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Escherichia coli strain:ATCC 8739

ABSTRACT: Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing

PROVIDER: PRJNA476837 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7412680_1.fastq.gz	Fastqsanger.gz
	SRR7412680_2.fastq.gz	Fastqsanger.gz
	SRR7412681_1.fastq.gz	Fastqsanger.gz
	SRR7412681_2.fastq.gz	Fastqsanger.gz
	SRR7412682_1.fastq.gz	Fastqsanger.gz

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Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing

Project description:Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing

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Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing

Project description:Investigation of spontaneous mutations by Next-Generation Sequencing technology has attracted extensive attention lately due to the fundamental roles of spontaneous mutations in evolution and pathological processes. However, these studies only focused on the mutations accumulated through many generations during long term --could be years of-- culturing, but not the freshly-generated spontaneous mutations that occurs at very low frequencies. In this study, we established a molecularly-barcoded deep sequencing strategy to detect low abundant spontaneous mutations in genomes of bacteria cell cultures. Genome-wide spontaneous mutations in 15 E. coli cell culture samples were defined with a high confidence (P < 0.01). We also developed a hotspot region-calling approach based on Run-Length Encoding algorithm to find the genomic regions that are vulnerable to the spontaneous mutations. The hotspots for the mutations appeared to be highly conserved across the bacteria samples. Further biological annotation of these regions indicated that most of the spontaneous mutations were located at the repeat domains or nonfunctional domains of the genomes, suggesting the existence of mechanisms that could somehow prevent the occurrence of mutations in crucial genic areas. This study provides a more faithful picture of mutation occurrence and spectra without the distortion of long term culturing.

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Clinical drug response and proteotype profiling elucidates targetable vulnerabilities of myelofibrosis

Project description:Myelofibrosis (MF) is a hematopoietic stem cell disorder belonging to the myeloproliferative neoplasms. MF patients frequently carry driver mutations in JAK2 and Calreticulin (CALR) and have limited therapeutic options. Here, we integrate ex vivo drug response and proteotype analyses across MF patient cohorts to discover targetable vulnerabilities and associated therapeutic strategies. Drug sensitivities of mutated and progenitor cells were measured in patient blood using high-content imaging and single-cell deep learning-based analyses. Integration with matched molecular profiling revealed three therapeutic vulnerabilities. First, CALR mutations drive BET and HDAC inhibitor sensitivity, particularly in the absence of high MAPK-Ras pathway protein levels. Second, an MCM complex-high proliferative signature corresponds to advanced disease and sensitivity to drugs targeting pro-survival signaling and DNA replication. Third, homozygous CALR mutations result in high ER stress, responding to ER stressors and UPR inhibition. Overall, our integrated analyses provide a molecularly-motivated roadmap for individualized MF patient treatment.

2023-10-12 | PXD036075 | Pride

Viability of Escherichia coli ATCC 8739 in Nutrient Broth, Luria-Bertani Broth and Brain Heart Infusion over 11 Weeks.

Project description:BackgroundEscherichia coli is a widely studied prokaryotic system. A recent study had demonstrated that reduced growth of E. coli after extended culture in Luria-Bertani broth is a result of depletion of fermentable sugars but able to sustain extended cell culture due to the presence of amino acids, which can be utilized as a carbon source. However, this had not been demonstrated in other media. The study aimed to determine the growth and viability of E. coli ATCC 8739 in 3 different media, Nutrient Broth (NB), Brain Heart Infusion (BHI) and Luria-Bertani Broth (LB) over 11 weeks.MethodsGrowth of E. coli ATCC 8739 was determined by optical density. Viability was determined by serial dilution/spread-plate enumeration. After 11 weeks, the media were exhausted by repeated culture. Glucose was added to the exhausted media to determine whether glucose is the growth-limiting factor.ResultsOur results showed that cell density in all 3 media increased to about 1 × 10(9) cells/ml by the end of week 1, from the inoculation density of 2.67 × 10(5) cells/ml, peaked at about 1 × 10(13) cells/ml at week 4, before declining to about 5 × 10(7) cells/ml at week 7. Cell density is highly correlated to genomic DNA content (r(2) = 0.93) but poorly correlated to optical density (r(2)< 0.2). Our results also showed that the spent media were able to support further growth after glucose-supplementation.ConclusionNB, LB and BHI are able to support extended periods of culture and glucose depletion is the likely reason for declining cell growth.

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2022-11-16 | PXD036025 | Pride

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