OMPwiki - User contributions [en]

PMID:18621901

2012-03-29T13:05:58Z

Obriantkm: Fill PMID: Page!

{{RightTOC}}



{| id="F4f745e35e5a35" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Tamae, C, Liu, A, Kim, K, Sitz, D, Hong, J, Becket, E, Bui, A, Solaimani, P, Tran, KP, Yang, H and Miller, JH''' (2008) Determination of antibiotic hypersensitivity among 4,000 single-gene-knockout mutants of Escherichia coli.''J. Bacteriol.'' '''190''':5981-8
|-
!align=left |Abstract
||
We have tested the entire Keio collection of close to 4,000 single-gene knockouts in Escherichia coli for increased susceptibility to one of seven different antibiotics (ciprofloxacin, rifampin, vancomycin, ampicillin, sulfamethoxazole, gentamicin, or metronidazole). We used high-throughput screening of several subinhibitory concentrations of each antibiotic and reduced more than 65,000 data points to a set of 140 strains that display significantly increased sensitivities to at least one of the antibiotics, determining the MIC in each case. These data provide targets for the design of "codrugs" that can potentiate existing antibiotics. We have made a number of double mutants with greatly increased sensitivity to ciprofloxacin, and these overcome the resistance generated by certain gyrA mutations. Many of the gene knockouts in E. coli are hypersensitive to more than one antibiotic. Together, all of these data allow us to outline the cell's "intrinsic resistome," which provides innate resistance to antibiotics.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18621901 PubMed]
Online version:[http://dx.doi.org/10.1128/JB.01982-07 10.1128/JB.01982-07]
|-
!align=left |Keywords
||
Ampicillin; Anti-Bacterial Agents; Ciprofloxacin; Escherichia coli; Genes, Bacterial; Gentamicins; Metronidazole; Microbial Sensitivity Tests; Mutation; Rifampin; Sulfamethoxazole; Vancomycin

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.2897.F4f745e35e5a35&page=2897&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| id="W4f745e36014ad" class=" tableEdit Phenotype_Table_2"
|-
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.2897.W4f745e36014ad&page=2897&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table] || || || || || || || || ||
|}
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:18621901

2012-03-29T13:05:57Z

Obriantkm: New PMID: Page!

PMID:20674514

2012-03-29T13:04:41Z

Obriantkm: Fill PMID: Page!

{{RightTOC}}



{| id="M4f745de906752" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Becket, E, Chen, F, Tamae, C and Miller, JH''' (2010) Determination of hypersensitivity to genotoxic agents among Escherichia coli single gene knockout mutants.''DNA Repair (Amst.)'' '''9''':949-57
|-
!align=left |Abstract
||
We have tested the KEIO collection of 3985 different viable single gene knockouts in Escherichia coli to identify genes whose loss increases sensitivity to one or more of six different chemotherapeutic agents and mutagens: Bleomycin (BLM), Cisplatin (CPT), ICR-191 (ICR), 5-azacytidine (5AZ), Zebularine (ZEB), and 5-bromo-2'-deoxyuridine (5BdU). We discovered a set of 156 strains that display a significant increase in sensitivity to at least one of the agents tested. Each genotoxic agent generates a distinct "sensitivity profile" that is characteristic of the agent. Comparison with an independent study of sensitivity profiles for an extensive set of antibiotics pinpoints those effects that are relatively specific for each agent. In some cases engineered double mutants have greatly increased effects. These results provide insight into the mechanism of action of each agent, and define targets for the design of co-drugs that can potentiate these agents. An example is the finding that mutants lacking one of several genes in the folate biosynthetic pathway are hypersensitive to ZEB, leading to a demonstration of synergy between trimethoprim and ZEB.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20674514 PubMed]
Online version:[http://dx.doi.org/10.1016/j.dnarep.2010.06.008 10.1016/j.dnarep.2010.06.008]
|-
!align=left |Keywords
||
Escherichia coli; Gene Knockout Techniques; Microbial Sensitivity Tests; Mutagens; Mutation

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.2896.M4f745de906752&page=2896&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| id="F4f745de9266a7" class=" tableEdit Phenotype_Table_2"
|-
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.2896.F4f745de9266a7&page=2896&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table] || || || || || || || || ||
|}
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]

PMID:20674514

2012-03-29T13:04:40Z

Obriantkm: New PMID: Page!

PMID:20065048

2012-03-23T13:00:26Z

Obriantkm: New PMID: Page!

PMID:20065048

2012-03-23T13:00:26Z

Obriantkm: Fill PMID: Page!

{{RightTOC}}



{| id="U4f6c73ea6ce9f" class=" tableEdit PMID_info_table"

|-
!align=left |Citation
||
'''Liu, A, Tran, L, Becket, E, Lee, K, Chinn, L, Park, E, Tran, K and Miller, JH''' (2010) Antibiotic sensitivity profiles determined with an Escherichia coli gene knockout collection: generating an antibiotic bar code.''Antimicrob. Agents Chemother.'' '''54''':1393-403
|-
!align=left |Abstract
||
We have defined a sensitivity profile for 22 antibiotics by extending previous work testing the entire KEIO collection of close to 4,000 single-gene knockouts in Escherichia coli for increased susceptibility to 1 of 14 different antibiotics (ciprofloxacin, rifampin [rifampicin], vancomycin, ampicillin, sulfamethoxazole, gentamicin, metronidazole, streptomycin, fusidic acid, tetracycline, chloramphenicol, nitrofurantoin, erythromycin, and triclosan). We screened one or more subinhibitory concentrations of each antibiotic, generating more than 80,000 data points and allowing a reduction of the entire collection to a set of 283 strains that display significantly increased sensitivity to at least one of the antibiotics. We used this reduced set of strains to determine a profile for eight additional antibiotics (spectinomycin, cephradine, aztreonem, colistin, neomycin, enoxacin, tobramycin, and cefoxitin). The profiles for the 22 antibiotics represent a growing catalog of sensitivity fingerprints that can be separated into two components, multidrug-resistant mutants and those mutants that confer relatively specific sensitivity to the antibiotic or type of antibiotic tested. The latter group can be represented by a set of 20 to 60 strains that can be used for the rapid typing of antibiotics by generating a virtual bar code readout of the specific sensitivities. Taken together, these data reveal the complexity of intrinsic resistance and provide additional targets for the design of codrugs (or combinations of drugs) that potentiate existing antibiotics.
|-
!align=left |Links
||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=20065048 PubMed]
Online version:[http://dx.doi.org/10.1128/AAC.00906-09 10.1128/AAC.00906-09]
|-
!align=left |Keywords
||
Automatic Data Processing; Databases, Genetic; Drug Resistance, Bacterial; Drug Resistance, Multiple, Bacterial; Escherichia coli; Gene Deletion; Gene Knockout Techniques; Genes, Bacterial; Microbial Sensitivity Tests

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.2888.U4f6c73ea6ce9f&page=2888&pagename={{FULLPAGENAMEE}}&type=1&template=PMID_info_table edit table] ||
|}


==Main Points of the Paper ==
{{LitSignificance}}

== Materials and Methods Used ==
{{LitMaterials}}

==Phenotype Annotations==
{{AnnotationTableHelp}}
<protect>

{| id="E4f6c73ea917e7" class=" tableEdit Phenotype_Table_2"
|-
!|Phenotype of!!Taxon Information!!Genotype Information (if known)!!Condition Information!!OMP ID!!OMP Term Name!!ECO ID!!ECO Term Name!!Notes!!Status

|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=d41d8cd98f00b204e9800998ecf8427e.2888.E4f6c73ea917e7&page=2888&pagename={{FULLPAGENAMEE}}&type=0&template=Phenotype_Table_2 edit table] || || || || || || || || ||
|}
</protect>

==Notes==

==References==
{{RefHelp}}
<references/>

[[Category:Publication]]