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699 results for “Biofilms”
Data from: eDNA-stimulated cell dispersion from Caulobacter crescentus biofilms upon oxygen limitation is dependent on a toxin-antitoxin system
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Data from: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro
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Disturbing the spatial structure of biofilms affects the expression of agr regulated virulence factors in Staphylococcus aureus
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Data from: Mechanisms of antibiofilm compounds JG-1 and M4 across multiple species: Alterations of protein interactions essential to biofilm formation
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Data from: Biofilms as self-shaping growing nematics
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Data for: Extensive cellular multi-tasking within Bacillus subtilis biofilms
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Data from: Multiscale mechanics of granular biofilms
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Data from: Innovative methodology for antimicrobial susceptibility determination in Mycoplasma biofilms
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Social evolution of shared biofilm matrix components
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Diversity, adaptation and metabolic potential of the microbiome in biofilms from a high-temperature hot spring
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The role of surface adhesion on the macroscopic wrinkling of biofilms
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Biofilm formation and plasmid-mediated quinolone resistance genes at varying quinolone inhibitory concentrations in quinolone-resistant bacteria superinfecting COVID-19 inpatients
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Confocal microscopy images for: Surface remodeling and inversion of cell-matrix interactions underlie community recognition and dispersal in Vibrio cholerae biofilms
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Disinfectant efficacy on mixed biofilms comprising Escherichia coli and spoilage microorganisms
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Pharmaceutical effects on biofilm functioning quantified via contaminant exposure substrates presented in Rosi et al. 2018.
An ongoing component of the Baltimore urban long-term ecological research (LTER) project (Baltimore Ecosystem Study, BES) is the use of the watershed approach and monitoring of stream water quality to evaluate the impacts of multiple chemical stressors on urban stream ecosystem functioning within Baltimore. The LTER research has focused on the Gwynns Falls watershed, which spans a gradient from highly urban, urban-residential, and suburban zones. In addition, a forested watershed serves as a reference. The long-term sampling network includes four longitudinal sampling sites along the Gwynns Falls mainstem, as well as several small (40-100 ha) watershed within or near the Gwynns Falls, providing data on water quality in different land use zones of the watersheds. Each study site is continuously monitored for discharge and is sampled weekly for water chemistry. Those data are available elsewhere on the BES website. We are interested in studying the effects of pharmaceuticals and personal care products (PPCPs) on stream biofilm functioning within urban streams. We constructed and deployed contaminant exposure substrates (CES) in four streams within the greater Baltimore, Maryland, USA area to measure the responses of biofilms in each of the four streams to caffeine, ciprofloxacin, cimetidine, diphenhydramine, and no PPCPs. We incubated CES for 2 weeks in the four different streams, with five replicate CES for each treatment being randomly placed on plastic L-bars within each stream. After the two-week deployment, we used the light-dark incubation approach to estimate gross primary production and community respiration via change in dissolved oxygen (DO) for biofilms colonizing substrates (either cellulose sponges to select heterotrophic biofilms or fritted glass disks to select for autotrophic biofilms) topping each CES. This dataset includes all of the raw data for the light-dark incubations used to calculate gross primary production and community respiration for the v
Repeated erosion of sediments with biofilms from Rowley River mud flats, year 2012, Rowley, MA
This study aims to explore the interplay between biofilms and erodability of cohesive sediments. Erosion experiments were run in four laboratory annular flumes with natural sediments. Mud from the Rowley River mudflats was taken at low tide and then placed in flumes. Two of the flumes were bleach to prevent biota, while the other two were allowed to grow; nutrients were also added to the flumes. On different intervals, the flumes were eroded and the amount of erosion and velocity of the flow were measured. Additionally, each day biofilm growth was measured using Pulse-Amplitude Modulation (PAM) Underwater Fluorometry. Reported here are 10 minute averages of shear stress (derived from velocity) and suspended sediment (uncalibrated, in NTUs) along with PAM measurements. The complete dataset is available upon request via .mat files, but the dataset is quite large (kendallv@bu.edu or pie_im@mbl.edu).
Supplementary online material for PhD thesis manuscript Proteomic approaches to the characterization of tolerance and virulence in bacterial biofilms
<p>These data belong to a PhD thesis manuscript Proteomic approaches to the characterization of tolerance and virulence in bacterial biofilms.</p> <p> </p> <p><strong>Supplementary online material 1</strong></p> <p>Theoretical proteome of <em>Staphylococcus aureus </em>ATCC 25923.</p> <p><strong>Supplementary online material 2</strong></p> <p>Theoretical proteome of <em>Pseudomonas aeruginosa </em>PAO1.</p> <p><strong>Supplementary online material 3</strong></p> <p>MaxQuant (v. 1.6.1.0) output of exoproteomic analysis carried out on a dual-species biofilm model.</p> <p><strong>Supplementary online material 4</strong></p> <p>MaxQuant (v. 1.6.1.0) output of surfaceomic analysis carried out on a dual-species biofilm model</p> <p><strong>Supplementary online material 5</strong></p> <p>Curated MaxQuant (v. 1.6.1.0) output of exoproteomic analysis carried out on a dual-species biofilm model.</p> <p><strong>Supplementary online material 6</strong></p> <p>Curated MaxQuant (v. 1.6.1.0) output of surfaceomic analysis carried out on a dual-species biofilm model.</p> <p><strong>Supplementary online material 7</strong></p> <p>Protein quantification of valid identifications in LC-MS/MS analysis of <em>Staphylococcus aureus </em>and <em>Pseudomonas aeruginosa </em>dual-species biofilms.</p>
Code and dataset for: Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy
<p>Dataset and codes for: Cell position fates and collective fountain flow in bacterial biofilms revealed by light-sheet microscopy.</p> <p>Published online via First Release, <strong>11 June 2020</strong></p> <p>B. Qin et al., Science, 10.1126/science.abb8501 (2020).</p> <p> </p>
Spatial structure affects phage efficacy in infecting dual-strain biofilms of Pseudomonas aeruginosa
Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a susceptible Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar. We found that both in liquid and in colonies, inter-strain competition reduced resistance evolution in the susceptible strain and decreased phage population size. However, while all sensitive bacteria died in liquid, bacteria in colonies could remain sensitive yet escape phage infection, due mainly to reduced growth in colony centers. In sum, spatial structure can protect bacteria against phage infection, while the presence of competing strains reduces the evolution of resistance to phage.
Data from: Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels
Phototrophic biofilms are ubiquitous in freshwater and marine environments where they are critical for biogeochemical cycling, food webs and in industrial applications. In streams, phototrophic biofilms dominate benthic microbial life and harbor an immense prokaryotic and eukaryotic microbial biodiversity with biotic interactions across domains and trophic levels. Here, we examine how community structure and function of these biofilms respond to varying light availability, as the crucial energy source for phototrophic biofilms. Using metatranscriptomics, we found that under light limitation dominant phototrophs, including diatoms and cyanobacteria, displayed a remarkable plasticity in their photosynthetic machinery manifested as higher abundance of messenger RNAs (mRNAs) involved in photosynthesis and chloroplast ribosomal RNA. Under higher light availability, bacterial mRNAs involved in phosphorus metabolism, mainly from Betaproteobacteria and Cyanobacteria, increased, likely compensating for nutrient depletion in thick biofilms with high biomass. Consumers, including diverse ciliates, displayed community shifts indicating preferential grazing on algae instead of bacteria under higher light. For the first time, we show that the functional integrity of stream biofilms under variable light availability is maintained by structure-function adaptations on several trophic levels. Our findings shed new light on complex biofilms, or "microbial jungles", where in analogy to forests, diverse and multi-trophic level communities lend stability to ecosystem functioning. This multi-trophic level perspective, coupling metatranscriptomics to process measurements, could advance understanding of microbial-driven ecosystems beyond biofilms, including planktonic and soil environments.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.