Journal: Molecular Vision

Article Title: Anterior segment mesenchymal dysgenesis in a large Australian family is associated with the recurrent 17 bp duplication in PITX3

doi:

Figure Lengend Snippet: Analysis of exon 4 of PITX3 . A : The gel of amplification products is shown. The 231 bp band containing the insertion is clearly separated from the 214 bp band. A heteroduplex band can also be seen in heterozygous individuals. –ve stands for the unaffected, control individual. M stands for the molecular weight marker, a HpaII digest of the plasmid pUC19. The bands either side of the amplification products are 190 and 242 bp. The heteroduplex runs with the 331 bp band. B : The sequence of exon 4, containing the insertion, for individual III-5 is shown.

Article Snippet: The molecular weight marker was HpaII-digested plasmid, pUC19 (catalog number DMWP-1; Geneworks, Adelaide, South Australia, Australia).

Techniques: Amplification, Control, Molecular Weight, Marker, Plasmid Preparation, Sequencing

Journal: Molecular Vision

Article Title: Anterior segment mesenchymal dysgenesis in a large Australian family is associated with the recurrent 17 bp duplication in PITX3

doi:

Figure Lengend Snippet: Prenatal diagnosis of the inherited duplication. Gels of amplification products are shown. Lanes 1 and 6 are a negative control. Lanes 2 and 5 are the positive control, III-5. Lanes 3 and 4 show two dilutions of the CVS material for IV-9. Lanes 7 and 8 show two dilutions of the CVS material for IV-10. M is the molecular weight marker, a HpaII digest of pUC19. IV-9 has the insertion band and IV-10 has only the normal band.

Article Snippet: The molecular weight marker was HpaII-digested plasmid, pUC19 (catalog number DMWP-1; Geneworks, Adelaide, South Australia, Australia).

Techniques: Biomarker Discovery, Amplification, Negative Control, Positive Control, Molecular Weight, Marker

Journal: bioRxiv

Article Title: Active DNA demethylation of developmental cis -regulatory regions predates vertebrate origins

doi: 10.1101/2021.11.07.467601

Figure Lengend Snippet: (A) Percentage of methylated and hydroxymethylated CpGs in embryonic and adult tissues of sea urchin, lancelet, and zebrafish. CpG sites with at least 80% methylation and CpG sites with at least 10% hydroxymethylation ( P adj. < 0.05) were included in the analysis. Only CpG sites with a minimum of 10x coverage were considered. (B) Concordance of hydroxymethylation levels between biological replicates. Sea urchin 48hpf and lancelet 60hpf samples are shown. (C, D) Ternary plots depicting the relationship between methylated (mC), hydroxymethylated (hmC) and unmethylated (C) CpG states in sea urchin (C) and lancelet (D) embryos and adult tissues. CpG sites hydroxymethylated at 48hpf in sea urchin (C) and 60 hpf in lancelet (D) ( P adj. < 0.05, proportion test), are shown. (E, F) Heatmaps depicting DNA hydroxymethylation dynamics (ACE-seq) of open chromatin regions (ATAC-seq) in sea urchin (E) and lancelet (F) . K-means clustering (k=2) of ACE-seq and ATAC-seq signal over ATAC-seq peaks. Boxplots of DNA hydroxymethylation and DNA methylation dynamics during sea urchin (E) and lancelet (F) development. (G) IGV browser tracks depicting DNA hydroxymethylation (ACE-seq and hMeDIP-seq) enrichment at open chromatin regions (ATAC-seq) coinciding with DNA demethylation (MethylC-seq) in sea urchin and lancelet genomes.

Article Snippet: Briefly, 100 ng of genomic DNA extracted from sea urchin, lancelet, and zebrafish embryos and adult tissues was spiked with 1 ng of CpG-methylated λ phage DNA (Wisegene) and 0.5 ng of all-C hydroxymethylated pUC19 plasmid DNA (Wisegene) and sonicated to ∼300 bp fragments using a M220 focused ultrasonicator (Covaris), with the following parameters: peak incident power, 50W; duty factor, 20%; cycles per burst, 200; treatment time, 75 sec. Sonicated DNA (125 μL total volume) was concentrated to 16.6 μL using AMPure beads (1 volume DNA : 2 volumes AMPure beads).

Techniques: Methylation, DNA Methylation Assay

Journal: ACS Omega

Article Title: Synthesis, Characterization, Crystal Structure, DNA and HSA Interactions, and Anticancer Activity of a Mononuclear Cu(II) Complex with a Schiff Base Ligand Containing a Thiadiazoline Moiety

doi: 10.1021/acsomega.1c05750

Figure Lengend Snippet: Cleavage of pUC19 DNA (200 ng) in Tris–HCl buffer (50 mM) at a pH 8.0 through the oxidative pathway at 37 °C. (a) Lane 1, DNA + H 2 O 2 (1 mM) control; lane 2, DNA + 1 (0.5 μM) + H 2 O 2 (1 mM); lane 3, DNA + 1 (1 μM) + H 2 O 2 (1 mM); lane 4, DNA + 1 (2.5 μM) + H 2 O 2 (1 mM); lane 5, DNA + 1 (5 μM) + H 2 O 2 (1 mM); lane 6, DNA + 1 (10 μM) + H 2 O 2 (1 mM); lane 7, DNA + 1 (10 μM) + H 2 O 2 (1 mM) + DMSO (2 μL); lane 8; DNA + 1 (10 μM) + H 2 O 2 (1 mM) + NaN 3 (500 μM).

Article Snippet: Calf thymus DNA was obtained from Sigma, and pUC19 DNA was supplied by Genetix Biotech.

Techniques: Control

Journal: ACS Omega

Article Title: Synthesis, Characterization, Crystal Structure, DNA and HSA Interactions, and Anticancer Activity of a Mononuclear Cu(II) Complex with a Schiff Base Ligand Containing a Thiadiazoline Moiety

doi: 10.1021/acsomega.1c05750

Figure Lengend Snippet: Cleavage of pUC19 DNA (200 ng) in Tris–HCl buffer (50 mM) at a pH 8.0 through the hydrolytic pathway at 37 °C. (a) Lane 1, only pUC19 DNA as the control; lane 2, pUC19 DNA + 1 (50 μM); lane 3, pUC19 DNA + 1 (100 μM); lane 4, pUC19 DNA + 1 (150 μM); lane 5, pUC19 DNA + 1 (200 μM); lane 6, pUC19 DNA + 1 (250 μM).

Article Snippet: Calf thymus DNA was obtained from Sigma, and pUC19 DNA was supplied by Genetix Biotech.

Techniques: Control

Journal: BMC Genomics

Article Title: GlaI digestion of mouse γ-satellite DNA: study of primary structure and ACGT sites methylation

doi: 10.1186/1471-2164-10-322

Figure Lengend Snippet: Mouse genomic DNA cleavage with enzymes GlaI, Sse9I, FatI, Bst2UI . 1,8% low melting point agarose, Tris-acetate buffer. M – DNA marker pUC19/MspI (the lengths of the fragments are shown at right).

Article Snippet: The following DNA preparations were used as DNA fragment length markers: 1 kbp DNA ladder and pUC19/MspI DNA ladder (SibEnzyme Ltd., Russia).

Techniques: Marker

Journal: BMC Genomics

Article Title: GlaI digestion of mouse γ-satellite DNA: study of primary structure and ACGT sites methylation

doi: 10.1186/1471-2164-10-322

Figure Lengend Snippet: A physical map of mouse γ-satellite DNA . A – gel photo of mouse genomic DNA cleavage with restriction enzymes (double digestions). Lanes: 4 – intact DNA; 1, 3, 5, 7, 9 – GlaI added; 1, 2 – AcsI added; 5, 6 – FatI added; 7, 8 – BstF5I added; 9, 10 – Bst2UI added; M – DNA marker pUC19/MspI. B-F – physical maps of mouse γ-satellite DNA with indication of experimentally obtained DNA fragments and theoretically predicted ones. B – GlaI; C – double digestion with GlaI and AcsI; D – double digestion with GlaI and FatI; E – double digestion with GlaI and BstF5I; F – double digestion with GlaI and Bst2UI. Experimental patterns of mouse DNA hydrolysis and DNA ladders are shown on a left side of each figure. Positions of cleavage sites are shown in brackets at the top. Intact GlaI fragments are shown in black, cleaved GlaI fragments are shown in grey, double digestion products are shown in brown. Horizontal dotted lines show a correspondence of predicted fragments (arrows) to those observed on gel photos.

Article Snippet: The following DNA preparations were used as DNA fragment length markers: 1 kbp DNA ladder and pUC19/MspI DNA ladder (SibEnzyme Ltd., Russia).

Techniques: Marker