Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1104242 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28792650_1.fastq.gz | Fastqsanger.gz | |||
| SRR28792650_2.fastq.gz | Fastqsanger.gz | |||
| SRR28792651_1.fastq.gz | Fastqsanger.gz | |||
| SRR28792651_2.fastq.gz | Fastqsanger.gz | |||
| SRR28792652_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 60 |
Similar Datasets
Project description:Escherichia coli is the leading cause of catheter-associated urinary tract infections, caused by biofilm formation on implanted biomaterial surfaces. Understanding the genes that cause cellular adhesion to diverse biomaterial surfaces may aid in the design of targeting anti-biofouling chemicals to prevent these biofilm infections, but our current knowledge on such surfaces is limited. Here, we incorporate a platform of six biomaterials of varying hydrophilicities and stiffnesses and a comprehensive genome-wide CRISPR interference (CRISPRi) library to elucidate genotype-phenotype relationships for cellular adhesion to physicochemically varied biomaterial surfaces in E. coli MG1655. After characterization of the biomaterials and CRISPRi tool, we designed a CRISPRi library of 34,315 unique designs targeting 99.0% of the genome in MG1655 (up to 8 designs per gene). We then performed pooled selections for adhesion to each biomaterial surface, elucidating over 400 novel gene hits to each biomaterial surface. Data analysis revealed greater correlations between biomaterials of the same hydrophilicity rather than stiffness, in addition to more gene hits associated with decreased adhesion across all six surfaces than increased adhesion. Monoclonal verification of select designs from the library exhibited strong correlations between results from the pooled selections and individual measurements for adhesion to each gel for most designs. The results from this study provide comprehensive gene sets for cellular adhesion to physicochemically diverse biomaterial surfaces that may be potential gene targets for the design of targeting anti-biofouling agents and offer insight that could be used for the design of “smart” biomaterials, both with potential to prevent biofilm infections.
2024-12-31 | GSE274727 | GEO
Project description:To combat dental implant-associated infections, there is a need for novel materials which effectively inhibit bacterial biofilm formation. In the present study, a titanium surface functionalization based on the “slippery liquid-infused porous surfaces” (SLIPS) principle was analyzed in an oral flow chamber system. The immobilized liquid layer was stable over 13 days of continuous flow. With increasing flow rates, the surface exhibited a significant reduction in attached biofilm of both the oral initial colonizer Streptococcus oralis and an oral multi-species biofilm composed of S. oralis, Actinomyces naeslundii, Veillonella dispar and Porphyromonas gingivalis. Using single cell force spectroscopy, reduced bacterial adhesion forces on the lubricant layer could be measured. Gene expression patterns in biofilms on SLIPS, on control surfaces and planktonic cultures were also compared. For this purpose, the genome of S. oralis strain ATCC® 9811TM was sequenced using PacBio Sequel technology. Even though biofilm cells showed clear changes in gene expression compared to planktonic cells, no differences could be detected between bacteria on SLIPS and on control surfaces. Therefore, it can be concluded that the ability of liquid-infused titanium to repel biofilms is solely due to weakened bacterial adhesion to the underlying liquid interface.
2020-05-10 | GSE129981 | GEO
Project description:Salmonella spp. biofilms have been implicated in persistence in the environment and plant surfaces. In addition, Salmonella is able to form biofilms on the surface on cholesterol gallstones. The ability of Salmonella spp. on these surfaces is superior to biofilm formation on surfaces on glass or plastic. Thus, we hypothesized that Salmonella gene expression is specific during biofilm development on cholesterol surfaces.
2013-07-09 | GSE48604 | GEO
Project description:Arabinogalactans decrease the expression of coaggregation protein FomA and modulate in vitro oral biofilm formation
| PRJNA574430 | ENA
Project description:Salmonella spp. biofilms have been implicated in persistence in the environment and plant surfaces. In addition, Salmonella is able to form biofilms on the surface on cholesterol gallstones. The ability of Salmonella spp. on these surfaces is superior to biofilm formation on surfaces on glass or plastic. Thus, we hypothesized that Salmonella gene expression is specific during biofilm development on cholesterol surfaces. Flow through assays were performed whereby S. Typhimurium was inoculated into chambers coated with glass or cholesterol. At 24h post-inoculation, planktonic (from the flow through), biofilms (from glass or cholesterol) were collected. Thus we had 4 samples: Planktonic (2) and Biofilms (2), each with 2 biological replicates
2013-07-09 | E-GEOD-48604 | biostudies-arrayexpress
Project description:Oral biofilms, comprising hundreds of bacteria and other microorganisms on oral mucosal and dental surfaces, play a central role in oral health and disease dynamics. Streptococcus oralis, a key constituent of these biofilms, contribute significantly to their formation, serving as an early colonizer and microcolony scaffold. The interaction between S. oralis and the orally predominant mucin, MUC5B, is pivotal in biofilm development, yet the mechanism underlying MUC5B degradation remains poorly understood. This study introduces MdpS (Mucin Degrading Protease from Streptococcus oralis), a protease that extensively hydrolyses MUC5B and offers an insight into its sequence homology, physicochemical properties, and substrate- and amino acid specificity. MdpS exhibits high sequence conservation within the species and also explicitly among early biofilm colonizing streptococci. It is characterized as a calcium or magnesium dependent serine protease with strict physicochemical preferences, including narrow pH and temperature tolerance, and high sensitivity to increased sodium chloride and reducing agent concentrations. Furthermore, MdpS primarily hydrolyze proteins with O-glycans, but also show activity towards immunoglobulins IgA1/2 and IgM, suggesting potential immunomodulatory effects. Significantly, MdpS extensively degrades MUC5B in the N- and C-terminal domains, emphasizing its role in mucin degradation with implications in carbon and nitrogen sequestration for S. oralis with a potential function by cross-feeding the oral biofilm. Moreover, the enzyme displays amino acid preferences of serine, threonine or cysteine depending on substrate glycosylation. Understanding the interplay between S. oralis and MUC5B, facilitated by MdpS, has significant implications for the management of a healthy eubiotic oral microenvironment, offering potential targets for interventions aimed at modulating oral biofilm composition and succession. Additionally, the MdpS data challenges the presently acknowledged model of MUC5B degradation, because contrarily MdpS does not necessitate O-glycan removal prior to extensive peptide backbone hydrolysis. These findings emphasize the necessity for further research in this field.
2024-02-14 | PXD046954 | Pride
Project description:Oral biofilms, comprising hundreds of bacteria and other microorganisms on oral mucosal and dental surfaces, play a central role in oral health and disease dynamics. Streptococcus oralis, a key constituent of these biofilms, contribute significantly to their formation, serving as an early colonizer and microcolony scaffold. The interaction between S. oralis and the orally predominant mucin, MUC5B, is pivotal in biofilm development, yet the mechanism underlying MUC5B degradation remains poorly understood. This study introduces MdpS (Mucin Degrading Protease from Streptococcus oralis), a protease that extensively hydrolyses MUC5B and offers an insight into its sequence homology, physicochemical properties, and substrate- and amino acid specificity. MdpS exhibits high sequence conservation within the species and also explicitly among early biofilm colonizing streptococci. It is characterized as a calcium or magnesium dependent serine protease with strict physicochemical preferences, including narrow pH and temperature tolerance, and high sensitivity to increased sodium chloride and reducing agent concentrations. Furthermore, MdpS primarily hydrolyze proteins with O-glycans, but also show activity towards immunoglobulins IgA1/2 and IgM, suggesting potential immunomodulatory effects. Significantly, MdpS extensively degrades MUC5B in the N- and C-terminal domains, emphasizing its role in mucin degradation with implications in carbon and nitrogen sequestration for S. oralis with a potential function by cross-feeding the oral biofilm. Moreover, the enzyme displays amino acid preferences of serine, threonine or cysteine depending on substrate glycosylation. Understanding the interplay between S. oralis and MUC5B, facilitated by MdpS, has significant implications for the management of a healthy eubiotic oral microenvironment, offering potential targets for interventions aimed at modulating oral biofilm composition and succession. Additionally, the MdpS data challenges the presently acknowledged model of MUC5B degradation, because contrarily MdpS does not necessitate O-glycan removal prior to extensive peptide backbone hydrolysis. These findings emphasize the necessity for further research in this field.
2024-04-18 | PXD046810 | Pride
Project description:Periodontal diseases are one of the most common human maladies and appear to be caused by the interaction of proximal pathogens such as Porphyromonas gingivalis but only as part of the polymicrobial community known as dental plaque. Streptococcus gordonii is an early colonizing oral organism that binds to oral surfaces and provides adherence for organisms such as P. gingivalis. Together P. gingivalis and S. gordonii form one of the simplest models of potentially pathogenic dental plaque. We used RNA sequencing to monitor the transcriptome of P. gingivalis over time in a biofilm model both in the presence and absence of S. gordonii. Samples were taken at 5, 30, 120, 240, and 360 minutes after shifing from planktonic to sessile conditions and growth media to PBS. When compared to planktonic cells increased transcripts were found for stress, amino acid catabolism, and comeptence and decreased transcripts for DNA replication. The presence of S. gordonii resulted in fewer changes from planktonic cells implying physiological support to Pl gingivalis making the transition from planktonic to sessile easier.
2017-01-15 | GSE80294 | GEO
Project description:This study investigates the mechanisms employed by Salmonella to colonise and establish itself on fresh produce at critical timepoints following infection. We established an alfalfa infection model and compared the findings to those obtained from glass surfaces. Our research revealed dynamic changes in the pathways associated with biofilm formation over time, with distinct plant-specific and glass-specific mechanisms for biofilm formation, alongside the identification of shared genes playing pivotal roles in both contexts.
2023-11-24 | E-MTAB-13495 | biostudies-arrayexpress