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Category:Team ppGpp 3 Times Fast

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SUPER BOWL ROUND Spring 2012

StatusPageUserDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
requireschangesPROMI:C2LKP1Devangam, Team ppGpp 3 Times Fast2012-04-15 16:04:37 CDTGO:0042710 biofilm formation (Figure 2 is a graph showing a viable cell count biofilm assay comparing the biofilm formation and growth of Wild type P. mirabilis cells, mutant cells without pstA gene, and mutant cells without pstS gene. The pstA and pstS mutants have much less biofilm formation than the wild type, indicating that the Pst family genes are involved in biofilm formation. )PMID:19372157IDA: Inferred from Direct Assay
challenge
requireschangesBRUAO:Q9FDD0Devangam, Team ppGpp 3 Times Fast2012-04-15 15:55:22 CDTGO:0045333 cellular respiration (P)PMID:11274104ECO:0000314 direct assay evidence used in manual assertion

Figure 2 demonstrates the survival rate of multiple strains of Brucella abortus. Strain BA582pSEK102 contains the cydB gene, and has a higher survival rate in response to respiratory inhibitors, whereas strain BA582 which lacks cydB gene, has a much lower survival rate in response to respiratory inhibitors. This indicates that cydB gene is involved in facilitating cellular respiration.

challenge
requireschangesBACSU:PLSYDevangam, Team ppGpp 3 Times Fast2012-04-15 15:37:14 CDTGO:0016747 transferase activity, transferring acyl groups other than amino-acyl groups (F)PMID:19282621ECO:0000314 direct assay evidence used in manual assertion

Figure 4 is a TLC plate that demonstrates the separation of protein fractions of wild type cells and protein fractions of mutant cells without PlsY gene. There is no separation for PlsY mutant cells when palmitoyl phosphate (an acyl phosphate) is added. This demonstrates that PlsY has acyl-phosphate transferase activity.

challenge
requireschangesMYCTU:CLPXDevangam, Team ppGpp 3 Times Fast2012-04-15 15:16:57 CDTGO:0051302 regulation of cell division (P)PMID:20625433ECO:0000314 direct assay evidence used in manual assertion

Figure 2A is a light scatter assay that shows the amount of FtsZ polymerization. FtsZ polymerization is necessary for FtsZ ring formation and cell division. Figure 2A shows that for M. tuberculosis mutant without a function ClpX gene has a higher level of FtsZ polymerization than the wild type strain. This indicates that ClpX inhibits cell division.

challenge
updatedbyinstructorMOUSE:SODMLabbeben, Team ppGpp 3 Times Fast2012-04-15 14:20:43 CDTGO:0016491 oxidoreductase activity (F)PMID:15205258ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 4 shows a Western blot that demonstrates the importance of Sod2 to the oxidation state of proteins in erythrocytes. In the progenitor stage and in both the cytosol and membranes of erythrocytes, the Sod2 -/- mutants have significantly more oxidation (here shown as darker bands, since the blot detected carbonyls resulting from reactive oxygen species activity). That Sod2 has direct oxidoreductase activity is further reinforced by the proteomics analysis in Table 2. Other proteins that might have significant oxidoreductase activity, such as Cytochrome C oxidase subunit Va, are not differentially expressed. Since the absence of Sod2 does not affect expression of these other oxidoreductases, the difference in oxidation states in the mutant is likely due to a lack of activity by Sod2 in this function, rather than as a transcription factor for other oxidoreductases.

challenge
acceptableSALTY:COBTDevangam, Team ppGpp 3 Times Fast2012-04-15 12:46:28 CDTGO:0008939 nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity (F)PMID:8206834ECO:0000314 direct assay evidence used in manual assertion

Figure 2 shows a TLC plate's separation of the reactants and products of the S. typhimurium CobT protein reaction with 2 different cell extracts: one with chromosomally (normal) encoded levels of CobT, and another with overexpressed levels of CobT. The separation indicates that the CobT-overexpressing cells have much greater alpha-ribazole-5'-P and the normal cells have much greater DMB (5,6-dimethylbenzimidazole). The separation indicates that CobT activity catalyzes the reaction from DMB to alpha-ribazole-5'-P, thus demonstrating nicotinate-nucleotide-dimethylbenzimadazole phosphoribosyltransferase activity.

challenge
acceptableCAMJE:FABZDevangam, Team ppGpp 3 Times Fast2012-04-15 12:21:52 CDTGO:0019171 3-hydroxyacyl-(acyl-carrier-protein) dehydratase activity (F)PMID:19280690ECO:0000314 direct assay evidence used in manual assertion

A spectrophotometric assay of fabZ activity is demonstrated by Figure 4. It shows the kinetics of fabZ dehydratase activity by showing the fabZ activity in response to varied levels of Crotonoyl-CoA and beta-hydroxybutyryl-CoA. Table 2 demonstrates that the Km value of beta-Hydroxybutyryl-CoA is greater than that of Crotonoyl-CoA, demonstrating that fabZ converts Beta-Hydroxybutyryl-CoA to Crotonoyl-CoA.

challenge
requireschangesBIFLO:Q8G545Devangam, Team ppGpp 3 Times Fast2012-04-15 11:35:44 CDTGO:0004360 glutamine-fructose-6-phosphate transaminase (isomerizing) activity (F)PMID:17943273ECO:0000314 direct assay evidence used in manual assertion

Figure 5 is a high-performance liquid chromatography study that detects elution profiles of phosphorylated monosaccharides. When purified GlmS protein was used (the gene product of Bifidobacterium longum gene glmS), a peak for glucosamine-6-phosphate was observed with addition of fructose-6-phosphate and glutamine. This demonstrates glutamine fructose-6-phosphate amidotransferase activity.

challenge
unacceptableECOLI:DNAKLabbeben, Team ppGpp 3 Times Fast2012-04-14 13:21:23 CDTGO:0005524 ATP binding (F)PMID:10521435ECO:0000021 physical interaction evidence

DnaK and DnaJ bind under certain circumstances- the abstract mentions that they have been shown to be co-chaperones. Figure 1, graph 1 demonstrates binding assays using immobilized DnaK on a sensor chip. The binding of DnaK to DnaJ occurs only in the presence of ATP, and not any other form of nucleotide. While this is not a direct analysis of the ATP-binding domain, from the graph it is possible to infer that DnaK requires the presence of ATP to bind DnaJ, and that the ATP is binding to DnaK (since it was only present in solution during the process of immobilizing DnaK, not when the DnaJ was added).

challenge
acceptableHUMAN:DDIT3Labbeben, Team ppGpp 3 Times Fast2012-04-14 12:36:53 CDTGO:0007050 cell cycle arrest (P)PMID:22496745ECO:0000314 direct assay evidence used in manual assertion

Figure 4 shows an assay of cells subjected to the condition of DDIT3 within the cytoplasm or the nucleus. After the cells were cultured for 12 hours, the nuclei were extracted and the gene expression pattern was analyzed. When DDIT3 is present in the nucleus, a much greater portion of cells accumulate in the G1 phase expression pattern, indicating that DDIT3 being present in the nucleus encourages cell cycle arrest in G1.

challenge


MSU Internal Competition

StatusPageUserDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
requireschangesMYXXD:Q1D7Q3Labbeben, Team ppGpp 3 Times Fast2012-04-01 16:16:30 CDTGO:0003677 DNA binding (F)PMID:1539954ECO:0000314 direct assay evidence used in manual assertion

Figure 2 demonstrates an example of one gene promoter region that FruA is able to bind to. E. coli containing a plasmid with the fruA gene was used to produce sufficient quantities of protein after induction with IPTG. 2A demonstrates that FruA was only produced after IPTG induction. The protein was then used in gel-shift assays with P32-labelled DNA, as shown in 2B. The sigma-4400 promoter region, which contains the proposed FruA binding site, forms a band that indicates binding only in the presence of IPTG-induced protein; in other words, only in the presence of FruA. The right side is another gene region from M. xanthus that does not contain the proposed FruA binding site, and acts as a negative control.

challenge
requireschangesGEOSE:NEPUDevangam, Team ppGpp 3 Times Fast2012-03-29 11:36:32 CDTGO:0005975 carbohydrate metabolic process (P)PMID:123897ECO:0000314 direct assay evidence used in manual assertion

Figure 1 shows results from a TLC plate that demonstrates that neopullulanase degrades amylose and small amounts of amylopectin into smaller subunits, mainly maltose and glucose. The TLC plate shows relative degradation of amylose and amylopectin, and it demonstrates that neopullulanase degrades amylose into glucose and maltose much more than it degrades amylopectin into glucose and maltose. Figure 2 is gel permeation chromatography that demonstrates that neopullulanase degrades amylose more than amylopectin over time. The degradation of starch by neopullulanase is evidence that it is involved in carbohydrate metabolism.

challenge
requireschangesGEOSE:NEPUDevangam, Team ppGpp 3 Times Fast2012-03-29 11:23:40 CDTGO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds (F)PMID:209598ECO:0000314 direct assay evidence used in manual assertion

Figures 1 & 2 demonstrates results from paper chromatograms that shows amount of sugars present over time when treated with neopullulanase. The increasing amounts of maltose and glucose that the enzyme degrades maltotriose, maltotriitol, isopanose, maltotetraose, 6^3-O-alpha-glucosyl-maltotriose, and 6^2-O-alpha-maltosyl-maltose.

challenge

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