Journal:

Article Title: Transcription-dependent recombination and the role of fork collision in yeast rDNA

doi: 10.1101/gad.1085403

Figure Lengend Snippet: Analysis of low-copy-rDNA strains. (A) Southern hybridization analysis of rDNA copy numbers. DNA was digested with BglII and subjected to electrophoresis followed by Southern analysis using the rDNA probe (Fig. 1). A single-copy gene, MCM2, was used as an internal control for normalization. (B) Quantitation of the intensities of the bands. NOY408-1b (wild-type strain), NOY408-1bf (fob1), TAK300 (fob1; low-copy rDNA strain), TAK301 (fob1 pol1; low-copy rDNA strain). (C) Collision between the transcription and the replication machineries analyzed by 2D gel analysis. DNA was prepared from the strains indicated, digested with BglII and SphI, and subjected to 2D agarose gel electrophoresis followed by Southern hybridization using the rDNA probe (see Fig. 1). A spot indicated by an arrowhead shows accumulation of Y-shaped DNA molecules at the RFB site (panel a). The slowdown region (SDR) is located between two arrows (panel c). The numbers in parentheses are copy numbers of rDNA in each strain. (Panel a) NOY408-1b (wild-type strain). (Panel b) NOY408-1bf (fob1). (Panel c) TAK300 (fob1; low-copy rDNA strain). (Panel d) TAK301 (fob1 pol1; low-copy rDNA strain). (Panel e) TAK301, complemented by a plasmid-borne RPA135 gene (fob1 POLI; low-copy rDNA strain).

Article Snippet: Replication fork blocking and slowdown activities were analyzed using 2D gel electrophoresis as described previously ( Brewer and Fangman 1987 ).

Techniques: Hybridization, Electrophoresis, Control, Quantitation Assay, Two-Dimensional Gel Electrophoresis, Agarose Gel Electrophoresis, Plasmid Preparation

Journal: Plant Physiology

Article Title: eIFiso4G Augments the Synthesis of Specific Plant Proteins Involved in Normal Chloroplast Function ^{1 [OPEN]}

doi: 10.1104/pp.19.00557

Figure Lengend Snippet: 2D-DIGE of proteins extracted from double or triple mutants. Protein extracts were cy2 (Col-0) or cy3 (i4g1 x i4g2 or i4f) dye-labeled and run on 2D-PAGE (Applied Biomics). A, Wild type (Col-0) and mutant (i4g1 x i4g2; i4f) 2D gels are shown. B, Superimposed images comparing wild-type and mutant protein extracts as indicated. Green indicates the protein is decreased relative to Col-0, red indicates the protein is increased relative to Col-0, and yellow indicates that the protein level remained the same. Proteins that were measurably increased or decreased were identified by mass spectrometry. See Supplemental Table S1 for all mutants.

Article Snippet: A more sensitive method using 2D differential gel electrophoresis (2D-DIGE; Applied Biomics) was used to identify more subtle changes in protein levels.

Techniques: Labeling, Mutagenesis, Mass Spectrometry

Journal: Plant Physiology

Article Title: eIFiso4G Augments the Synthesis of Specific Plant Proteins Involved in Normal Chloroplast Function ^{1 [OPEN]}

doi: 10.1104/pp.19.00557

Figure Lengend Snippet: Confirmation by western blotting of protein targets identified as decreased by 2D-DIGE in double or triple mutants. Total plant extracts were probed with antibodies to protein targets identified by 2D-DIGE in wild-type and mutant plants. A, Proteins that were the most decreased evidenced by 2D-DIGE: Lhcb3, Lhcb1, RCA, and CA1; i4G and i4E and actin are included as controls. B, Additional proteins identified as decreased in the 2D-DIGE: PsbP, VIPP1, PsbQ, and PsbO. See Supplemental Figure S4A for an example of the Stain-Free gel for protein loading comparison. MW, molecular weight.

Article Snippet: A more sensitive method using 2D differential gel electrophoresis (2D-DIGE; Applied Biomics) was used to identify more subtle changes in protein levels.

Techniques: Western Blot, Mutagenesis, Staining, Molecular Weight