Journal:

Article Title: Involvement of Superoxide Dismutases in the Response of Escherichia coli to Selenium Oxides

doi: 10.1128/JB.184.6.1556-1564.2002

Figure Lengend Snippet: Comparative 2D gel electrophoresis analyses of total E. coli proteins expressed in response to selenium oxide treatment. Autoradiograms of 2D gels performed with total E. coli extracts from [35S] methionine-labeled cells as described in Materials and Methods are shown. The extracts were prepared from control untreated cells (A), from cells exposed to SeO42− (2 mM) for 30 min (B), and from cells exposed to SeO32− (2 mM) for 30 min (C). Proteins whose synthesis rate is stimulated upon SeO42− or SeO32− exposure were identified by mass spectrometry and are indicated on the map. Protein spots induced but not characterized are also indicated by an arrow. Proteins repressed by SeO42− or SeO32− are indicated by a black bar in panel A.

Article Snippet: The spots on the radioactive gels were recorded by PhosphorImager technology (Molecular Dynamics) and analyzed with a 2D gel analysis software (MelanieII; Bio-Rad).

Techniques: Two-Dimensional Gel Electrophoresis, Electrophoresis, Labeling, Mass Spectrometry

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

Journal: BioMed Research International

Article Title: Proteomic Analysis of Fetal Ovaries Reveals That Primordial Follicle Formation and Transition Are Differentially Regulated

doi: 10.1155/2017/6972030

Figure Lengend Snippet: Representative 2D-DIGE gel image of differentially expressed proteins of fetal ovaries at day 55 and day 90 of gestation. The proteins extracted from the fetal ovaries at day 55 and day 90 of gestation samples were labelled with cy3 and cy5, respectively. An internal standard protein sample (a mixture of fetal ovaries at day 55 and day 90 of gestation samples) was labelled with the Cy2 dye. The number in the figure corresponds to the number shown in .

Article Snippet: The 2D DIGE gel images were analyzed by the Image Master 2D platinum 7.0 software (GE Healthcare Life Sciences, NJ, USA) and the protein abundance changes for spot picking detection were calculated using cy3/cy2 and cy5/cy2 differential in-gel analysis ratios.

Techniques:

Journal: BMC Plant Biology

Article Title: Integration of proteomic and genomic approaches to dissect seed germination vigor in Brassica napus seeds differing in oil content

doi: 10.1186/s12870-018-1624-7

Figure Lengend Snippet: The 2D-DIGE maps and the functional categorization of DEPs in germinating B. napus seeds with high and low oil content. a - e represent the 2D-DIGE maps of 12WH191 (H) and KenC8 (L) germinating seeds at 0, 12, 24, 36 and 48 HAI. f represents the functional categorization of DEPs. Arrows show the protein spots that were highly expressed in low oil-containing seeds; lines show the protein spots that were highly expressed in high oil-containing seeds

Article Snippet: For 2D-DIGE analysis, the labeled proteins were mixed with 2D-DIGE buffer (7 M urea, 2 M thiourea, 4% CHAPS, 0.4% DTT, 0.5% IPG buffer) and separated with isoelectric focusing after being loaded on an immobilized pH gradient strip (IPG, pH 4–7, 24 cm; Amersham Biosciences, Uppsala, Sweden) [ ].

Techniques: Functional Assay