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Cacao

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GO:0030655beta-lactam antibiotic catabolic processPMID:30588046ECO:0000338 IDA: Inferred from Direct AssayBiological Process
30 EPKP (ESBL-producing K. pneumoniae) isolates collected by the authors were screened with various antimicrobial drugs, and it was found that 63.33% had the ESBL (extended-spectrum β-lactamase) gene (Table 1). Transconjugants containing plasmids of ESBL genes were created, which had the bla CTX M-15. S1-nuclease digestion was followed up with pulsed-field gel electrophoresis for all isolates and transconjugants to observe whether the resistance genes had been encoded into the plasmids (Table 2). In this study, they identified the CTX-M-15 enzyme as the most prevalent ESBL in VAP patients. Their results indicate that IncF-related plasmids carrying blaCTX-M-15 were a major vehicle for the resistance genes in K. pneumoniae isolates.
complete
This annotation made on page: STRCO:CYC2
By: CShee (group Team Green B 2019) on 2019-03-10 17:26:08 CDT.




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Entry TypeChallenging User,GroupTime/DateChallenge ReasonPoints/Assessment
Public
Assessment		Ivanerill2019-03-27 10:07:18 CDTNo notes given.Acceptable
✔ Protein
✔ Publication
✔ Qualifier
✔ Go term
✔ Evidence
✔ With/From
✔ Notes
✔ Unique/Original
Public
Assessment		DanielRenfro2019-03-26 19:44:07 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:0044550 secondary metabolite biosynthetic process PMID:12563033 ECO:0006091 IMP: Inferred from Mutant Phenotype P In this paper, the researchers used PCR targeting, gene replacement cassette, and transposon mutagenesis to determine whether genes cyc1 and cyc2 were both required for production of geosmin, a substance that gives soil its distinctive scent. GC-MS was used to detect geosmin production by each mutant. In Table 3, it is shown that when cyc2 is deleted, (strains J3001, J3002) there is no production of geosmin. When cyc1 is mutated using a transposon, geosmin is still produced. This indicates that cyc2, not cyc1, is required for the production of geosmin. To confirm this, the researchers reintroduced the cyc2 gene (complementation) via a vector into the strain, and geosmin production was restored. complete
CACAO 13559
on STRCO:CYC2
Flagged
Public
Assessment		Ivanerill2019-03-25 12:24:32 CDT

"figure out whether cyc1 and cyc2 exhibited functional redundancy, a substance that gives soil its distinctive scent. " please revise

Requires Changes
✔ Protein
✔ Publication
✔ Qualifier
✔ Go term
✔ Evidence
✔ With/From
✗ Notes
✔ Unique/Original
Public
Assessment		DanielRenfro2019-03-25 10:23:44 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
GO:0044550 secondary metabolite biosynthetic process PMID:12563033 ECO:0006091 IMP: Inferred from Mutant Phenotype P In this paper, they used PCR targeting, gene replacement cassette, and transposon mutagenesis to figure out whether cyc1 and cyc2 exhibited functional redundancy, a substance that gives soil its distinctive scent. GC-MS was used to detect geosmin production by each mutant. In Table 3, it is shown that when cyc2 is deleted, (strains J3001, J3002) there is no production of geosmin. This indicates that cyc2 is directly involved in production of Geosmin. To confirm this, the researchers reintroduced (complementation) cyc2 gene via a vector; geosmin production was restored. complete
CACAO 13559
on STRCO:CYC2
Flagged
Public
Assessment		Ivanerill2019-03-25 08:53:37 CDT

Move Annotation 13559 from KLEPN:Q2PUH3 to STRCO:CYC2

Updated by Instructor
Public
Assessment		Ivanerill2019-03-13 09:10:12 CDT

The authors only check that resistant isolates carry a resistance gene, but in no way seem to prove that the gene product is directly involved in the resistance process that they are annotating to. Evidence should be further specified (IDA is a root term). Please use the cross-linked evidence terms from ECO (i.e. those that end in "used in manual assertion" or "used in automatic assertion" Most instances of evidence you will come across will be of type "used in manual assertion". Terms with "used in automatic assertion" imply that the authors did not make a conscious effort to analyze the results of an experiment, letting an algorithm make the call. For instance, if somebody were to use BLAST to determine that a bunch of proteins are homologous (and hence have the same function as the query) and they do not assess the BLAST results in any way (just accept whatever BLAST returns as significant given a preestablished threshold) that could be thought of as an "automatic assertion".


Requires Changes
✔ Protein
✔ Publication
✔ Qualifier
✗ Go term
✗ Evidence
✗ Notes
✔ Unique/Original
Public
Assessment		DanielRenfro2019-03-12 12:54:59 CDT

This annotation has been flagged because it has been edited since last assessment

Qualifier GO ID GO term name Reference ECO ID ECO term name with/from Aspect Extension Notes Status
Contributes to GO:0030655 beta-lactam antibiotic catabolic process PMID:30588046 ECO:0000338 IDA: Inferred from Direct Assay P 30 EPKP (ESBL-producing K. pneumoniae) isolates collected by the authors were screened with various antimicrobial drugs, and it was found that 63.33% had the ESBL (extended-spectrum β-lactamase) gene (Table 1). Transconjugants containing plasmids of ESBL genes were created, which had the bla CTX M-15. S1-nuclease digestion was followed up with pulsed-field gel electrophoresis for all isolates and transconjugants to observe whether the resistance genes had been encoded into the plasmids (Table 2). In this study, they identified the CTX-M-15 enzyme as the most prevalent ESBL in VAP patients. Their results indicate that IncF-related plasmids carrying blaCTX-M-15 were a major vehicle for the resistance genes in K. pneumoniae isolates. complete
CACAO 13559
on KLEPN:Q2PUH3
Flagged
Private
Assessment		Ivanerill2019-03-11 16:09:11 CDTYou need to be an instructor to view these notes.Requires Changes
Private
Assessment		Ivanerill2019-03-11 10:46:41 CDTYou need to be an instructor to view these notes.Requires Changes
✔ Protein
✔ Publication
✔ Qualifier
✗ Go term
✗ Evidence
✗ Notes
✔ Unique/Original


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