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699 results for “Biofilms”
Aquatic biofilm autotrohic index, carbon dioxide flux, and environmental conditions for the APEX water table experiment 2021-2023
To better understand linkages between hydrology and ecosystem carbon flux in northern aquatic ecosystems, we evaluated the relationship between plant communities, biofilm development, and carbon dioxide (CO2) exchange following long-term changes in hydrology in an Alaskan fen. We quantified seasonal variation in biofilm composition and CO2 exchange in response to lowered and raised water-table position (relative to a control) during years with varying levels of background dissolved organic carbon (DOC). We then used nutrient-diffusing substrates to evaluate cause-effect relationships between changes in plant subsidies (i.e., leachates) and biofilm composition among water-table treatments. We found that background DOC concentration determined whether plant subsidies promoted net autotrophy or heterotrophy on nutrient diffusing substrates. In conditions where background DOC was <= 40 mg L-1, plant subsidies promoted an autotrophic biofilm. Conversely, when background DOC concentration was >= 50 mg L-1, plant subsidies promoted heterotrophy. Greater light attenuation associated with elevated levels of DOC may have overwhelmed the stimulatory effect of nutrients on autotrophic microbes by constraining photosynthesis while simultaneously allowing heterotrophs to outcompete autotrophs for available nutrients. At the ecosystem level, conditions that favored an autotrophic biofilm resulted in net CO2 uptake among all water-table treatments, whereas the site was a net source of CO2 to the atmosphere in conditions that supported greater heterotrophy. Taken together, these findings show that hydrologic history interacts with changes in dominant plant functional groups to alter biofilm composition, which has consequences for ecosystem CO2 exchange.
Vanishing_Glaciers_Epilithic_Biofilms
<p>- Dataset containing the separate output files from IMP, METABOLIC, gRodon, Anvi'o, MANTIS etc. for downstream analyses of epilithic biofilms from the NOMIS Vanishing Glacier's project</p>
Data from Sand aggradation alters biofilm standing crop and metabolism in a low-gradient Lake Superior tributary
We conducted a comparative study of biofilm standing crop and metabolism in the Salmon Trout River, a tributary of Lake Superior where watershed disturbances have led to 3-fold increases in streambed fine sediments, predominately sand, in the past decade. We compared biofilm standing crop and metabolism rates using light–dark chambers in reaches where substrate consisted of predominately exposed rock or sand substrates. This data archive includes rates of primary production and respiration, biomass measurements from chambers, and benthic standing crop and water chemistry data collected from the same river sites over the course of a summer. All data were published in Journal of Great Lakes research in 2015, https://doi.org/10.1016/j.jglr.2015.09.004
Interlaboratory study for the evaluation of three microtiter plate-based biofilm quantification methods
<p>Data collected in the Print-aid interlaboratory study (ring trial) to evaluate the repeatability and reproducibility of three microtiter plate based methods: crystal violet, resazurin and plate counts. The files contain all the raw data collected for each laboratory as well as the tranformed data. Analysis and protocol details can be found in the following publication https://www.nature.com/articles/s41598-021-93115-w </p>
The potential of nitric acid-functionalized carbon nanotubes to mitigate bacterial biofilms
<p>Pristine multi-walled carbon nanotubes were functionalized with nitric acid, followed by thermal treatment at 600 °C, and incorporated into a poly(dimethylsiloxane) matrix. The composites were characterized and their antibiofilm activity and antibacterial mechanisms were assessed by biofilm cell culturability and flow cytometry, respectively.</p>
Analyzing marine biofilms developed on carbon nanotube-modified surfaces by 3D OCT approach
<p>Glass, epoxy resin, and carbon nanotubes (CNT) composite were analyzed regarding wettability by water contact angle measurement, and roughness by atomic force microscopy. Cyanobacterial biofilms formed by Nodosilinea cf. nodulosa LEGE 10377 were developed on these surfaces for seven weeks and under controlled hydrodynamic conditions. Biofilm wet weight and structural parameters such as biofilm thickness, contour coefficient, biovolume, porosity, and average size of non-connected pores obtained from Optical Coherence Tomography (OCT) were assessed.</p>
The potential of graphene oxide surfaces to reduce biofilms formed by uropathogens
<p>Polydimethylsiloxane (PDMS), 5 wt.% GNP/PDMS (GNP/PDMS), 1 wt.% graphene oxide (GO)/PDMS (GO1/PDMS), 3 wt.% GO/PDMS (GO3/PDMS), 5 wt.% GO/PDMS (GO5/PDMS)) were analyzed regarding hydrophobicity and roughness. Staphylococcus aureus and Pseudomonas aeruginosa biofilms were developed on these different surfaces under static conditions for 24h at 37°C. The number of biofilm total and culturable cells was quantified by flow cytometry and plate counts, respectively, whereas the biofilm amount was determined by crystal violet staining. Moreover, the mechanisms of action of GO were characterized using the flow cytometer.</p>
The impact of graphene composite surfaces in the architecture of cyanobacterial biofilms
<p>Glass, epoxy resin and graphene nanoplatelet (GNP) composite were analyzed regarding wettability and roughness. Cyanobacterial biofilms from Lusitaniella coriacea LEGE 07157 were developed on these surfaces for seven weeks and under controlled hydrodynamic conditions. Biofilm wet weight, structural parameters (biofilm thickness, empty spaces, and average size of empty spaces) obtained from Optical Coherence Tomography (OCT), and biovolume and surface coverage obtained by Confocal Laser Scanning Microscopy (CLSM) were analyzed.</p>
Effect of chitosan-based surfaces on biofilms formed by Cobetia marina
<p>The characterization (roughness and water contact angle) of poly (lactic acid) surfaces coated with chitosan of different molecular weights and concentrations obtained from the <i>Loligo opalescens</i> pen was performed. The antifouling activity of these surfaces against <i>Cobetia marina</i> biofilm formation was evaluated, as well as the mechanism of action of this type of chitosan.</p>
Source data for publication "Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation"
<p><strong>This dataset contains the source data for the figures in the following publication: </strong></p> <p><strong>Title: </strong>Bacteria use exogenous peptidoglycan as a danger signal to trigger biofilm formation</p> <p><strong>Authors: </strong>Sanika Vaidya, Dibya Saha, Daniel K.H. Rode, Gabriel Torrens, Mads F. Hansen, Praveen K. Singh, Eric Jelli, Kazuki Nosho, Hannah Jeckel, Stephan Göttig, Felipe Cava, Knut Drescher</p> <p><strong>Journal: </strong>Nature Microbiology, 2025</p> <p> </p> <p><strong>Description of the dataset: </strong></p> <p>The data is organized by figures in the publication receferenced above. For each figure, there is a XLSX-file that contains the processed data and a ZIP-archive that contains the raw image data. The ZIP-archive also contains readme documents with more detailed descriptions for every set of raw image data. </p> <p>Example: For Figure 1 in the main text of the publication, there following data are available:</p> <ul> <li>raw data: Figure_01.zip</li> <li>processed data: Processed_Source_Data_Figure1.xlsx</li> </ul> <p>Similarly, XLSX-files and ZIP-archives are available for the main text Figures 1-6. For the Extended Data (ED) Figures 1-10, there are XLSX-files available that present the data shown in each figure. Only some of the Extended Data Figures present results based on image data - therefore raw image data ZIP-archives are only available for ED Figures 3, 6, 7, 8, 9, 10.</p>
Vanishing_Glaciers_Epilithic_Biofilms_Data
<p>Metagenomic data from epilithic biofilms obtained from Glacer-fed streams as part of the Vanishing Glaciers Project, funded by NOMIS</p>
DATASET: Near-Infrared Photothermal Ablation of Biofilms using Protein-Functionalized Gold Nanospheres with a Tunable Temperature Response
<p>This dataset contains the DLS, TEM, temperature data, and other experimental data to accompany the manuscript.</p>
Baltimore Ecosystem Study: Stream biofilm bacterial community composition
The Baltimore Ecosystem Study stream biofilm bacterial community composition was obtained from 8 long-term sampling network sites in and near the Gwynns Falls watershed to examine how bacterial communities differ along an urban-rural gradient. Sampling was conducted at the same time as stream chemistry sampling on 18 June 2014 and 21 Oct 2014. Note: biofilm samples were taken about 50 meters east from the Carroll Park monitoring station, just under the I95 highway overpass, due to high water depth, high water flow, and lack of rock substrates for sampling. This dataset presents the number of sequences matching the taxonomic classifications in a reference database of 16S rRNA genes. See the full metadata record for detailed methods.
Effects of nutrients and organic carbon on the relative proportion of primary producers (microalgae) and heterotrophic decomposers (bacteria and fungi) during aquatic biofilm development in boreal peatland located near Fairbanks Alaska - 2018
1. Producer-decomposer interactions within aquatic biofilms can range from mutualistic associations to competition depending on available resources. The outcomes of such interactions have implications for biogeochemical cycling, and as such, may be especially important in northern peatlands, which are a global carbon sink and are expected to experience changes in resource availability with climate change. The purpose of this study was to evaluate the effects of nutrients and organic carbon on the relative proportion of primary producers (microalgae) and heterotrophic decomposers (bacteria and fungi) during aquatic biofilm development in a boreal peatland. Given that decomposers are often better competitors for nutrients than primary producers in aquatic ecosystems, we predicted that labile carbon subsidies would shift the biofilm composition towards heterotrophy owing to the ability of decomposers to outcompete primary producers for available nutrients in the absence of carbon limitation. 2. We manipulated nutrients (nitrate and phosphate) and organic carbon (glucose) in a full factorial design using nutrient-diffusing substrates in an Alaskan fen. 3. Heterotrophic bacteria were limited by organic carbon and algae were limited by inorganic nutrients. However, the outcomes of competitive interactions depended on background nutrient levels. Heterotrophic bacteria were able to outcompete algae for available nutrients when organic carbon was elevated and nutrient levels remained low, but not when organic carbon and nutrients were both elevated through enrichment. 4. Fungal biomass was significantly lower in the presence of glucose alone, possibly owing to antagonistic interactions with heterotrophic bacteria. In contrast to bacteria, fungi were stimulated along with algae following nutrient enrichment. 5. The decoupling of algae and heterotrophic bacteria in the presence of glucose alone shifted the biofilm trophic status towards heterotrophy. This effect was overturned
Cryo-OrbiSIMS for 3D molecular imaging of a bacterial biofilm in its native state
<p>We developed a method for analysis and imaging of biological samples in their native state, by combining a cryo-OrbiSIMS instrument with cryogenic sample handling and high-pressure freezing. By using this method, we did analysis and imaging of frozen-hydrated mature <em>Pseudomonas aeruginosa</em> biofilm, which allows the identification and map of quorum sensing signaling molecules, nucleobases and bacterial membrane molecules with high spatial-resolution and high mass-resolution. Some of quorum sensing signaling molecules were further confirmed by MS/MS. By comparing the analysis of frozen-hydrated <em>Pseudomonas aeruginosa</em> biofilm with the freeze-dried one, we dicover that signal intensity of all interesting molecules get enhanced in the frozen-hydrated state. Especially for polar molecules, such as amino acid, it could even achieve 10,000 fold increasing. Here, we provide the original OrbiSIMS data including MS and MS/MS spectra, depth profile and images of frozen-hydrated and freeze-dried <em>Pseudomonas aeruginosa</em> biofilm. The data could be open by using SurfaceLab Version 7.0 (ION-TOF, Germany).</p>
Dataset - The influence of the crowding assumptions in biofilm simulations
<p><strong>Dataset simulated for the manuscript "The influence of the crowding assumptions in biofilm simulations" by Angeles-Martinez and Hatzimanikatis.</strong></p>
3D cell tracking dataset of bacterial biofilm deformation and recovery under shear flow
<p>This MAT file includes dataset in the scientific article "<i>In vivo</i> microrheology reveals elastic and plastic responses inside three-dimensional bacterial biofilms" by the following authors: Takuya Ohmura, Dominic Skinner, Konstantin Neuhaus, Gary Choi, Jörn Dunkel, Knut Drescher. This MAT file can be conveniently opened with Matlab. </p><p>When you open this file with Matlab, you will find 4 variables stored in the file "Data_v3_loop2_newRxy_bidx1_274.mat"</p><p><strong>Variable 1: name_parameter</strong></p><p>Names of 31 parameters for columns in 3 variables: 'deformation_all', 'recovery_all' , 'plasticity_all'. The parameters have cell displacements, orientations, coordinates, biofilm indexes and experimental conditions. When the parameters have units, they are shown in the names. </p><ul><li>'x_Frame1[um]'</li><li>'y_Frame1[um]'</li><li>'z_Frame1[um]'</li><li>'Normalized_x_Frame1'</li><li>'Normalized_y_Frame1'</li><li>'Normalized_z_Frame1'</li><li>'LocalDensity_Frame1(VolumeFractionAround30px)'</li><li>'LocalCellNumberDensity_Frame1(VolumeFractionAround30px)'</li><li>'NematicOrderParameter_Frame1'</li><li>'AlignmentFlow_Frame1[rad]'</li><li>'AlignmentRadial_Frame1[rad]'</li><li>'AlignmentZaxis_Frame1[rad]'</li><li>'d_x[um]'</li><li>'d_y[um]'</li><li>'d_z[um]'</li><li>'Normalized_d_x'</li><li>'Normalized_d_y'</li><li>'Normalized_d_z'</li><li>'d_LocalDensity'</li><li>'d_LocalNumberDensity[um^-3]'</li><li>'d_NematicOrderParameter'</li><li>'d_AlignmentFlow[rad]'</li><li>'d_AlignmentRadial[rad]'</li><li>'d_AlignmentZaxis[rad]'</li><li>'CrossProduct[um^2]'</li><li>'BiofilmIndexNumber'</li><li>'Biofilm_width[um]'</li><li>'Biofilm_height[um]'</li><li>'Biofilm_volume[um^3]'</li><li>'FlowRate[ul/min]'</li><li>'Duration[min]'</li></ul><p><strong>Variable 2: deformation_all</strong></p><p>The rows indicate 704198 single-cell trackings in deformations of 274 bacterial biofilms. Each of the 274 bacterial biofilms has a different 'BiofilmIndexNumber'. The columns indicate 31 parameters which names are shown in 'name_parameter'.</p><p><strong>Variable 3: recovery_all</strong></p><p>The rows indicate 685991 single-cell trackings in recoveries of 274 bacterial biofilms. Each of the 274 bacterial biofilms has a different 'BiofilmIndexNumber'. The columns indicate 31 parameters which names are shown in 'name_parameter'.</p><p><strong>Variable 4: plasticity_all</strong></p><p>The rows indicate 665749 single-cell trackings in plasticities of 274 bacterial biofilms. Each of the 274 bacterial biofilms has a different 'BiofilmIndexNumber'. The columns indicate 31 parameters which names are shown in 'name_parameter'.</p><p> </p><p>To plot the cell tracked data in the figures of the article, use our MATLAB code uploaded in our GitHub (https://github.com/knutdrescher/biofilm-rheology).</p>
Metadata for Confocal Laser Scanning Microscopy Images of Monoculture and Mixed-Species Biofilms Formed by Bacterial Isolates of Dairy Origin
<p>In a project conducted by ILVO (Belgium), a wide variety of bacterial species were recovered from the surface of a dairy pasteurizer after cleaning and disinfection (C&D). The biofilm-forming ability of these bacteria was determined in both single-species and various mixed-culture combinations. Some work related to this study has been published in Frontiers: "Synergistic interactions in multispecies biofilm combinations of bacterial isolates recovered from diverse food processing industries". Bacterial species were mixed in different combinations to assess the community biofilm mass and growth dynamics of individual species. ILVO and the University of Copenhagen conducted experiments aimed at revealing the structural characteristics and spatial organization of bacterial species within different mixed-species biofilms. In our research, we employed oligonucleotide FISH probes, each conjugated with a unique fluorescent dye: Cy5 for <em>Stenotrophomonas rhizophila</em> (B68), Cy3 for <em>Bacillus licheniformis</em> (B65), and FAM for <em>Microbacterium lacticum</em> (B30). C1 combination refers to a combination containing B68 and B30. </p> <p><span>Images of the biofilms formed on the coupons were captured using a confocal laser scanning microscope (LSM 800, Zeiss) with a Plan-Apochromat 63x/1.4 oil-immersion objective. Z-stacks were recorded to obtain three-dimensional (3D) images. Standard images were made with an image size of 1024 × 1024 pixels, corresponding to physical dimensions of 101.4 × 101.4 μm for each image. For each image, two separate channels were applied to detect any dual-species combination using a flexible detector (GaAsP-PMT) in the LSM 800 system. Representative 3D views of images were generated using the 3D model function in the ZEN system 3.7.</span></p> <p>Biofilms were grown in BHI for 24 h on plastic coupons. The samples were imaged at different time points: 6h, 12h, 18h and 24h. Each samples had three replicates and for each replicate imaging was performed from 3-6 different positions. </p> <p>Details of the oligonucleotide probes are given below:</p> <table> <tbody> <tr> <td> <p><strong><span>Name of the species</span></strong></p> </td> <td> <p><strong><span>Sequences</span></strong></p> </td> <td> <p><strong><span>Max. excitation</span></strong></p> </td> <td> <p><strong><span>Max. emission</span></strong></p> </td> <td> <p><strong><span>Fluorophores</span></strong></p> </td> </tr> <tr> <td> <p><em><span>S. rhizophila</span></em><span> B68<span> </span></span></p> </td> <td> <p><span>GGGCCTTTACCCCGCCA</span></p> </td> <td> <p><span>649 nm</span></p> </td> <td> <p><span>670 nm</span></p> </td> <td> <p><span>Cy5</span></p> </td> </tr> <tr> <td> <p><em><span>B. licheniformis</span></em><span> B65</span></p> </td> <td> <p><span>ACCGCCTGCGCGCGCTT</span></p> </td> <td> <p><span>550 nm</span></p> </td> <td> <p><span>570 nm</span></p> </td> <td> <p><span>Cy3</span></p> </td> </tr> <tr> <td> <p><em><span>M. lacticum</span></em><span> B30</span></p> </td> <td> <p><span>CCCCACCCTTTCGCTCC</span></p> </td> <td> <p><span>495 nm</span></p> </td> <td> <p><span>520 nm</span></p> </td> <td> <p><span>FAM</span></p> </td> </tr> </tbody> </table>
When does antimicrobial resistance increase bacterial fitness? Effects of dosing, social interactions and frequency dependence on the benefits of AmpC β-lactamases in broth, biofilms and a gut infection model.
<p><span>One of the longstanding puzzles of antimicrobial resistance is why the frequency of resistance persists at intermediate levels.<span> </span>Theoretical explanations for the lack of fixation of resistance include cryptic costs of resistance or negative frequency-dependence but are seldom explored experimentally. <span> </span><em>β</em>-lactamases, which detoxify penicillin-related antibiotics, have well-characterized frequency-dependent dynamics driven by cheating and cooperation.<span> </span>However, bacterial physiology determines whether <em>β</em>-lactamases are cooperative and we know little about the sociality or fitness of <em>β</em>-lactamase producers in infections.<span> </span>Moreover, media-based experiments constrain how we measure fitness, and ignore important parameters such as infectivity and transmission among hosts.<span> </span>Here, we investigated the fitness effects of broad-spectrum AmpC <em>β</em>-lactamases in <em>Enterobacter cloacae</em> in broth, biofilms and gut infections in a model insect. <span> </span>We quantified frequency- and dose-dependent fitness using cefotaxime, a third-generation cephalosporin.<span> </span>We predicted that infection dynamics would be similar to those observed in biofilms, with social protection extending over a wide dose range.<span> </span>We found evidence for the sociality of <em>β</em>-lactamases in all contexts with negative frequency-dependent selection ensuring the persistence of wild-type bacteria although cooperation was less prevalent in biofilms, contrary to predictions.<span> </span>While competitive fitness in gut infections and broth had similar dynamics, incorporating infectivity into measurements of fitness in infections<em> </em>significantly affected conclusions. <span> </span>Resistant bacteria had reduced infectivity which limited the fitness benefits of resistance to infections challenged with low antibiotic doses and having low initial frequencies of resistance. <span> </span>The fitness of resistant bacteria in more physiologically tolerant states (in biofilms, in infections) could be constrained by the presence of wild-type bacteria, high antibiotic doses and limited availability of <em>β</em>-lactamases.<span> </span>One conclusion is that increased tolerance of <em>β</em> -lactams does not necessarily increase selection pressure for resistance.<span> </span>Overall, both cryptic fitness costs and frequency-dependence curtailed the fitness benefits of resistance in this study.<span> </span></span></p> <p><span> </span></p>
Data from: Photoinactivation of Yeast and Biofilm Communities of Candida albicans Mediated by ZnTnHex-2-PyP4+ Porphyrin
<p>Data supporting the figures presented in the research article Photoinactivation of Yeast and Biofilm Communities of <em>Candida albicans</em> Mediated by ZnTnHex-2-PyP<sup>4+</sup> Porphyrin.</p> <p> </p> <p><em>Candida albicans</em> is the main cause of superficial candidiasis. While the antifungals available are defied by biofilm formation and resistance emergence, antimicrobial photodynamic inactivation (aPDI) arises as an alternative antifungal therapy. The tetracationic metalloporphyrin Zn(II) <em>meso</em>-tetrakis(<em>N</em>-n-hexylpyridinium-2-yl)porphyrin (ZnTnHex-2-PyP<sup>4+</sup>) has high photoefficiency and improved cellular interactions. We investigated the ZnTnHex-2-PyP<sup>4+</sup> as a photosensitizer (PS) to photoinactivate yeasts and biofilms of <em>C. albicans</em> strains (ATCC 10231 and ATCC 90028) using a blue light-emitting diode. The photoinactivation of yeasts was evaluated by quantifying the colony forming units. The aPDI of ATCC 90028 biofilms was assessed by the MTT assays, propidium iodide (PI) labeling, and scanning electron microscopy. Mammalian cytotoxicity was investigated in Vero cells using MTT assay. The aPDI (4.3 J/cm<sup>2</sup>) promoted eradication of yeasts at 0.8 and 1.5 µM of PS for ATCC 10231 and ATCC 90028, respectively. At 0.8 µM and same light dose, aPDI-treated biofilms showed intense PI labeling, about 89% decrease in the cell viability, and structural alterations with reduced hyphae. No considerable toxicity was observed in mammalian cells. Our results introduce the ZnTnHex-2-PyP<sup>4+</sup> as a promising PS to photoinactivate both yeasts and biofilms of <em>C. albicans</em>, stimulating studies with other <em>Candida </em>species and resistant isolates.</p>
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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)
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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.