Ontology highlight
ABSTRACT:
PROVIDER: PRJNA994497 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR25258300.fastq.gz | Fastqsanger.gz | |||
| SRR25258301.fastq.gz | Fastqsanger.gz | |||
| SRR25258302.fastq.gz | Fastqsanger.gz | |||
| SRR25302582_1.fastq.gz | Fastqsanger.gz |
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Project description:Biofilm formation by microorganisms is a major cause of recurring infections and removal of biofilms has proven to be extremely difficult given their inherent drug resistance. Understanding the biological processes that underlie biofilm formation is thus extremely important and could lead to the development of more effective drug therapies, resulting in better infection outcomes. Using the yeast S. cerevisiae as a biofilm model, overexpression screens identified DIG1, SFL1, HEK2, TOS8, SAN1 and ROF1/YHR177W as regulators of biofilm formation. Subsequent RNA-seq analysis of biofilm and non-biofilm forming strains revealed that all of the overexpression strains, other than DIG1 and TOS8, were adopting a single differential expression profile, although induced to varying degrees. TOS8 adopted a separate profile, while the expression profile of DIG1 reflected the common pattern seen in most of the strains, plus substantial DIG1-specific expression changes. We interpret the existence of the common transcriptional pattern seen across multiple, unrelated overexpression strains as reflecting a real transcriptional state, that the yeast cell can access through regulatory signaling mechanisms, allowing an adaptive morphological change between biofilm-forming and non-biofilm states.
2017-04-25 | GSE98079 | GEO
Project description:The formation of Listeria monocytogenes biofilms contributes to persistent contamination in food processing facilities. A microarray comparison of L. monocytogenes between the transcriptome of the strong biofilm forming strain (Bfms) Scott A and the weak biofilm forming (Bfmw) strain F2365 was conducted to identify genes potentially involved in biofilm formation. Among 951 genes with significant difference in expression between the two strains, a GntR-family response regulator encoding gene (LMOf2365_0414), designated lbrA, was found to be highly expressed in Scott A relative to F2365. A Scott A lbrA-deletion mutant, designated AW3, formed biofilm to a much lesser extent as compared to the parent strain by a rapid attachment assay and scanning electron microscopy. Complementation with lbrA from Scott A restored the Bfms phenotype in the AW3 derivative. A second microarray assessment using the lbrA deletion mutant AW3 and the wild type Scott A revealed a total of 304 genes with expression significantly different between the two strains, indicating the potential regulatory role of LbrA in L. monocytogenes. A cloned copy of Scott A lbrA was unable to confer enhanced biofilm forming potential in F2365, suggesting that additional factors contributed to weak biofilm formation by F2365. Findings from the study may lead to new strategies to modulate biofilm formation.
2012-09-06 | GSE40598 | GEO
Project description:To reveal the transcriptional profiles of Actinobacillus pleuropneumoniae under biofilm and planktonic growth, we established a biofilm-forming culture method and constructed a mutant strain Δpga with defect in biofilm formation. Wild-type and Δpga mutant strains of Actinobacillus pleuropneumoniae strain 4074 were cultured in bottles with shaking for planktonic (WT_PK) and in microplates in static status for biofilm (WT_BF, Δpga), respectively. The bacteria in logarithmic growth period of different culture groups were collected for RNA seq.
2023-05-31 | GSE221940 | GEO
Project description:LC-MS/MS analyses of 20 MeOH/ACN/water cyanobacterial extracts from Guadeloupe mangroves in the DDA mode.
ESI +
| MSV000090244 | GNPS
Project description:The formation of Listeria monocytogenes biofilms contributes to persistent contamination in food processing facilities. A microarray comparison of L. monocytogenes between the transcriptome of the strong biofilm forming strain (Bfms) Scott A and the weak biofilm forming (Bfmw) strain F2365 was conducted to identify genes potentially involved in biofilm formation. Among 951 genes with significant difference in expression between the two strains, a GntR-family response regulator encoding gene (LMOf2365_0414), designated lbrA, was found to be highly expressed in Scott A relative to F2365. A Scott A lbrA-deletion mutant, designated AW3, formed biofilm to a much lesser extent as compared to the parent strain by a rapid attachment assay and scanning electron microscopy. Complementation with lbrA from Scott A restored the Bfms phenotype in the AW3 derivative. A second microarray assessment using the lbrA deletion mutant AW3 and the wild type Scott A revealed a total of 304 genes with expression significantly different between the two strains, indicating the potential regulatory role of LbrA in L. monocytogenes. A cloned copy of Scott A lbrA was unable to confer enhanced biofilm forming potential in F2365, suggesting that additional factors contributed to weak biofilm formation by F2365. Findings from the study may lead to new strategies to modulate biofilm formation. Two comparisons were performed between 1) strong biofilm former Listeria monocytogenes strain ScottA versus weak biofilm former Listeria monocytogenes strain F2365; 2) Listeria monocytogenes ScottA LbrA deletion mutant strain versus Listeria monocytogenes ScottA. Four replicates were loaded for the first comparison and two replicates were loaded for the second comparison.
2012-09-06 | E-GEOD-40598 | biostudies-arrayexpress
Project description:Staphylococcus epidermidis is a Gram-positive, coagulase-negative (CoNS) bacterium that is carried asymptomatically on the skin and mucous membranes of virtually all human beings. It is a major cause of nosocomial infections and associated with invasive procedures (Méric et al., 2018). Virulent S. epidermidis strains contaminate indwelling medical devices, such as catheters or implants (Sabaté Brescó et al., 2017), showing pathogenicity traits, e.g., biofilm formation, cell toxicity, or methicillin resistance (Méric et al., 2018). Apart from that, even the low-virulent, low-biofilm forming strain of S. epidermidis ATCC 12228 was shown to form a biofilm under decreased oxygen conditions (Uribe-Alvarez et al., 2015). As a member of the skin and mucosal microbiome, S. epidermidis prevents the colonization of Staphylococcus aureus (Otto, 2011). Its well-studied metabolism and the ability to grow on known media make S. epidermidis a possible reconstruction candidate. A reconstruction of a genome-scale metabolic model (GEM) of S. epidermidis was created using CarveMe (Machado et al., 2018) and carefully refined in subsequent manual curation efforts, using the S. epidermidis ATCC 12228 strain sequence. The model was experimentally validated on multiple media under varying growth conditions, such as different carbon sources.
2025-05-19 | MODEL2012220002 | BioModels
Project description:The biofilm proteome profile of endodontic and systemic pathogen E. faecalis has been analysed in this study to identify markers associated with its biofilm formation. Strong and weak biofilm forming E. faecalis clinical isolates were compared with two standard ATCC strains of E. faecalis in order to elucidate the biological pathways associated with the biofilm formation capability of E. faecalis.
2018-01-29 | PXD006542 | Pride
Project description:Cyanobacterial blooms associated with the benthic mat have been rising. Besides the ongoing concern about toxins production, cyanobacteria are actively involved in marine biofilms, representing several economic and environmental impacts. Proteomic studies on cyanobacterial biofilms could be an effective approach to establish metabolic pathways that affect these fouling organisms and, consequently, obtain novel control strategies against them. Currently, there are few studies in this field on filamentous cyanobacteria. Thus, standard methodologies for following cyanobacterial biofilm development for a long-term assay and a quantitative proteomics analysis were performed in this work. Biofilm development from unidentified filamentous Synechococcales LEGE 06021 was evaluated on different surfaces, glass and perspex, and at two significant shear rates for marine environments (4 s-1 and 40 s-1). Higher biofilm development was observed at 4 s-1, and these biofilms showed a lower roughness coefficient value than those formed at higher shear. Overall, about 1,877 proteins were identified, and differences in proteome were more noticeable between the two hydrodynamic conditions than those found between the two surfaces. 20 Differentially Expressed Proteins (DEPs) were found between 4 s-1 vs. 40 s-1, of which 15 DEPs were found on glass, whereas five DEPs were found on perspex. On the glass, some of these DEPs include phage tail proteins, orange carotenoid protein, enzymes like cyanophynase, glutathione-dependent formaldehyde dehydrogenase, and MoaD/ThiS family protein, while on perspex, the DEPs include enzymes such as transketolase, dihydroxy-acid dehydratase, iron ABC transporter substrate-binding protein or transcription termination/antitermination protein NusG. In summary, the biofilm structure, chlorophyll a content, total biomass, and proteomic profile are more affected by the hydrodynamic conditions than by the surfaces employed. These findings suggest that most of the metabolic changes could be produced to counterbalance the different shear rates. However, the differential expression of some proteins could be associated with the surfaces used. This study helps to consolidate the knowledge of the main factors affecting biofilm development, and sheds new lights on putative targets to address new antimicrobial strategies.
2022-10-13 | PXD029048 | Pride