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: Dose-Response

Article Title: Biological Entanglement–Like Effect After Communication of Fish Prior to X-Ray Exposure

doi: 10.1177/1559325817750067

Figure Lengend Snippet: Representative 2-D gel showing protein spots selected for identification. Nine canalicular multispecific organic ion transporter/multidrug resistance–associated protein 2, 14 intermediate filament protein, 18 α-enolase, 21 bifunctional P-450/NADPH-P450 reductase, 22 canalicular multispecific organic ion transporter/multidrug resistance–associated protein 2, 30 ubiquitin-40S ribosomal protein, 36 intermediate filament protein, 45 glucose-6-phosphate 1-dehydrogenase, 64 glycine-tRNA ligase β subunit, 69 14-3-3 protein β subunit, 74 gasdermin, 80 fructose bisphosphate aldolase, 82 Tubulin β-1 chain, 89 vacuolar membrane–associated protein IML1, 95 tropomyosin α-1 chain/β chain, 101 tropomyosin α-3 chain, 111 glucose-6-phosphate 1-dehydrogenase, 123 ABC transporter G family member. 2-D, 2-dimensional

Article Snippet: Gel image analysis was carried out using the Phoretix 2-D software (Progenesis PG200, Phoretix International, United Kingdom) with protein expression being quantitatively expressed as “normalized spot volume,” a parameter which combines the spot size and intensity.

Techniques:

Journal: The FEBS journal

Article Title: A novel 2D-based approach to the discovery of candidate substrates for the metalloendopeptidase meprin.

doi: 10.1111/j.1742-4658.2008.06592.x

Figure Lengend Snippet: Fig. 1. Simple 2D IEF ⁄ SDS ⁄ PAGE-based image analysis procedure. The procedure is based on qualitative differences among reference gels (level 1 match-sets) of each group of five gel replicates (three pooled biological gel replicates and two more technical gel repli- cates). Gel replicates of each group (activated meprin versus non-activated meprin) were cut virtually into four equally spaced quadrants for four independent image analyses. Reference gels of each group were then clustered into a new set for higher-level image analysis. The spot matching features of PDQUEST (version 7.3.1) allowed for detection of unique protein spots. The combined higher- level match-set is the final fusion of all annotated unique spots into one big 2D reference map.

Article Snippet: 2D IEF ⁄ SDS ⁄PAGE-based image analysis was performed using the program pdquest, version 7.3.1 (Bio-Rad Laboratories).

Techniques:

Journal: The FEBS journal

Article Title: A novel 2D-based approach to the discovery of candidate substrates for the metalloendopeptidase meprin.

doi: 10.1111/j.1742-4658.2008.06592.x

Figure Lengend Snippet: Fig. 2. Application of a simple 2D IEF ⁄ SDS ⁄ PAGE-based protease proteomic approach in substrate finding. A representative image analysis of the first quadrant is shown. Two hundred and fifty micrograms of conditioned medium protein from trypsin activated and non-activated MDCKa ⁄ b cells was separated by IEF in a 24 cm long IPG pH 3–10 NL strip. Vertical separation was according to mass in a 12.5% SDS gel. Optimized Ruthenium staining: for each condition (activated meprin versus non-activated meprin), three pooled biological gel replicates (from 18 dishes per pooled sample) and two more technical gel replicates (of one pooled sample) were produced for subsequent image analysis. Unique protein spots are labelled in level 1 and higher-level match-sets with SSP assigned by the image analysis software.

Article Snippet: 2D IEF ⁄ SDS ⁄PAGE-based image analysis was performed using the program pdquest, version 7.3.1 (Bio-Rad Laboratories).

Techniques: Stripping Membranes, SDS-Gel, Staining, Produced, Software

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: 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