Journal: Development (Cambridge, England)

Article Title: Cellular analysis of cleavage-stage chick embryos reveals hidden conservation in vertebrate early development

doi: 10.1242/dev.118604

Figure Lengend Snippet: Mitotic division orientation and yolk syncytial nuclei. (A-C) Increase in cell layer number is not caused by oriented mitotic division. (A) Schematic view of three representative mitotic plane angles (0°, 45° and 90°). The last (90°) scenario was hypothesized as the cause for blastoderm cell-layer number increase by Eyal-Giladi and colleagues. (B) Representative section views of EGK-III to EGK-V embryos stained with DAPI to reveal mitotic cells. Top: one-cell layer region; bottom: 2- to 3-cell-layer region. Only anaphase and telophase nuclei were counted. Mitotic plane orientation was calculated as the angle between the blastoderm surface and the line passing through two separating nuclei. Red lines: surface-located cell divisions (s). Green line: deep cell division (d). (C) Rose diagrams showing the distribution of mitotic plane orientation. Left: dividing surface cells ( n =143). Right: dividing deep cells ( n =97). A vast majority of surface cells divide with their mitotic planes orientated at a less than 30° angle to the surface, likely producing two surface daughter cells. Mitotic planes of non-surface cells exhibit a more randomized distribution. (D-H) Yolk syncytial nuclei are detected in three different avian species. (D) DAPI staining of EGK-V (left) and EGK-VIII (right) chick embryos. DAPI-positive structures (arrows) are detected underneath the yolk cell surface. (E) In post-ovipositional chick (EGK-XI, left panels) and pre-ovipositional quail (EGK-VIII, right panels) embryos, double-staining with DAPI (nucleus) and Rhodamine-WGA (membrane) reveals that DAPI-positive signals (arrows) are located underneath the yolk cell membrane. (F) Four examples of zebra finch embryos (two EGK-VI and two EGK-VII) showing DAPI-positive syncytial nuclei (arrows) located underneath the yolk cell membrane. (G) A composite view (assembled from four images) of a zebra finch embryo cross-section, showing an intact yolk cell membrane and many syncytial nuclei (arrows) underneath it. (H) A schematic view of the YSL in an avian embryo.

Article Snippet: Yolk cell membrane was marked using rhodamine-labeled wheat germ agglutinin (WGA) (Vector Laboratories, Cat# RL-1022).

Techniques: Staining, Double Staining

Journal: Developmental cell

Article Title: YAP Partially Reprograms Chromatin Accessibility to Directly Induce Adult Cardiogenesis in Vivo

doi: 10.1016/j.devcel.2019.01.017

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Rhodamine-conjugated WGA used was from Vector labs Cat#RL-1022.

Techniques: Plasmid Preparation, Recombinant, Imaging, SYBR Green Assay, Expressing, Software, Next-Generation Sequencing

Journal: BMC Pharmacology & Toxicology

Article Title: Interaction between AhR and HIF-1 signaling pathways mediated by ARNT/HIF-1β

doi: 10.1186/s40360-022-00564-8

Figure Lengend Snippet: Primer sequences for real-time reverse transcription-PCR and plasmid construction

Article Snippet: The chemicals used were purchased from the following companies: RPMI-1640 medium (Hyclone, Logan, UT, USA), fetal bovine serum (Gibco, Grand Island, NY, USA), HIF-1α stabilizing regent CoCl 2 and AhR ligand BaP (Sigma-Aldrich, St. Louis, MO, USA), pDsRed-Monomer-N1 expression vector and pAcGFP1-N1 expression vector (Clontech, Mountain View, CA, USA), Revert Aid First Strand cDNA synthesis kit (Thermo Fisher Scientific, Waltham, MA, USA, Cat. K1621), BglII, KpnI enzyme (Takara, Shiga, Japan), Hoechst 33342(Thermo Fisher Scientific, Waltham, MA, USA, Cat. 1022) CAIX antibody (Santa Cruz Biotechnology, Dallas, TX, USA, Cat. sc-365,900), CYP1B1 antibody (Abcam, Cambridge, UK, Cat. ab33586), CYP1A1 antibody (Abcam, Cambridge, UK, Cat. ab3568), VEGF antibody (Abcam, Cambridge, UK, Cat. ab32152), HIF-1α antibody (Abcam, Cambridge, UK, Cat. ab1), and AhR antibody (Abcam, Cambridge, UK, Cat. ab84833), HIF-1β/ARNT antibody (Cell Signaling Technology, Danvers, MA, USA, Cat. 3781S).

Techniques: Plasmid Preparation, Sequencing

Journal: BMC Pharmacology & Toxicology

Article Title: Interaction between AhR and HIF-1 signaling pathways mediated by ARNT/HIF-1β

doi: 10.1186/s40360-022-00564-8

Figure Lengend Snippet: Effects of BaP on CAIX ( A ), VEGF ( B ), CYP1A1 ( C ), and CYP1B1 ( D ) expression at the mRNA level without (□) or with (■) CoCl 2 and with 0–8 μM BaP. Data are presented as the fold-increase compared to without B(α) P and CoCl 2 , * P < 0.05, ** P < 0.01. Without (□) or with (■) CoCl 2 and with 0–8 μM BaP. Data are presented as the fold-increase compared to without BaP and CoCl 2 , * P < 0.05, ** P < 0.01, n = 3

Article Snippet: The chemicals used were purchased from the following companies: RPMI-1640 medium (Hyclone, Logan, UT, USA), fetal bovine serum (Gibco, Grand Island, NY, USA), HIF-1α stabilizing regent CoCl 2 and AhR ligand BaP (Sigma-Aldrich, St. Louis, MO, USA), pDsRed-Monomer-N1 expression vector and pAcGFP1-N1 expression vector (Clontech, Mountain View, CA, USA), Revert Aid First Strand cDNA synthesis kit (Thermo Fisher Scientific, Waltham, MA, USA, Cat. K1621), BglII, KpnI enzyme (Takara, Shiga, Japan), Hoechst 33342(Thermo Fisher Scientific, Waltham, MA, USA, Cat. 1022) CAIX antibody (Santa Cruz Biotechnology, Dallas, TX, USA, Cat. sc-365,900), CYP1B1 antibody (Abcam, Cambridge, UK, Cat. ab33586), CYP1A1 antibody (Abcam, Cambridge, UK, Cat. ab3568), VEGF antibody (Abcam, Cambridge, UK, Cat. ab32152), HIF-1α antibody (Abcam, Cambridge, UK, Cat. ab1), and AhR antibody (Abcam, Cambridge, UK, Cat. ab84833), HIF-1β/ARNT antibody (Cell Signaling Technology, Danvers, MA, USA, Cat. 3781S).

Techniques: Expressing

Journal: BMC Pharmacology & Toxicology

Article Title: Interaction between AhR and HIF-1 signaling pathways mediated by ARNT/HIF-1β

doi: 10.1186/s40360-022-00564-8

Figure Lengend Snippet: Effects of BaP on CAIX, VEGF, CYP1A1 and CYP1B1 expression at the protein level without (□) or with (■) CoCl 2 and with 0–8 μM BaP. Data are presented as the fold-increase compared to without B(α) P and CoCl 2 , * P < 0.05, ** P < 0.01. Without (□) or with (■) CoCl 2 and with 0–8 μM BaP. Data are presented as the fold-increase compared to without B(α) P and CoCl 2 , * P < 0.05, ** P < 0.01, n = 3

Article Snippet: The chemicals used were purchased from the following companies: RPMI-1640 medium (Hyclone, Logan, UT, USA), fetal bovine serum (Gibco, Grand Island, NY, USA), HIF-1α stabilizing regent CoCl 2 and AhR ligand BaP (Sigma-Aldrich, St. Louis, MO, USA), pDsRed-Monomer-N1 expression vector and pAcGFP1-N1 expression vector (Clontech, Mountain View, CA, USA), Revert Aid First Strand cDNA synthesis kit (Thermo Fisher Scientific, Waltham, MA, USA, Cat. K1621), BglII, KpnI enzyme (Takara, Shiga, Japan), Hoechst 33342(Thermo Fisher Scientific, Waltham, MA, USA, Cat. 1022) CAIX antibody (Santa Cruz Biotechnology, Dallas, TX, USA, Cat. sc-365,900), CYP1B1 antibody (Abcam, Cambridge, UK, Cat. ab33586), CYP1A1 antibody (Abcam, Cambridge, UK, Cat. ab3568), VEGF antibody (Abcam, Cambridge, UK, Cat. ab32152), HIF-1α antibody (Abcam, Cambridge, UK, Cat. ab1), and AhR antibody (Abcam, Cambridge, UK, Cat. ab84833), HIF-1β/ARNT antibody (Cell Signaling Technology, Danvers, MA, USA, Cat. 3781S).

Techniques: Expressing

Journal: Developmental cell

Article Title: YAP Partially Reprograms Chromatin Accessibility to Directly Induce Adult Cardiogenesis in Vivo

doi: 10.1016/j.devcel.2019.01.017

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Phospho-YAP(Ser127) antibody Cell signaling technology Cat#4911 Rabbit YAP1 antibody Novus biologicals Cat#NB110-583538 Donkey anti-Rabbit, Alexa 488 Thermo Fisher Scientific Cat#A-21206 Donkey anti-Rabbit, Alexa 647 Thermo Fisher Scientific Cat#A-31573 Donkey anti-Rabbit, Alexa 546 Thermo Fisher Scientific Cat#A-10040 Donkey anti-Mouse, Alexa 488 Thermo Fisher Scientific Cat#A-21202 Donkey anti-Mouse, Alexa 546 Thermo Fisher Scientific Cat#A-10036 Donkey anti-chicken, Alexa 488 Thermo Fisher Scientific Cat#A-11039 Donkey anti-rat, Alexa 488 Thermo Fisher Scientific Cat#A-11006 IRDye ® 800CW Goat anti-Mouse IgG LI-COR Cat#925-32210 IRDye ® 680RD Goat anti-Rabbit IgG LI-COR Cat#925-68071 Mouse anti-cTnT Thermo Fisher Scientific Cat#MA5-12960 Mouse anti-cTnT-Alexa 647 conjugate BD Pharmingen cat#565744 Mouse anti-AuroraKB Novus Cat#NBP2-50039 Rat anti-PHH3 Abcam Cat#ab10543 Mouse anti-M2Flag Sigma-Aldrich Cat#F1804 Mouse anti-GAPDH Millipore Cat#CB1001 Rabbit Anti-PCM-1 Sigma-Aldrich Cat#HPA023370 Chicken anti-β-gal Abcam Cat#ab9361 Rabbit anti-N-cadherin Abcam Cat#ab76057 Rat anti-BrdU Accurate Chemical & Scientific corp Cat#OBT0030 Rabbit DYKDDDDK Tag Antibody Cell signaling technology Cat#2368 Bacterial and Virus Strains pCMV-flag YAP25SA Addgene, Kun-Liang Guan plasmid # 27371 Chemicals, Peptides, and Recombinant Proteins Tamoxifen Sigma-Aldrich Cat#T5648 Collagenase A Sigma-Aldrich Cat#10103586001 Blebbistatin Sigma-Aldrich Cat#B0560 di-4-ANEPS Invitrogen Cat#D-1199 BglII NEB Cat#R0143S EcoRI-HF® NEB Cat#R3101 BsrGI-HF® NEB Cat#R3575L T4 DNA ligase (3C) NEB Cat#R3575L Proteinase K Sigma-Aldrich Cat#P2308-25MG RNAse A Sigma-Aldrich Cat#10109142001 Protein-G Dynabeads ThermoFisher Scientific Cat#10004D Rhodamine conjugated WGA Vector Labs Cat#RL-1022 DAPI Thermo Fisher Scientific Cat#62248 OptiPrem Density Gradient Medium Sigma-Aldrich Cat#D1556 Critical Commercial Assays Click-iT EdU Alexa Fluor 647 Imaging Kit ThermoFisher Scientific Cat# {"type":"entrez-nucleotide","attrs":{"text":"C10340","term_id":"1535411","term_text":"C10340"}} C10340 iTaq ™ Universal SYBR ® Green Supermix Bio-Rad Cat#1725120 DpnII NEB Cat#R0543M T4 DNA ligase (4C) Roche Cat#10799009001 Proteinase K (4C) Thermo Fisher Cat#EO0491 NucleoMag 96 PCR kit Macherey-Nagel Cat#744100.1 Csp6I Thermo Fisher Cat#ER0211 Expand Long template polymerase Roche Cat#11681842001 Agencourt AMPure XP beads Beckman Coulter Cat#A63881 Tissue-Tek ® O.C.T.

Techniques: Virus, Plasmid Preparation, Recombinant, Imaging, SYBR Green Assay, Expressing, Software, Next-Generation Sequencing