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

Journal: Oncotarget

Article Title: MicroRNA-1291 targets the FOXA2-AGR2 pathway to suppress pancreatic cancer cell proliferation and tumorigenesis

doi: 10.18632/oncotarget.9999

Figure Lengend Snippet: ( A–C ) 2D-DIGE images of proteins in the control and miR-1291-expression PANC-1 cells labeled with green and red fluorescent dye, respectively, and the overlaid graph indicating the difference in the abundance of proteins. The protein downregulated in miR-1291-expressing PANC-1 cells to the greatest degree was identified as AGR2. ( D, E ) Immunocytochemistry analysis confirmed the sharp downregulation of AGR2 (brown staining) in miR-1291-expressing PANC-1 cells (400 ×).

Article Snippet: Proteins were extracted from miR-1291-expressing PANC-1 cells and control cells, and subjected to 2D-DIGE and protein identification by MALDI-TOF and tandem MS (Applied Biomics, Hayward, CA), as described [ , ].

Techniques: Expressing, Labeling, Immunocytochemistry, Staining

Journal: Oncotarget

Article Title: MicroRNA-1291 targets the FOXA2-AGR2 pathway to suppress pancreatic cancer cell proliferation and tumorigenesis

doi: 10.18632/oncotarget.9999

Figure Lengend Snippet: Proteins differentially expressed in miR-1291-expressing and control PANC-1 cells, which were identified by 2D-DIGE, MALDI-TOF and MS/MS proteomic profiling study

Article Snippet: Proteins were extracted from miR-1291-expressing PANC-1 cells and control cells, and subjected to 2D-DIGE and protein identification by MALDI-TOF and tandem MS (Applied Biomics, Hayward, CA), as described [ , ].

Techniques: Binding Assay

Journal: Oncotarget

Article Title: MicroRNA-1291 targets the FOXA2-AGR2 pathway to suppress pancreatic cancer cell proliferation and tumorigenesis

doi: 10.18632/oncotarget.9999

Figure Lengend Snippet: Network of interactions was constructed using IPA software. The input was all miR-1291-altered proteins (in bold) in PANC-1 cells identified by 2D-DIGE, MALDI-TOF and MS/MS proteomic profiling study.

Article Snippet: Proteins were extracted from miR-1291-expressing PANC-1 cells and control cells, and subjected to 2D-DIGE and protein identification by MALDI-TOF and tandem MS (Applied Biomics, Hayward, CA), as described [ , ].

Techniques: Construct, Software, Tandem Mass Spectroscopy

Journal: The FASEB Journal

Article Title: Cyclophilin A contributes to aortopathy induced by postnatal loss of smooth muscle TGFBR1

doi: 10.1096/fj.201900601RR

Figure Lengend Snippet: Deletion of Tgfbr1 promotes aberrant TGFBR2 signaling and induction of CypA production in Tgfbr1iko SMCs. A) Two-dimensional DIGE was used to profile proteins extracted from Tgfbr1iko SMCs with or without TGF-β1 treatment (1.0 ng/ml, 24 h). Proteins differentially expressed in treated vs. untreated cells were identified by LC-MS/MS, and 1 highly induced protein was found to be CypA. B) CypA production in Tgfbr1iko SMCs after TGF-β1 stimulation. C) CypA production in Tgfbr1iko SMCs after treatment with TGF-β1, LY2109761 (a TGFBR2 kinase inhibitor), or LY2109761 and TGF-β1. D) CypA production in Tgfbr1iko SMCs after treatment with GDF15, LY2109761, or LY2109761 and GDF15. E) Effect of Tgfbr2 siRNA silencing on CypA production in Tgfbr1iko SMCs after TGF-β1 stimulation. F) TGF-β1–induced CypA production in Tgfbr1iko SMCs pretreated with SIS3 (a SMAD3 inhibitor). Expression data (B–F) were obtained by Western blot analysis. Data are expressed as band intensity normalized to the levels of GAPDH, and significance was analyzed using 1-way ANOVA.

Article Snippet: Two-dimensional (2D) difference gel electrophoresis (DIGE) protein expression profiling and liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis of cell lysates was performed by Applied Biomics (Hayward, CA, USA).

Techniques: Liquid Chromatography with Mass Spectroscopy, Expressing, Western Blot