Journal: Nucleic Acids Research

Article Title: Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis

doi: 10.1093/nar/gkq162

Figure Lengend Snippet: GW motif proteins identified in Arabidopsis genome after applying threshold filters on dos and ics scores

Article Snippet: AT5G07540.1 , 122.96 , 3.85 E –07 , 1.82 , GLYCINE-RICH PROTEIN 16 (GRP16); Oleosin (InterPro:IPR000136); FUNCTIONS IN: lipid binding, nutrient reservoir activity; INVOLVED IN: sexual reproduction, lipid storage;.

Techniques: Binding Assay, Activity Assay, DNA Methylation Assay, Methylation

Journal: Genes & Development

Article Title: Constitutive mTORC1 activation by a herpesvirus Akt surrogate stimulates mRNA translation and viral replication

doi: 10.1101/gad.1978310

Figure Lengend Snippet: Stimulation of Akt substrate phosphorylation by Us3. (A) NHDFs were mock-infected (Mock) or infected (MOI = 5) with Us3-deficient (ΔUs3) or wild-type HSV-1 (WT) in the presence (+) or absence (−) of Akt inhibitor VIII. At 16 hpi, total protein was isolated, fractionated by SDS-PAGE, and analyzed by immunoblotting with the indicated antisera. (B) U2OS cells transfected with the indicated plasmids (described in Fig. 4A) were treated with DMSO (−) or Akt inhibitor VIII (+). Proteins were analyzed as described in Figure 4A. In the p-FOXO immunoblot, the asterisk represents a nonspecific band insensitive to Akt inhibitor routinely observed in U2OS cells. (C) α Herpesvirus Us3 protein sequences (HSV-1, VZV, HSV-2, bovine herpesvirus, Mareks, and Pseudorabies) were aligned using ClustalW2 (Larkin et al. 2007), with a broad selection of kinases representing the range of subfamilies in the InterPro Protein Kinase superfamily (CL0016), including AKT1 (AAL55732), KAPCA (P17612), KPCA (P17252), p90_RPS6Ka3 (NP_004577), PIM-1 (P11309), ABCA1 (NP_005493), PAS_domain_STpK (NP_055963), PTKII (NP_751911), MAPK7 (O43318), INSR (P06213), EGFR (P00533), KALRN (O60229), TRIO (O75962), neuronal adhesion A (NP_001032209), Galactose-binding (O14786), PDZ-LIM (O00151), and PRIC1 (Q96MT3). The evolutionary history was inferred using the Minimum Evolution (ME) method (Rzhetsky and Nei 1992). The optimal tree with the sum of the branch length = 16.70884448 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (500 replicates) are shown next to the branches (Felsenstein 1985). The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Poisson correction method and are in the units of the number of amino acid substitutions per site. The ME tree was searched using the Close Neighbor Interchange (CNI) algorithm (Nei and Kumar 2000) at a search level of 1. The neighbor-joining algorithm (Saitou and Nei 1987) was used to generate the initial tree. All positions containing gaps and missing data were eliminated from the data set (complete deletion option). There were a total of 137 positions in the final data set. Phylogenetic analyses were conducted in MEGA4 (Tamura et al. 2007).

Article Snippet: In the p-FOXO immunoblot, the asterisk represents a nonspecific band insensitive to Akt inhibitor routinely observed in U2OS cells. ( C ) α Herpesvirus Us3 protein sequences (HSV-1, VZV, HSV-2, bovine herpesvirus, Mareks, and Pseudorabies) were aligned using ClustalW2 ( Larkin et al. 2007 ), with a broad selection of kinases representing the range of subfamilies in the InterPro Protein Kinase superfamily (CL0016), including AKT1 ( {"type":"entrez-protein","attrs":{"text":"AAL55732","term_id":"18027298","term_text":"AAL55732"}} AAL55732 ), KAPCA ( {"type":"entrez-protein","attrs":{"text":"P17612","term_id":"125205","term_text":"P17612"}} P17612 ), KPCA ( {"type":"entrez-protein","attrs":{"text":"P17252","term_id":"317373571","term_text":"P17252"}} P17252 ), p90_RPS6Ka3 ( {"type":"entrez-protein","attrs":{"text":"NP_004577","term_id":"4759050","term_text":"NP_004577"}} NP_004577 ), PIM-1 ( {"type":"entrez-protein","attrs":{"text":"P11309","term_id":"83305339","term_text":"P11309"}} P11309 ), ABCA1 ( {"type":"entrez-protein","attrs":{"text":"NP_005493","term_id":"21536376","term_text":"NP_005493"}} NP_005493 ), PAS_domain_STpK ( {"type":"entrez-protein","attrs":{"text":"NP_055963","term_id":"35038528","term_text":"NP_055963"}} NP_055963 ), PTKII ( {"type":"entrez-protein","attrs":{"text":"NP_751911","term_id":"26667203","term_text":"NP_751911"}} NP_751911 ), MAPK7 ( {"type":"entrez-protein","attrs":{"text":"O43318","term_id":"12643557","term_text":"O43318"}} O43318 ), INSR ( {"type":"entrez-protein","attrs":{"text":"P06213","term_id":"308153655","term_text":"P06213"}} P06213 ), EGFR ( {"type":"entrez-protein","attrs":{"text":"P00533","term_id":"2811086","term_text":"P00533"}} P00533 ), KALRN ( {"type":"entrez-protein","attrs":{"text":"O60229","term_id":"160380714","term_text":"O60229"}} O60229 ), TRIO ( {"type":"entrez-protein","attrs":{"text":"O75962","term_id":"257050981","term_text":"O75962"}} O75962 ), neuronal adhesion A ( {"type":"entrez-protein","attrs":{"text":"NP_001032209","term_id":"81158226","term_text":"NP_001032209"}} NP_001032209 ), Galactose-binding ( {"type":"entrez-protein","attrs":{"text":"O14786","term_id":"206729912","term_text":"O14786"}} O14786 ), PDZ-LIM ( {"type":"entrez-protein","attrs":{"text":"O00151","term_id":"20178312","term_text":"O00151"}} O00151 ), and PRIC1 ( {"type":"entrez-protein","attrs":{"text":"Q96MT3","term_id":"59800163","term_text":"Q96MT3"}} Q96MT3 ).

Techniques: Phospho-proteomics, Infection, Isolation, SDS Page, Western Blot, Transfection, Selection, Binding Assay

Journal:

Article Title: PANDORA: keyword-based analysis of protein sets by integration of annotation sources

doi: 10.1093/nar/gkg769

Figure Lengend Snippet: PANDORA graph of 140 proteins annotated by InterPro as ‘Homebox protein, antennapedia type’. Resolution is maximal (no simplification). Select annotations on nodes (InterPro in italics, SwissProt underlined): (A) ‘Homebox protein, antennapedia type’; (B) ‘Homeobox’, ‘DNA-binding’, ‘Nuclear protein’; (C) ‘Developmental protein’; (D) ‘Ribosomal protein’, ‘Mitochondrion’; (E) ‘ABC transporter’, ‘Nitrate assimilation’, ‘Membrane’; (F) ‘Chymotrypsin Serine protease S1’, ‘Zymogen’. Nodes D, E and F appear biologically distinct in the graph, and are falsely annotated as ‘Homebox protein, antennapedia type’ proteins.

Article Snippet: Select annotations on nodes (InterPro in italics, SwissProt underlined): (A) ‘ Homebox protein, antennapedia type ’; (B) ‘ Homeobox ’, ‘ DNA-binding ’, ‘ Nuclear protein ’; (C) ‘ Developmental protein ’; (D) ‘ Ribosomal protein ’, ‘ Mitochondrion ’; (E) ‘ ABC transporter ’, ‘ Nitrate assimilation ’, ‘ Membrane ’; (F) ‘ Chymotrypsin Serine protease S1 ’, ‘ Zymogen ’.

Techniques: Binding Assay, Membrane