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ABSTRACT:
PROVIDER: PRJNA1288547 | ENA |
REPOSITORIES: ENA
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Project description:The aim of this experiment was to compare the transciptome of the peach-potato aphid (Myzus persicae) clone 4106a (a laboratory insecticide-susceptible standard collected from potato in Scotland in 2000) with clone FRC (an insecticide resistant aphid clone collected from peach in France in 2009) to identify which genes are over or underexpressed in the resistant phenotype. The custom microarray used in this study was designed using the Agilent eArray platform (Agilent Technologies) by the Georg Jander Lab and is based on a previously described array containing probes for >10, 000 M. persicae unigenes produced by Sanger sequencing (Ramsey, Wilson et al. 2007) augmented with an additional 30, 517 probe set designed on EST unigene sequences identified in a 454 sequencing project (Ramsey, Rider et al. 2010). The final slide layout consists of four arrays of 45, 220 60-mer probes and these are produced by Agilent by in situ oligonucleotide synthesis. References: Ramsey, J. S., D. S. Rider, et al. (2010). "Comparative analysis of detoxification enzymes in Acyrthosiphon pisum and Myzus persicae." Insect Molecular Biology 19: 155-164. Ramsey, J. S., A. C. C. Wilson, et al. (2007). "Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design." BMC Genomics 8.
2013-07-29 | GSE24629 | GEO
Project description:The aim of this experiment was to compare the transciptome of the peach-potato aphid (Myzus persicae) clone 4106a (a laboratory insecticide-susceptible standard collected from potato in Scotland in 2000) with clone FRC (an insecticide resistant aphid clone collected from peach in France in 2009) to identify which genes are over or underexpressed in the resistant phenotype. The custom microarray used in this study was designed using the Agilent eArray platform (Agilent Technologies) by the Georg Jander Lab and is based on a previously described array containing probes for >10, 000 M. persicae unigenes produced by Sanger sequencing (Ramsey, Wilson et al. 2007) augmented with an additional 30, 517 probe set designed on EST unigene sequences identified in a 454 sequencing project (Ramsey, Rider et al. 2010). The final slide layout consists of four arrays of 45, 220 60-mer probes and these are produced by Agilent by in situ oligonucleotide synthesis. References: Ramsey, J. S., D. S. Rider, et al. (2010). "Comparative analysis of detoxification enzymes in Acyrthosiphon pisum and Myzus persicae." Insect Molecular Biology 19: 155-164. Ramsey, J. S., A. C. C. Wilson, et al. (2007). "Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design." BMC Genomics 8. Two-condition experiment, 4106a vs. FRC Myzus persicae clones. Biological replicates: 4 pools of RNA extracted from ten 15 day old aphids of each clone. Technical Replicates: Two technical reps incorporating a dye swap. Total replication: eight replicates for each clone.
2013-07-29 | E-GEOD-24629 | biostudies-arrayexpress
Project description:Streptococcus pneumoniae (pneumococcus) is a leading human respiratory pathogen that causes a variety of serious mucosal and invasive diseases. D39 is an historically important serotype 2 strain that was used in experiments by Avery and coworkers to demonstrate that DNA is the genetic material. Although isolated nearly a century ago, D39 remains extremely virulent in murine infection models and is perhaps the strain used most frequently in current studies of pneumococcal pathogenicity. To date, the complete genome sequences have been reported for only two S. pneumoniae strains; TIGR4, a recent serotype 4 clinical isolate, and laboratory strain R6, an avirulent, unencapsulated derivative of strain D39. We report herein the genome sequences of two different isolates of strain D39 and the corrected sequence and updated annotation of strain R6. Comparisons of these three related sequences allowed deduction of the likely sequence of the D39 progenitor and mutations that arose in each isolate. Despite its numerous repeated sequences and IS elements, the serotype 2 genome has remained remarkably stable during cultivation, and one of the D39 isolates contains only 5 relatively minor mutations compared to the deduced D39 progenitor. In contrast, laboratory strain R6 contains 71 single base pair changes, 6 deletions, 4 insertions, and has lost the cryptic pDP1 plasmid compared to the D39 progenitor strain. Many of these mutations are in or affect the expression of genes that play important roles in regulation, metabolism, and virulence. The nature of the mutations that arose spontaneously in these three strains, relative global transcription patterns determined by microarray analyses, and the implications of the D39 genome sequences to studies of pneumococcal physiology and pathogenesis are presented and discussed. Keywords: bacterial strain comparison, bacterial isolate comparison
2006-10-09 | GSE5375 | GEO
Project description:Proteomic characterization of outer membrane vesicles from urinary E. coli strains and lab strain
2022-07-11 | PXD035215 |
Project description:Carbapenem-resistant Acinetobacter baumannii (CRAB) is a recognized nosocomial pathogen with limited therapeutics options. Lactic acid bacteria (LAB) constitute a promising therapeutic alternative. Here we aimed to study the antibacterial properties of a collection of LAB strains using phenotypic and transcriptomic analysis against A. baumannii clinical strains. One strain, Lacticaseibacillus rhamnosus CRL 2244, exerts a strong inhibitory capacity on A. baumannii with a strong killing activity. Scanning electron microscopy images showed changes in the morphology of A. baumannii with an increase formation of outer membrane vesicles. Significant changes in the expression levels a wide variety of genes were observed. Interestingly, most of the modified genes were involved in metabolic pathway known to be associated with bacterial survival. The paa operon, Hut system, and fatty acid degradation were some of the pathways that have been induced. The data reveals the impact of Lcb. rhamnosus CRL 2244 on A. baumannii response, resulting in bacterial stress and subsequent cell death. These findings highlight the antibacterial properties of Lcb. rhamnosus CRL 2244 and its potential as an alternative or complementary strategy for treating infections. Further exploration and development of this LAB as a treatment option could provide valuable alternatives for combating CRAB infections.
2023-09-14 | GSE236782 | GEO
Project description:Tan2012 - Antibiotic Treatment, Inoculum Effect
The efficacy of many antibiotics decreases with increasing bacterial density, a phenomenon called the ‘inoculum effect’ (IE). This study reveals that, for ribosome-targeting antibiotics, IE is due to bistable inhibition of bacterial growth, which reduces the efficacy of certain treatment frequencies.
This model is described in the article:
The inoculum effect and band-pass bacterial response to periodic antibiotic treatment.
Tan C, Phillip Smith R, Srimani JK, Riccione KA, Prasada S, Kuehn M, You L.
Mol Syst Biol. 2012 Oct 9; 8:617
Abstract:
The inoculum effect (IE) refers to the decreasing efficacy of an antibiotic with increasing bacterial density. It represents a unique strategy of antibiotic tolerance and it can complicate design of effective antibiotic treatment of bacterial infections. To gain insight into this phenomenon, we have analyzed responses of a lab strain of Escherichia coli to antibiotics that target the ribosome. We show that the IE can be explained by bistable inhibition of bacterial growth. A critical requirement for this bistability is sufficiently fast degradation of ribosomes, which can result from antibiotic-induced heat-shock response. Furthermore, antibiotics that elicit the IE can lead to 'band-pass' response of bacterial growth to periodic antibiotic treatment: the treatment efficacy drastically diminishes at intermediate frequencies of treatment. Our proposed mechanism for the IE may be generally applicable to other bacterial species treated with antibiotics targeting the ribosomes.
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2024-09-02 | BIOMD0000000425 | BioModels
Project description:Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: comparative genomic hybridizations (CGH) comparing different yeast strains
2008-09-05 | GSE10267 | GEO