Journal: Genome Research

Article Title: Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns

doi: 10.1101/gr.101535.109

Figure Lengend Snippet: High-resolution genome-wide methylation profiling and genome-wide DNA methylation trends. (A) Browser view of Methyl-MAPS data from the genomic region spanning the BIK gene. Individual mapped sequence reads are shown in the top raw data tracks. Red sequences were resistant to methylation-sensitive restriction endonucleases (RE) and are therefore methylated. Blue sequences were resistant to the methylation-dependent McrBC complex and are unmethylated. Tick marks in both tracks along the top of the figure and within each sequence indicate locations of individual RE and McrBC recognition sequences. Methylation data is also presented in a concise view, where each CpG is assigned a methylation score from the ratio of methylated to total (unmethylated and methylated) sequences covering each CpG site. The bulk of the BIK gene is methylated, while the CpG-rich promoter is unmethylated. (B) Methylation of the SVA retrotransposon in a repeat-rich region of chr 19. While the CpG density is comparable to that of the CpG island of the BIK gene shown in A, the SVA retrotransposon is densely methylated.

Article Snippet: A 100 molar ratio excess of CAP adaptors (containing EcoP15I sites) was ligated onto the end-polished, EcoP15I-methylated DNA molecules (1× Invitrogen ligase buffer [5×], 30 U of Ambion T4 DNA ligase), followed by PCP.

Techniques: Genome Wide, Methylation, DNA Methylation Assay, Sequencing

Journal: Genome Research

Article Title: Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns

doi: 10.1101/gr.101535.109

Figure Lengend Snippet: (A,B) CpG distributions and methylation patterns in human genes. m5CpG and CpG densities are shown in relation to enhancers (A), TSS, exon splice sites, stop codons, and poly(A) sites (B). Note spikes in CpG and m5CpG densities at the 5′ and 3′ ends of exons and internal to the stop codon in the last exon. (C) Comparison of methylation patterns in normal breast tissue from two individuals. Methylation status of each CpG with high coverage is computed for each sample. The frequency of such points is then plotted as a function of the methylation score for each sample. Heat map indicates frequency. Values in the left corner are unmethylated in both samples. Values in the right corner are methylated in both samples. Values along the horizontal are equivalently methylated in each sample. Some sequence classes have a wide range of methylation states, such as intronic and intergenic single-copy sequences and LINEs, LTRs, and DNA transposons. Other classes such as SINEs, exons, simple repeats, and promoters are polarized.

Article Snippet: A 100 molar ratio excess of CAP adaptors (containing EcoP15I sites) was ligated onto the end-polished, EcoP15I-methylated DNA molecules (1× Invitrogen ligase buffer [5×], 30 U of Ambion T4 DNA ligase), followed by PCP.

Techniques: Methylation, Comparison, Sequencing

Journal: ADMET & DMPK

Article Title: Synthetic routes to theranostic applications of carbon-based quantum dots

doi: 10.5599/admet.1747

Figure Lengend Snippet: Summary of top-down approaches used for the preparation of CDs for various biomedical applications

Article Snippet: The team utilized the hydrothermal method by heating the solution at a constant temperature of 140 °C for 10 h. The prepared CDs ranging from 2-6 nm led to the formation of fluorescence molecules (1,2,3,5-tetrahydro-50oxo-imidazo[1,2- a ] pyridine-7-carboxylic acid, IPCA) via amidation reaction to form the branched polymers.

Techniques: Quantitation Assay, Imaging, Fluorescence, Irradiation

Journal: ADMET & DMPK

Article Title: Synthetic routes to theranostic applications of carbon-based quantum dots

doi: 10.5599/admet.1747

Figure Lengend Snippet: Summary of the hydrothermal method used for the preparation of CDs for various biomedical applications

Article Snippet: The team utilized the hydrothermal method by heating the solution at a constant temperature of 140 °C for 10 h. The prepared CDs ranging from 2-6 nm led to the formation of fluorescence molecules (1,2,3,5-tetrahydro-50oxo-imidazo[1,2- a ] pyridine-7-carboxylic acid, IPCA) via amidation reaction to form the branched polymers.

Techniques: Labeling, Activity Assay, Fluorescence

Journal: ADMET & DMPK

Article Title: Synthetic routes to theranostic applications of carbon-based quantum dots

doi: 10.5599/admet.1747

Figure Lengend Snippet: Summary of carbon dots prepared for theranostic tumor applications

Article Snippet: The team utilized the hydrothermal method by heating the solution at a constant temperature of 140 °C for 10 h. The prepared CDs ranging from 2-6 nm led to the formation of fluorescence molecules (1,2,3,5-tetrahydro-50oxo-imidazo[1,2- a ] pyridine-7-carboxylic acid, IPCA) via amidation reaction to form the branched polymers.

Techniques: Imaging, Fluorescence, Activity Assay, Formulation, In Vivo, In Vitro, Membrane, Synthesized, Inhibition, Optical Imaging, Irradiation