Ontology highlight
ABSTRACT:
PROVIDER: PRJNA752693 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15365158_1.fastq.gz | Fastqsanger.gz | |||
| SRR15365158_2.fastq.gz | Fastqsanger.gz | |||
| SRR15365159_1.fastq.gz | Fastqsanger.gz | |||
| SRR15365159_2.fastq.gz | Fastqsanger.gz | |||
| SRR15365160_1.fastq.gz | Fastqsanger.gz |
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Project description:Mycoplasma genitalium is the causative agent of non-gonococcal, chlamydia-negative urethritis in men and has been linked to reproductive tract disease syndromes in women. As with other mycoplasmas, M. genitalium lacks many regulatory genes because of its streamlined genome and total dependence on a parasitic existence. Therefore, it is important to understand how gene regulation occurs in M. genitalium, particularly in response to environmental signals likely to be encountered in vivo. In this study, we developed an oligonucleotide-based microarray to investigate transcriptional changes in M. genitalium following osmotic shock. Using a physiologically relevant osmolarity condition (0.3 M sodium chloride), we identified 39 up-regulated and 72 down-regulated genes. Of the up-regulated genes, 21 were of unknown function and 15 encoded membrane-associated proteins. The majority of down-regulated genes encoded enzymes involved in energy metabolism and components of the protein translation process. These data provide insight into the in vivo response of M. genitalium to hyperosmolarity conditions and identify candidate genes that may contribute to mycoplasma survival in the urogenital tract.
2010-11-15 | GSE22661 | GEO
Project description:Suthers2009 - Genome-scale metabolic network
of Mycoplasma genitalium (iPS189)
This model is described in the article:
A genome-scale metabolic
reconstruction of Mycoplasma genitalium, iPS189.
Suthers PF, Dasika MS, Kumar VS,
Denisov G, Glass JI, Maranas CD.
PLoS Comput. Biol. 2009 Feb; 5(2):
e1000285
Abstract:
With a genome size of approximately 580 kb and approximately
480 protein coding regions, Mycoplasma genitalium is one of the
smallest known self-replicating organisms and, additionally,
has extremely fastidious nutrient requirements. The reduced
genomic content of M. genitalium has led researchers to suggest
that the molecular assembly contained in this organism may be a
close approximation to the minimal set of genes required for
bacterial growth. Here, we introduce a systematic approach for
the construction and curation of a genome-scale in silico
metabolic model for M. genitalium. Key challenges included
estimation of biomass composition, handling of enzymes with
broad specificities, and the lack of a defined medium.
Computational tools were subsequently employed to identify and
resolve connectivity gaps in the model as well as growth
prediction inconsistencies with gene essentiality experimental
data. The curated model, M. genitalium iPS189 (262 reactions,
274 metabolites), is 87% accurate in recapitulating in vivo
gene essentiality results for M. genitalium. Approaches and
tools described herein provide a roadmap for the automated
construction of in silico metabolic models of other
organisms.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180052.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
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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2015-07-30 | MODEL1507180052 | BioModels
Project description:Interferons (IFNs) possess broad-spectrum antiviral activity to resist virus epidemic. However, IFNs antiviral efficacy needs to be greatly improved. Here, we reveal that LATS1 is a vital signal transmitter governing full type-I-interferon (IFN-I) signaling activity. Importantly, LATS1 deficiency restricts IFN-I signaling and attenuates host antiviral immune response.
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2021-09-08 | GSE183474 | GEO
Project description:CID 70698683 is a novel broad-spectrum antiviral compound. To understand the broad-spectrum antiviral mechanism, the cellular gene expression changes by the treatment of CID70698683 was measured.
2015-11-25 | GSE72167 | GEO
Project description:Mycoplasma genitalium is the causative agent of non-gonococcal, chlamydia-negative urethritis in men and has been linked to reproductive tract disease syndromes in women. As with other mycoplasmas, M. genitalium lacks many regulatory genes because of its streamlined genome and total dependence on a parasitic existence. Therefore, it is important to understand how gene regulation occurs in M. genitalium, particularly in response to environmental signals likely to be encountered in vivo. In this study, we developed an oligonucleotide-based microarray to investigate transcriptional changes in M. genitalium following osmotic shock. Using a physiologically relevant osmolarity condition (0.3 M sodium chloride), we identified 39 up-regulated and 72 down-regulated genes. Of the up-regulated genes, 21 were of unknown function and 15 encoded membrane-associated proteins. The majority of down-regulated genes encoded enzymes involved in energy metabolism and components of the protein translation process. These data provide insight into the in vivo response of M. genitalium to hyperosmolarity conditions and identify candidate genes that may contribute to mycoplasma survival in the urogenital tract. To examine the effects of hyperosmolarity on M. genitalium transcription, four 50 ml cultures of strain G37 in 75 cm2 tissue culture flasks (Corning) were grown to exponential phase, as determined by medium colour change and colony density. Then, NaCl was added to three flasks to achieve final concentrations of 0.1, 0.2 and 0.3 M. Parallel cultures of M. genitalium in the absence of NaCl served as controls. All cultures were incubated for 1 h at 37M-bM-^DM-^C prior to RNA extraction. Experiments were repeated six times, which produced six independent RNA sample pairs from NaCl-treated cultures and control cultures for each NaCl condition. Dye swap was performed on three of six RNA pairs to minimize effects caused by biased labelling efficiencies.
2010-11-15 | E-GEOD-22661 | biostudies-arrayexpress
Project description:Enoxacin shows a broad-spectrum antiviral activity against diverse viruses by enhancing antiviral RNAi in insects
| PRJNA781957 | ENA
Project description:CID 70698683 is a novel broad-spectrum antiviral compound. To understand the broad-spectrum antiviral mechanism, the cellular gene expression changes by the treatment of CID70698683 was measured. HEp-2 cells grown in 6-well plates were treated with 5 microM of CID 70698683 for overnight and the cellular RNA was extracted (Treatment group). For control, DMSO was used instead of CID 70698683 (final concentration of 0.25%). Three replicates per group used.
2015-11-25 | E-GEOD-72167 | biostudies-arrayexpress
Project description:Mycoplasma genitalium and M. pneumoniae are two significant mycoplasmas that infect the urogenital and respiratory tracts of humans. Despite distinct tissue tropisms, they both have similar pathogenic mechanisms and infect/invade epithelial cells in the respective regions and persist within these cells. However, the pathogenic mechanisms of these species in terms of bacterium-host interactions are poorly understood. To gain insights on this, we infected HeLa cells independently with M. genitalium and M. pneumoniae and assessed gene expression by whole transcriptome sequencing (RNA-seq) approach. The results revealed that HeLa cells respond to M. genitalium and M. pneumoniae differently by regulating various protein-coding genes. Though there is a significant overlap between the genes regulated by these species, many of the differentially expressed genes were specific to each species. KEGG pathway and signaling network analyses revealed that the genes specific to M. genitalium are more related to cellular processes. In contrast, the genes specific to M. pneumoniae infection are correlated with immune response and inflammation, possibly suggesting that M. pneumoniae has some inherent ability to modulate host immune pathways.
2021-10-07 | GSE179051 | GEO
Project description:Yeast with broad-spectrum, zymocidal activity
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