Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA595907 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:To better understand the impact of infection on oocyte quality we employed global transcriptomics of oocytes collected from heifers after receiving intrauterine infusion of pathogenic Escherichia coli and Trueperella pyogenes. We hypothesized that oocyte transcriptome would be altered in response to intrauterine infection. A total of 452 differentially expressed genes were identified in oocytes collected from heifers 4 days after bacteria infusion compared to vehicle infusion, while 539 differentially expressed genes were identified in oocytes collected from heifers 60 days after bacteria infusion. Only 42 genes were differentially expressed in bacteria infused heifers at both day 4 and day 60. Interferon, HMGB1, ILK, IL-6 and TGF-beta signaling pathways were downregulated in oocytes collected at day 4 from bacteria infused heifers, while interferon, ILK and IL-6 signaling were upregulated in oocytes collected at day 60 from bacteria infused heifers. These data suggest that bacterial infusion alters the oocyte transcriptome differently at day 4 and day 60, suggesting different follicle stages are susceptible to damage. Characterizing the long-term impacts of uterine infection on oocyte transcriptome aids in our understanding of how infection causes infertility in dairy cattle.
2020-01-01 | GSE141307 | GEO
Project description:Liquid-infused structured titanium surfaces for dental implants: antiadhesive mechanism to repel bacterial biofilms
| PRJNA533328 | ENA
Project description:Purpose: Use RNA-seq to investigate the transcriptional response of Pseudomonas aeruginosa when adhering to different surfaces. Methods: Coupons of silicone, glass, and polycarbonate plastic were purchased from Biosurfaces Technologies (Catalog numbers: RD128-Si, RD128-GL, RD128-PC). Coupons were placed into a 24-well plate and conditioned in LB for at least 10 min prior to bacterial addition. LB was removed and replaced with 2mL of logarithmic phase bacterial culture in LB (OD600 0.7). At the indicated time point, the coupon was rinsed twice in PBS and placed into 1 mL of Trizol. Trizol was collected and stored at -80°C for RNA isolation. HiSeq 4000 sequencing was performed, generating approximately 300 million total paired end 300 bp reads. Reads were aligned to the reference PAO1 genome using Rockhopper. Results: A total of 833 genes were differentially expressed across the three surfaces. Most genes were reduced (522 genes) rather than elevated (269 genes), with 42 genes showing both elevated and reduced RNA levels across two or more surfaces. Conclusion: Bacteria had a nearly unique transcriptional response on each surface, with the vast majority regulated on only one surface
2022-02-03 | GSE195826 | GEO
Project description:The aim of this experiment was to determine if the development of resistance to antibiotics can be driven by the concentration and speciation of Cu. Experimental setup was designed to investigate two hypotheses for which two strains of Gram- bacteria have been selected: - Do TE enhance AR in resistant bacteria? Resistant strain: Bioluminescent Pseudomonas aeruginosa PAO1 (Xen41, Tetracycline resistant) - Do TE induce AR in sensitive bacteria? Sensitive strain: Pseudomonas aeruginosa PAO1 (Wild Type)
2020-10-28 | GSE160188 | GEO
Project description:Pseudomonas aeruginosa is a pathogenic micro-organism responsible for many hospital-acquired infections. It is able to adhere to solid surfaces and develop an immobilised community or so-called biofilm. Many studies have been focusing on the use of specific materials to prevent the formation of these biofilms, but the reactivity of the bacteria in contact to surfaces remains unknown. In order to evaluate the impact of different materials on the physiology of Pseudomonas aeruginosa during the first stage of biofilm formation, i.e. adhesion, we investigated the total proteome of cells adhering to three materials: stainless steel, glass and polystyrene. Using tandem mass spectrometry performed at the PAPPSO proteomic platform, 930 proteins were identified, 70 of which were differentially expressed between the materials. Dysregulated proteins belonged to 19 PseudoCAP (Pseudomonas Community Annotation Project) functional classes, with a particular abundance of proteins involved in small molecule transport and membrane proteins. Notably, ten porins or porin precursors were under-produced in bacteria adhering to stainless steel when compared to those adhering to polystyrene and glass. Although adhesion to solid surfaces is an extracellular phenomenon, it involves not only extracellular proteins but also intracellular reactions, as observed with the dysregulation of 11 proteins involved in various metabolisms and five in protein translation. Overall, this work showed that during bacterial adhesion, P. aeruginosa senses the materials concerned and is able to modulate its physiology accordingly.
2018-10-24 | PXD006881 | Pride
Project description:Clostridium perfringens is a Gram-positive anaerobic pathogen that causes multiple diseases in humans and animals. C. perfringens lack flagella but have type IV pili (TFP) and can glide on agar surfaces by forming filaments of cells aligned end to end. When cells are placed on agar surfaces, they become elongated, flexible and have TFP on their surface. To understand the basis of these phenotypes, cells were grown in three types of liquid media and on agar plates with the same medium to compare gene expression using RNA-seq. Hundreds of genes were differentially expressed, including genes associated with TFP functions, which were higher on plates than in liquid. The gusA gene, encoding the enzyme β-glucuronidase, was inserted into the chromosome downstream of TFP promoters and expression measured in liquid and on plates. β-glucuronidase activity was proportional to the amount of transcripts seen with RNA-seq n liquid-grown cells, but not plate-grown cells, suggesting post-transcriptional regulation of these genes on surfaces. An sRNA adjacent to pilA1 (SR79) was expressed at higher levels on plates in all media; overexpression of this sRNA resulted in longer cells on plates and shorter lag times in liquid suggesting SR79 plays a role in adapting to surface growth.
2018-06-30 | GSE99224 | GEO
Project description:Dictyostelium amoebae feed on bacteria, which are taken up by phagocytosis. Using DNA microarrays we have investigated gene expression during phagocytosis of Dictyostelium cells incubated with Escherichia coli. The gene expression profiles of cells incubated for a short time with bacteria were compared with cells either exposed to axenic culture medium or exponentially growing on bacteria. Transcriptional changes during exponential growth either in axenic medium or on bacteria were also compared, in order to identify genes differentially expressed during growth on bacteria. We recognized 443 and 59 genes, which are differentially regulated by phagocytosis or growth on bacteria, respectively, and 102 genes, which are common to both processes. Roughly one third of the genes is up- and two third down-regulated compared to growth in axenic medium. Functional annotation of differentially regulated genes revealed that phagocytosis induces profound changes in carbohydrate, aminoacid and lipid metabolism, in the translation machinery and in cytoskeletal components. Among the up-regulated genes are genes encoding proteins involved in transcription and translation, sterol metabolism and mitochondrial biogenesis. Very few changes were detected in genes required for endocytosis and intracellular traffic, suggesting that the intracellular traffic machinery is mostly in common between phagocytosis and pinocytosis. A few putative receptor or adhesion proteins and components of signal transduction have been identified, which could be involved in regulating phagocytosis.
2009-01-31 | E-TABM-415 | biostudies-arrayexpress
Project description:Background:
- Some bacteria found in the large and small intestines help keep people healthy and aid digestion. They may also affect a person s risk of developing cancer. Researchers want to study the relationship between intestinal bacteria and breast cancer risk factors. They can do this by looking at stool and urine samples from postmenopausal women.
Objectives:
- To study intestinal bacteria and its relationship to urine-based markers of breast cancer risk in women.
Eligibility:
- Women between 55 and 69 years of age with a recent mammogram that showed no signs of cancer.
Design:
* Participants will be screened with a medical history and basic health questionnaire.
* At home, participants will complete questionnaires about cancer risk factors and food consumption.
* Participants will also collect urine and stool samples. They will send the samples to the designated labs for study.
* No treatment will be provided as part of this protocol.
| 2114858 | ecrin-mdr-crc
Project description:16S high-throughput sequencing of bacteria from leaf surfaces of 11 tree species Raw sequence reads
| PRJNA705503 | ENA