF aptamer (RNA based oligonucleotide which binds VEGF) Direct inhibition of VEGF; intravitreal injection Humans 243 rhu Fab (Genentech) Anti-VEGF monoclonal antibody fragment Small fragment; good penetration; intravitreal injection Monkeys 244 Semaxanib ( SU 5416, Sugen Inc) Competitive inhibitor of Flk-1/KDR > Flt1-1 Specific receptor synthetic inhibitor Humans 245 SU 6668 (Sugen Inc) Flk-1/KDR, PDGFR β and FGFR-1 receptor inhibitor Oral administration Humans 245 Angiozyme (Ribozyme Pharmaceutical) Ribozyme-cleave mRNA for Flt-1 and Flk-1/KDR — Humans 245 CGP41251 Protein kinase C and VEGF receptor kinase inhibition — Humans 246 siRNA targeting VEGF Inhibits VEGF or VEGF receptors Subconjunctival injection, intravenous injection Mice 247 Soluble VEGF receptor sFlt-1 binds VEGF Intravitreal injection Rats 248 VEGF peptide Inhibits VEGF from binding the receptor Intravitreal injection Mice 249 Squalamine(Evizon) Inhibit VEGF mediated endothelial Systematic Human 250 VEGF Trap VEGF Trap binds VEGF IV systematic Human 251 Bevacizumab(Avastin) Anti-VEGF monoclonal antibody(whole antibody) Intravitreal injection Human 252 Open in a separate window VEGF INHIBITORS The proposed mechanisms for endostatin functioning are characterized as follows: (i) endostatin inhibits vascular endothelial tube formation by inhibiting nitric oxide synthase 206 ; (ii) endostatin attenuates vascular endothelial cell migration by downregulating c-myc mRNA expression, which was abrogated with the introduction of the c-myc gene into vascular endothelial cells 207 ; (iii) endostatin induces endothelial cell apoptosis by activating caspase-3 enzymatic activity, reducing antiapoptotic protein BcL-2, and reducing MAP kinases activities 184 ; (iv) endostatin regulates the Wnt signaling pathway by promoting β catenin degradation in the Xenopus system 208 ; (v) endostatin causes G1 arrest of endothelial cells by decreasing the hyperphosphorylation of retinoblastoma gene product and decreasing the mRNA and protein of cyclin D1.

Techniques: Inhibition, Injection, Binding Assay

Journal: Tissue Engineering. Part A

Article Title: Amorphous Silicon Oxynitrophosphide-Coated Implants Boost Angiogenic Activity of Endothelial Cells

doi: 10.1089/ten.tea.2019.0051

Figure Lengend Snippet: Gene and Specific TagMan Assay Identification

Article Snippet: The housekeeping gene was 18S , and the studied genes were: VEGF-A , HIF-1α , Ang-1 , nesprin-2 , SOD-1 , Cat-1 , and NOS-3 ( ). table ft1 table-wrap mode="anchored" t5 Table 2. caption a7 Gene Assay identification VEGF-A Hs00900055_m1 HIF-1α Hs00153153_m1 Ang-1 Hs00919202_m1 Nesprin-2 ( SYNE2 ) Hs00794881_m1 SOD-1 Hs00533490_m1 Cat-1 ( CAT ) Hs00156308_m1 e-NOS ( NOS3 ) Hs01574665_m1 Open in a separate window CAT-1 , catalase-1; HIF-1α , hypoxia-inducible factor-1α; SOD-1 , superoxide dismutase 1; VEGF-A , vascular endothelial growth factor A. Gene and Specific TagMan Assay Identification Statistics The data are shown as the mean ± standard deviation.

Techniques:

Journal: Toxicological Sciences

Article Title: Microglia Activation and Gene Expression Alteration of Neurotrophins in the Hippocampus Following Early-Life Exposure to E-Cigarette Aerosols in a Murine Model

doi: 10.1093/toxsci/kfx257

Figure Lengend Snippet: Taqman Gene Expression Assays Used in RT-qPCR

Article Snippet: Quantified mRNA expression levels were calculated using the ΔΔCT method and normalized to the reference gene, glyceraldehyde-3-phosphate dehydrogenase ( Gapdh ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Gene Gene Symbol Assay ID Amplicon Length Reference Sequence Nerve growth factor receptor Ngfr Mm00446296_m1 77 {"type":"entrez-nucleotide","attrs":{"text":"NM_033217.3","term_id":"118131161","term_text":"NM_033217.3"}} NM_033217.3 Brain derived neurotrophic factor Bdnf Mm04230607_s1 92 {"type":"entrez-nucleotide","attrs":{"text":"NM_007540.4","term_id":"114326462","term_text":"NM_007540.4"}} NM_007540.4 Glial cell line derived neurotrophic factor Gdnf Mm00599849_m1 101 {"type":"entrez-nucleotide","attrs":{"text":"NM_010275.2","term_id":"118129978","term_text":"NM_010275.2"}} NM_010275.2 Glyceraldehyde-3-phosphate dehydrogenase Gapdh Mm99999915_g1 109 {"type":"entrez-nucleotide","attrs":{"text":"NM_001289726.1","term_id":"576080554","term_text":"NM_001289726.1"}} NM_001289726.1 Open in a separate window Taqman Gene Expression Assays Used in RT-qPCR

Techniques: Expressing, Amplification, Sequencing, Derivative Assay

Journal: Toxicological Sciences

Article Title: Microglia Activation and Gene Expression Alteration of Neurotrophins in the Hippocampus Following Early-Life Exposure to E-Cigarette Aerosols in a Murine Model

doi: 10.1093/toxsci/kfx257

Figure Lengend Snippet: Decreases in hippocampal expression levels for Ngfr and Bdnf after early-life exposure to e-cigarette aerosols with and without nicotine. All data are represented as mean values (n = 6–10) ± SEM. *Significantly different from filtered air control p < .001. Results were calculated using the 2^(–ΔΔCT) method.

Article Snippet: Quantified mRNA expression levels were calculated using the ΔΔCT method and normalized to the reference gene, glyceraldehyde-3-phosphate dehydrogenase ( Gapdh ). table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 Gene Gene Symbol Assay ID Amplicon Length Reference Sequence Nerve growth factor receptor Ngfr Mm00446296_m1 77 {"type":"entrez-nucleotide","attrs":{"text":"NM_033217.3","term_id":"118131161","term_text":"NM_033217.3"}} NM_033217.3 Brain derived neurotrophic factor Bdnf Mm04230607_s1 92 {"type":"entrez-nucleotide","attrs":{"text":"NM_007540.4","term_id":"114326462","term_text":"NM_007540.4"}} NM_007540.4 Glial cell line derived neurotrophic factor Gdnf Mm00599849_m1 101 {"type":"entrez-nucleotide","attrs":{"text":"NM_010275.2","term_id":"118129978","term_text":"NM_010275.2"}} NM_010275.2 Glyceraldehyde-3-phosphate dehydrogenase Gapdh Mm99999915_g1 109 {"type":"entrez-nucleotide","attrs":{"text":"NM_001289726.1","term_id":"576080554","term_text":"NM_001289726.1"}} NM_001289726.1 Open in a separate window Taqman Gene Expression Assays Used in RT-qPCR

Techniques: Expressing

Journal:

Article Title: In Vitro Activity of TD-6424 against Staphylococcus aureus

doi: 10.1128/AAC.47.11.3602-3604.2003

Figure Lengend Snippet: In vitro activities of TD-6424 and comparator antibiotics against MRSA and MSSA

Article Snippet: Linezolid at 8 μg/ml reduced the initial inoculum from log 10 5.76 ± 0.07 CFU/ml to log 10 2.73 ± 0.08 CFU/ml by 4 h, and vancomycin at 32 μg/ml decreased it from log 10 5.76 ± 0.07 CFU/ml to log 10 4.82 ± 0.02 CFU/ml over this period. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 1. caption a7 Time-kill curves for MSSA (ATCC 13709) (A), MRSA (ATCC 33591) (B), and GISA (HIP 5836) (C). (A) Vancomycin at 4 times the MIC (⧫), nafcillin at 4 times the MIC (▪), linezolid at 4 times the MIC (▴), and TD-6424 at 4 times the MIC (▵); (B) vancomycin at 8 times the MIC (⧫), linezolid at 8 times the MIC (▴), and TD-6424 at 8 (▵) and 32 (▪) times the MIC; (C) linezolid at 4 times the MIC (▴), vancomycin at 4 times the MIC (⧫), and TD-6424 at 4 (▵), 8 (▪), and 16 (□) times the MIC.

Techniques: In Vitro

Journal:

Article Title: In Vitro Activity of TD-6424 against Staphylococcus aureus

doi: 10.1128/AAC.47.11.3602-3604.2003

Figure Lengend Snippet: Time-kill curves for MSSA (ATCC 13709) (A), MRSA (ATCC 33591) (B), and GISA (HIP 5836) (C). (A) Vancomycin at 4 times the MIC (⧫), nafcillin at 4 times the MIC (▪), linezolid at 4 times the MIC (▴), and TD-6424 at 4 times the MIC (▵); (B) vancomycin at 8 times the MIC (⧫), linezolid at 8 times the MIC (▴), and TD-6424 at 8 (▵) and 32 (▪) times the MIC; (C) linezolid at 4 times the MIC (▴), vancomycin at 4 times the MIC (⧫), and TD-6424 at 4 (▵), 8 (▪), and 16 (□) times the MIC. ✻, bacterial growth control. The nafcillin MIC was 1 μg/ml for ATCC 13709. Vancomycin MICs were 1, 1, and 8 μg/ml for ATCC 13709, ATCC 33591, and HIP 5836, respectively; the corresponding values were 2, 2, and 2 μg/ml for linezolid and 1, 1, and 2 μg/ml for TD-6424.

Article Snippet: Linezolid at 8 μg/ml reduced the initial inoculum from log 10 5.76 ± 0.07 CFU/ml to log 10 2.73 ± 0.08 CFU/ml by 4 h, and vancomycin at 32 μg/ml decreased it from log 10 5.76 ± 0.07 CFU/ml to log 10 4.82 ± 0.02 CFU/ml over this period. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 1. caption a7 Time-kill curves for MSSA (ATCC 13709) (A), MRSA (ATCC 33591) (B), and GISA (HIP 5836) (C). (A) Vancomycin at 4 times the MIC (⧫), nafcillin at 4 times the MIC (▪), linezolid at 4 times the MIC (▴), and TD-6424 at 4 times the MIC (▵); (B) vancomycin at 8 times the MIC (⧫), linezolid at 8 times the MIC (▴), and TD-6424 at 8 (▵) and 32 (▪) times the MIC; (C) linezolid at 4 times the MIC (▴), vancomycin at 4 times the MIC (⧫), and TD-6424 at 4 (▵), 8 (▪), and 16 (□) times the MIC.

Techniques: Control

Journal:

Article Title: In Vitro Activity of TD-6424 against Staphylococcus aureus

doi: 10.1128/AAC.47.11.3602-3604.2003

Figure Lengend Snippet: PAE for TD-6424 and comparator antibiotics

Article Snippet: Linezolid at 8 μg/ml reduced the initial inoculum from log 10 5.76 ± 0.07 CFU/ml to log 10 2.73 ± 0.08 CFU/ml by 4 h, and vancomycin at 32 μg/ml decreased it from log 10 5.76 ± 0.07 CFU/ml to log 10 4.82 ± 0.02 CFU/ml over this period. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 1. caption a7 Time-kill curves for MSSA (ATCC 13709) (A), MRSA (ATCC 33591) (B), and GISA (HIP 5836) (C). (A) Vancomycin at 4 times the MIC (⧫), nafcillin at 4 times the MIC (▪), linezolid at 4 times the MIC (▴), and TD-6424 at 4 times the MIC (▵); (B) vancomycin at 8 times the MIC (⧫), linezolid at 8 times the MIC (▴), and TD-6424 at 8 (▵) and 32 (▪) times the MIC; (C) linezolid at 4 times the MIC (▴), vancomycin at 4 times the MIC (⧫), and TD-6424 at 4 (▵), 8 (▪), and 16 (□) times the MIC.

Techniques:

Journal: Mucosal immunology

Article Title: Short ragweed pollen promotes M2 macrophage polarization via TSLP/TSLPR/OX40L signaling in allergic inflammation

doi: 10.1038/s41385-019-0187-8

Figure Lengend Snippet: TaqMan gene expression assays used for RT-qPCR

Article Snippet: So the fold for control always equal to 1 without error bar. table ft1 table-wrap mode="anchored" t5 Table 1. caption a7 TaqMan gene Assay ID GAPDH Mm99999915_g1 Arg1 Mm00475988_m1 Ym1 Mm00657889_mH FIZZ1 Mm00445109_m1 TSLP Mm00498739_m1 TSLPR Mm00497362_m1 OX40L Mm00437214_m1 TARC Mm00516136_m1 MDC Mm00436439_m1 IL-4 Mm00445259_m1 IL-5 Mm99999063_m1 IL-13 Mm00434204_m1 Open in a separate window TaqMan gene expression assays used for RT-qPCR

Techniques: Gene Expression, Gene Assay

Journal: Tissue Engineering and Regenerative Medicine

Article Title: Fabrication of Functional Cell Sheets with Human Thyrocytes from Non-Tumorous Thyroid Tissue

doi: 10.1007/s13770-019-00198-8

Figure Lengend Snippet: List of TaqMan ® gene expression assay mix (20x)/PCR primers used in RT-qPCR studies

Article Snippet: The conditions for the reactions were set at 95 °C for 20 s and 40 cycles at 95 °C for 1 s and 60 °C for 20 s. The cycle threshold values were determined automatically by the Applied Biosystems StepOnePlus Real-Time PCR System, and the fold-change in the gene expression was calculated by the 2 −ΔΔCT method. table ft1 table-wrap mode="anchored" t5 Table 2 caption a7 Gene symbol Gene name Assay ID Species Amplicon length TPO Thyroid peroxidase Hs00892519_m1 Human 53 TG Thyroglobulin Hs00174974_m1 Human 69 TGFB Transforming growth factor beta 1 Hs00998133_m1 Human 57 IL6 Interleukin 6 Hs00985639_m1 Human 66 EGF Epidermal growth factor Hs01099999_m1 Human 70 Open in a separate window List of TaqMan ® gene expression assay mix (20x)/PCR primers used in RT-qPCR studies Fabrication of cell sheets Human primary thyroid cell sheets were constructed using TRCDs.

Techniques: Gene Expression, Amplification

Journal: Tissue Engineering and Regenerative Medicine

Article Title: Fabrication of Functional Cell Sheets with Human Thyrocytes from Non-Tumorous Thyroid Tissue

doi: 10.1007/s13770-019-00198-8

Figure Lengend Snippet: Changes in the gene expression of thyroid cell markers and cytokines. A-E RT-qPCR analyses of TPO, TG, IL-6, TGFB and EGF for cells cultured in DMEM and HDM. GAPDH was set as the housekeeper gene. TPO: thyroid peroxidase; TG: thyroglobulin; TGFB: transforming growth factor-β; EGF: epidermal growth factor. *p < 0.05, **p < 0.01, **p < 0.01, ***p < 0.001 (two-way ANOVA), n.s.: non significance, n = 6 in 2 cases

Article Snippet: The conditions for the reactions were set at 95 °C for 20 s and 40 cycles at 95 °C for 1 s and 60 °C for 20 s. The cycle threshold values were determined automatically by the Applied Biosystems StepOnePlus Real-Time PCR System, and the fold-change in the gene expression was calculated by the 2 −ΔΔCT method. table ft1 table-wrap mode="anchored" t5 Table 2 caption a7 Gene symbol Gene name Assay ID Species Amplicon length TPO Thyroid peroxidase Hs00892519_m1 Human 53 TG Thyroglobulin Hs00174974_m1 Human 69 TGFB Transforming growth factor beta 1 Hs00998133_m1 Human 57 IL6 Interleukin 6 Hs00985639_m1 Human 66 EGF Epidermal growth factor Hs01099999_m1 Human 70 Open in a separate window List of TaqMan ® gene expression assay mix (20x)/PCR primers used in RT-qPCR studies Fabrication of cell sheets Human primary thyroid cell sheets were constructed using TRCDs.

Techniques: Gene Expression, Quantitative RT-PCR, Cell Culture