Klebsiella pneumoniae strain:MGH 66
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ABSTRACT:
PROVIDER: PRJNA1309751 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To investigate the whole-genome gene expression difference between the wild-type and capsule deletion mutant in Klebsiella pneumoniae MGH 78578. The mutants analyzed in this study are further described in Huang T.W., Stapleton J.C., Chang H.Y., Tsai S.F., Palsson B.O., Charusanti P. Capsule removal via lambda-Red knockout system perturbs biofilm formation and fimbriae extression in Klesiella pneumoniae MGH 78578 (manuscript submission) A six chip study using total RNA recovered from three separate wild-type cultures and three separate cultures of a capsule deltion mutant of Klebsiella pneumoniae MGH 78578. The capsule gene cluster (KPN_02493 to KPN_02515) was entirely removed in the capsule deletion mutant. Each chip measures the expression level of 5,305 genes from Klebsiella pneumoniae MGH 78578 and the associated five plasmids (pKPN3, pKPN4, pKPN5, pKPN6 and pKPN7) with 50-mer oligo tiling array with 30-mer spacer.
2013-12-31 | E-GEOD-40011 | biostudies-arrayexpress
Project description:To investigate the whole-genome gene expression difference between the wild-type and capsule deletion mutant in Klebsiella pneumoniae MGH 78578. The mutants analyzed in this study are further described in Huang T.W., Stapleton J.C., Chang H.Y., Tsai S.F., Palsson B.O., Charusanti P. Capsule removal via lambda-Red knockout system perturbs biofilm formation and fimbriae extression in Klesiella pneumoniae MGH 78578 (manuscript submission)
2013-12-31 | GSE40011 | GEO
Project description:Sequences of 11 amino acids belonging to the KPN_00363 protein and KPN_00459 protein from Klebsiella pneumoniae MGH 78578 which was previously identified as potentially immunogenic was analyzed via alanine scanning to narrow down the significant amino acid residues within the sequence.
2014-08-22 | GSE60588 | GEO
Project description:Genome-wide gene expression analysis was performed with the cells in exponential and stationary growth phases. Through these two growth status, 89.6% of currently annotated genes were expressed. High-density oligonucleotide tiling arrays consisting of 379,528 50-mer probes spaced 30 bp apart across the whole Klebsiella pneumoniae MGH 78578 genome was used (Roche NimbleGen).
2012-12-31 | E-GEOD-35926 | biostudies-arrayexpress
Project description:Genome-wide identification of RNA polymerase (RNAP) binding sites were performed in Klebsiella pneumoniae MGH 78578 (KP). Anti-RNAP is used to capture the RNAP in KP. ChIP-chip was performed on tiling array specifically made for KP.
2012-12-31 | GSE35927 | GEO
Project description:The screening of a cDNA derived expression library of Klebsiella pneumoniae MGH 78578 expressed in E.coli using a fusion construct and specific HaloTag interaction to a modified surface is shown. Thus, 1536 different clones were screened including positive (ompA, mdh) and negative (pyrC, gapA) reference proteins. The goal of the screening was to identify potential novel immunogenic proteins from K. pneumoniae by selecting clones showing a high signal intensity in comparison to the known antigens used as positve markers. Afterwards, the most promising clones were sequenced to identify the gene and corresponding protein and these proteins were then investigated further. Consequently, 14 novel immunogenic proteins could be identified.
2014-02-02 | GSE52536 | GEO
Project description:Genome-wide identification of RNA polymerase (RNAP) binding sites were performed in Klebsiella pneumoniae MGH 78578 (KP). Anti-RNAP is used to capture the RNAP in KP. ChIP-chip was performed on tiling array specifically made for KP. Comparison ChIP by anti-RNAP antibody vs ChIP by normal mouse IgG (control, mock IP)
2012-12-31 | E-GEOD-35927 | biostudies-arrayexpress
Project description:Liao2011 - Genome-scale metabolic
reconstruction of Klebsiella pneumoniae (iYL1228)
This model is described in the article:
An experimentally validated
genome-scale metabolic reconstruction of Klebsiella pneumoniae
MGH 78578, iYL1228.
Liao YC, Huang TW, Chen FC,
Charusanti P, Hong JS, Chang HY, Tsai SF, Palsson BO, Hsiung
CA.
J. Bacteriol. 2011 Apr; 193(7):
1710-1717
Abstract:
Klebsiella pneumoniae is a Gram-negative bacterium of the
family Enterobacteriaceae that possesses diverse metabolic
capabilities: many strains are leading causes of
hospital-acquired infections that are often refractory to
multiple antibiotics, yet other strains are metabolically
engineered and used for production of commercially valuable
chemicals. To study its metabolism, we constructed a
genome-scale metabolic model (iYL1228) for strain MGH 78578,
experimentally determined its biomass composition,
experimentally determined its ability to grow on a broad range
of carbon, nitrogen, phosphorus and sulfur sources, and
assessed the ability of the model to accurately simulate growth
versus no growth on these substrates. The model contains 1,228
genes encoding 1,188 enzymes that catalyze 1,970 reactions and
accurately simulates growth on 84% of the substrates tested.
Furthermore, quantitative comparison of growth rates between
the model and experimental data for nine of the substrates also
showed good agreement. The genome-scale metabolic
reconstruction for K. pneumoniae presented here thus provides
an experimentally validated in silico platform for further
studies of this important industrial and biomedical
organism.
This model is hosted on
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and identified by:
MODEL1507180054.
To cite BioModels Database, please use:
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quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
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2024-10-15 | BIOMD0000001094 | BioModels
Project description:The screening of a cDNA derived expression library of Klebsiella pneumoniae MGH 78578 expressed in E.coli using a fusion construct and specific HaloTag interaction to a modified surface is shown. Thus, 1536 different clones were screened including positive (ompA, mdh) and negative (pyrC, gapA) reference proteins. The goal of the screening was to identify potential novel immunogenic proteins from K. pneumoniae by selecting clones showing a high signal intensity in comparison to the known antigens used as positve markers. Afterwards, the most promising clones were sequenced to identify the gene and corresponding protein and these proteins were then investigated further. Consequently, 14 novel immunogenic proteins could be identified. In total 1536 (4 x 384) different lysates were spotted on different microarray slides. Each slides contained 3600 distinct spots, seperated into two compartments of 1800 spots each. Each compartment comprised quadruplicate replicates of each sample lysate with controls being analysed with more replicates. As controls we used: ompA1, ompA2 and mdh (3 x 40 replicates) as positive reference proteins, as they have been described as immunogenic before. gapA and pyrC (2 x 40 replicates) as negative reference proteins, additionally two sets of E.coli cell lysates without fusionprotein expressed, namely Acella electrocompetent cells (40 replicates) and KRX (32 replicates). Last but not least a buffer control (24 replicates) was included. Therefore, each set of replicate slides contained 376 different samples and 8 controls. Each screening was performed with three replicate slides. Consequently, a total number of 12 slides were screened (4 sets of samples x 3 replicates). For identification rabbit polyclonal antibody to K. pneumoniae (Acris AP00792PU-N) as primary and Goat polyclonal to Rabbit IgG conjugated with ChromeoTM-546 (Abcam ab60317) as secondary antibody were used. The top compartment was incubated first with primary antibody, while the bottom compartment was incubated with PBS at the same time. Afterwards both compartments were incubated with secondary antibody.
2014-02-02 | E-GEOD-52536 | biostudies-arrayexpress
Project description:A strain of Klebsiella pneumoniae exposed to native and heat-inactivated serum for different time points
2023-10-16 | MSV000093124 | MassIVE