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Category:Team Bucky's Bugs

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StatusPageUserDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
unacceptableECOLI:SUFECneitzel2, Team Bucky's Bugs2013-11-10 16:21:07 CSTGO:0097361 CIA complex (C)PMID:24196966ECO:0000314 direct assay evidence used in manual assertion

Figure 3. SufS-SufE complex formation.

challenge
unacceptableMYCTU:PKNHCneitzel2, Team Bucky's Bugs2013-11-10 15:51:12 CSTGO:0045927 positive regulation of growth (P)PMID:22383473ECO:0000314 direct assay evidence used in manual assertion

Figure 4b. pknH is required for diazotrophic growth

challenge
unacceptableKLEPN:NIFJCneitzel2, Team Bucky's Bugs2013-11-10 15:19:13 CSTGO:0008901 ferredoxin hydrogenase activity (F)PMID:21317262ECO:0000314 direct assay evidence used in manual assertion

Table 2. Hydrogenase activities.

challenge
unacceptableDROME:ATLASEmuehlenkamp, Team Bucky's Bugs2013-11-04 19:32:46 CSTPMID:19573020ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 4. Vesicle formation from swollen tubules or ER.

challenge
unacceptableDROME:ATLASEmuehlenkamp, Team Bucky's Bugs2013-11-04 19:17:20 CSTGO:0071787 endoplasmic reticulum tubular network assembly (P)PMID:19573020ECO:0000314 direct assay evidence used in manual assertion

Fig. 3. Atlastin induces formation of tubules characteristic of the ER.

challenge
unacceptableDROME:ATLASEmuehlenkamp, Team Bucky's Bugs2013-11-04 18:33:48 CSTGO:0016050 vesicle organization (P)PMID:19573020ECO:0000314 direct assay evidence used in manual assertion

Fig. 2. Atlastin helps form vesicles with VSV-G and increases sensitivity to VSV-G.

challenge
unacceptableDROME:TERAEmuehlenkamp, Team Bucky's Bugs2013-11-04 14:33:17 CSTGO:0016485 protein processing (P)PMID:23790629ECO:0000314 direct assay evidence used in manual assertion

Fig. 5. Loss of VCP causes a suppression of the atlastin overexpression phenotype, rough or small eyes.

challenge
unacceptableDROME:TERAEmuehlenkamp, Team Bucky's Bugs2013-11-04 14:26:54 CSTGO:0016485 protein processing (P)PMID:23790629ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 4. VCP contributes to atlastin function. VCP expression directly influences atlastin expression as seen by large or rough eyes.

challenge
requireschangesDROME:TERAEmuehlenkamp, Team Bucky's Bugs2013-11-04 14:21:33 CSTGO:0007029 endoplasmic reticulum organization (P)PMID:23790629ECO:0000314 direct assay evidence used in manual assertion

Fig. 2B,C, and D all show atlastin and VCP in ER regions.

challenge
unacceptableDROME:TERAEmuehlenkamp, Team Bucky's Bugs2013-11-04 14:12:55 CSTGO:0016485 protein processing (P)PMID:23790629ECO:0000316 genetic interaction evidence used in manual assertion

Fig. 2A. VCP is confirmed to interact with atlastin, known to function in protein processing, through co-immunoprecipitation.

challenge
unacceptableDROME:TERAEmuehlenkamp, Team Bucky's Bugs2013-11-04 13:57:33 CSTGO:0016485 protein processing (P)PMID:23790629ECO:0000317 genomic context evidence used in manual assertion

Fig. 1B. Proteins are identified through DAVID and again through DroPNet and constructed into a web through Cytoscape. Valosin-containing protein (VCP) homologue (TER94) is found in th protein processing section of the atlastin interactome web.

challenge
unacceptable9FLAV:Q9J1B7Kbohning, Team Bucky's Bugs2013-10-27 14:33:02 CDTGO:0008166 viral replication (P)PMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Figure 4 (B) Association of Hsp70 with NS3 and NS5 proteins and viral RNA in JEV-infected cells. 293T cells were transfected with Hsp70-Myc expressing plasmid or vector before being mock-infected or infected with JEV at an MOI of 1.0. Cell lysates were harvested at 36 h p.i. and subjected to immunoprecipitation with antibody against Myc, followed by Western blotting for the detection of NS3 and NS5. The RNA were extracted from the precipitates and then subjected to RT-PCR for detecting viral RNA. RNA extracted from cells infected and uninfected with JEV was used as positive control (PC) and negative control (NC) respectively.

challenge
unacceptable9FLAV:Q9J1B7Kbohning, Team Bucky's Bugs2013-10-27 14:31:47 CDTPMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Figure 4A. Interaction of Hsp70 with components of the JEV replicase complex.

Interaction of Hsp70 with JEV NS3. 293T cells were co-transfected with Myc-tagged Hsp70 plasmid and Flag-tagged NS3 plasmid or vector. Cell lysates were harvested 36 h after transfection for co-IP experiments with anti-Flag antibody. The precipitates were then analyzed by Western blotting with anti-Flag or anti-Myc antibody.

challenge
requireschanges9FLAV:Q9J1B7Kbohning, Team Bucky's Bugs2013-10-27 14:28:17 CDTGO:0008166 viral replication (P)PMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Figure 3D.The direct interaction between GST-NS5 RdRp domain and His-Hsp70 was analyzed by GST pull-down assay and Western blotting.

challenge
unacceptable9FLAV:Q9J1B7Kbohning, Team Bucky's Bugs2013-10-27 14:26:37 CDTGO:0008166 viral replication (P)PMID:24086464ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3C.The purified proteins of GST-NS5 (406-905) and His-Hsp70 were analyzed by SDS-PAGE.

challenge
unacceptable9FLAV:Q9J1B7Kbohning, Team Bucky's Bugs2013-10-27 14:25:17 CDTGO:0008166 viral replication (P)PMID:24086464ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 3B.Interaction of Hsp70 with deletion mutants of NS5 protein. Hsp70-Myc and a series of deletion mutants of Flag-NS5 were co-transfected in 293T cells, precipitated with mouse anti-Flag MAb and then subjected to Western blotting.

challenge
unacceptable9FLAV:Q9J1B7Kbohning, Team Bucky's Bugs2013-10-27 14:23:33 CDTGO:0008166 viral replication (P)PMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Figure 2B.Interaction of the JEV NS5 protein with identified cellular proteins. 293T cells were transfected with expression plasmids encoding Flag-NS5 and eEF-1α-Myc.

challenge
unacceptable9FLAV:Q9J1B7Kbohning, Team Bucky's Bugs2013-10-27 14:20:33 CDTGO:0008166 viral replication (P)PMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Figure 2C. Interaction of the JEV NS5 protein with identified cellular proteins.293T cells were transfected with expression plasmids encoding Flag-NS5 and Ran-Myc.

challenge
unacceptable9FLAV:Q9J1B7Kbohning, Team Bucky's Bugs2013-10-27 14:15:55 CDTGO:0008166 viral replication (P)PMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Figure 2A. Interaction of the JEV NS5 protein with identified cellular proteins.293T cells were transfected with expression plasmids encoding Flag-NS5 and Hsp70-Myc.

challenge
unacceptable9FLAV:Q9J1B7Kbohning, Team Bucky's Bugs2013-10-27 14:12:42 CDTGO:0008166 viral replication (P)PMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Figure 1B. Western Blot analysis of the purified proteins. Anti-Flag antibody was used to detect Flag-HA-NS5 protein. In lane 1 of both panels, the black arrowheads mark the expected full length Flag-HA-NS5.

challenge
unacceptable9FLAV:Q9J1B7Kbohning, Team Bucky's Bugs2013-10-27 14:10:52 CDTGO:0008166 viral replication (P)PMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Figure 1A.Purification of NS5-interacting proteins using the TAP method

challenge
unacceptableDROME:TERAEmuehlenkamp, Team Bucky's Bugs2013-10-21 15:21:34 CDTGO:0046907 intracellular transport (P)PMID:23790629ECO:0000255 match to sequence model evidence used in manual assertion

Table 1.Valosin-containing protein (VCP) homologue function categorized by DAVID and receiving the highest MASCOT score in anti-myc affinity purification and mass-spectrometry with the protein atlastin.

challenge
unacceptableBACSU:TILSKbohning, Team Bucky's Bugs2013-10-13 17:28:52 CDTGO:0016563 transcription activator activity (F)PMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Fig.7 In vitro transcription analyses.

challenge
unacceptableBACSU:TILSKbohning, Team Bucky's Bugs2013-10-13 17:26:30 CDTGO:0016563 transcription activator activity (F)PMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 Gel filtration chromatograms for His-tagged TilS alone.

challenge
unacceptableBACSU:TILSKbohning, Team Bucky's Bugs2013-10-13 17:21:16 CDTGO:0016563 transcription activator activity (F)PMID:24086464ECO:0000314 direct assay evidence used in manual assertion

Figure 4. SDS Page Analysis of co-purification of TilS and HprT by

Ni-NTA affinity chromatography.

challenge
unacceptable9FLAV:G4XII4Kbohning, Team Bucky's Bugs2013-09-26 19:03:32 CDTGO:0019079 viral genome replication (P)PMID:22796133ECO:0000314 direct assay evidence used in manual assertion

Figure 3B.Binding capacities of NS5 of Tick-borne encephalitis and West Nile virus encephalitis.

challenge
acceptable9FLAV:G4XII4Kbohning, Team Bucky's Bugs2013-09-26 18:56:55 CDTGO:0019079 viral genome replication (P)PMID:22796133ECO:0000314 direct assay evidence used in manual assertion

Figure 3.A. Contains SDS-PAGE of cytoplasmic fractions. The NS5 specific antibody revealed a band at the expected size of TBEVNS5 (103 kDa), but also an additional band around 70 kDa.

challenge
acceptable9FLAV:G4XII4Kbohning, Team Bucky's Bugs2013-09-26 18:50:28 CDTGO:0019079 viral genome replication (P)PMID:22796133ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 2. Mutations is the NS5 protein in viral replication of Tick-borne encephalitis

challenge
unacceptablePSEAE:LASRKbohning, Team Bucky's Bugs2013-09-25 14:13:36 CDTGO:0003700 sequence-specific DNA binding transcription factor activity (F)PMID:23066081ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 1.section 3 shows the mutant strain in the Lux R protein and what happens in the presence of adenosine.

challenge

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Pages in category "Team Bucky's Bugs"

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