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699 results for “Biofilms”
Development of a flow chamber system for the reproducible in vitro analysis of biofilm formation on implant materials
<p>The data provided are the original data from the microscopic investigation of oral bacterial biofilms. Bacteria were stained with a life/dead staining. Viable cells are represented in red, non-viable cells are shown in green. The biofilms were gained by 50 stacks each with a CLSM. The biofilms were formed in a flow chamber system with a flow velocity of 100µL/min over 24-72 hours. The biofilms were grown on tintanium discs.</p>
Spectrophotometrical raw data of viability and total sugar content included in the paper "Promastigote EPS secretion and haptomonad biofilm formation as evolutionary adaptations of trypanosomatid parasites for colonizing honeybee hosts"
<p>Raw data of spectrophotometrical data included in the paper: "Promastigote EPS secretion and haptomonad biofilm formation as evolutionary adaptations of trypanosomatid parasites for colonizing honeybee hosts" published in npj biofilms and Microbiomes. </p>
Basic data that show effect of Panax ginseng and Symphytum officinale boost metronidazole on quorum sensing and biofilm disruption in Porphyromonas gingivalis
<p>Basic data that show effect of Panax ginseng and Symphytum officinale boost metronidazole on quorum sensing and biofilm disruption in Porphyromonas gingivalis</p>
DATASET: Using a Bacterial Protein to Selectively Target Bacterial Biofilms: Treatment of S. epidermidis Biofilms with Targeted Photothermal Gold Nanoparticles
<p>Supporting data for the manuscript.</p>
Data from: Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts
The molecular and evolutionary processes underlying fungal domestication remain largely unknown despite the importance of fungi to bioindustry and for comparative adaptation genomics in eukaryotes. Wine fermentation and biological aging are performed by strains of S. cerevisiae with, respectively, pelagic fermentative growth on glucose, and biofilm aerobic growth utilizing ethanol. Here, we use environmental samples of wine and flor yeasts to investigate the genomic basis of yeast adaptation to contrasted anthropogenic environments. Phylogenetic inference and population structure analysis based on single nucleotide polymorphisms (SNPs) revealed a group of flor yeasts separated from wine yeasts. A combination of methods revealed several highly differentiated regions between wine and flor yeasts, and analyses using codon-substitution models for detecting molecular adaptation identified sites under positive selection in the high affinity transporter gene ZRT1. The Cross Population Composite Likelihood Ratio (XP-CLR) revealed selective sweeps at three regions, including in the hexose transporter gene HXT7, the yapsin gene YPS6 and the membrane protein coding gene MTS27. Our analyses also revealed that the biological aging environment has led to the accumulation of numerous mutations in proteins from several networks, including Flo11 regulation and divalent metal transport. Together, our findings suggest that the tuning of FLO11 expression and zinc transport networks are a distinctive feature of the genetic changes underlying the domestication of flor yeasts. Our study highlights the multiplicity of genomic changes underlying yeast adaptation to man-made habitats, and reveals that flor/wine yeast lineage can serve as a useful model for studying the genomics of adaptive divergence.
Modelling the growth of biofilms on soft substrates
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PIV vector fields from: Boundary layer hydrodynamics of patchy biofilms
<p>This dataset contains the instantaneous velocity vector fields from PIV data taken over large acrylic plates fouled with diatomaceous biofilm of varying patchiness. </p> <p>See associated article, Boundary layer hydrodynamics of patchy biofilms, for methods description.</p> <p>Each zip folder contains data for one of the 4 non-uniform biofilms examined, PB-1 (patchy biofilm 1); PB-2 (patchy biofilm 2); SB-1 (sparse biofilm 1); SB-2 (sparse biofilm 2). For each biofilm, the corresponding folder contains 4000 statistically independent instantaneous velocity vector fields. Each vector field is saved in a .mat file, and the workspace variable that contains the data is called ‘vecfield’. </p> <p>Size calibration and water temperature are provided in the spreadsheet ‘experiment_metadata.xlsx’</p> <p> </p> <p>Column 1: X (streamwise distance [pixels]) </p> <p>Column 2: Y (wall-normal distance from bottom of frame [pixels])</p> <p>Column 3: U (streamwise velocity vector [pixels / 250 microseconds]) </p> <p>Column 4: V (vertical velocity vector [pixels / 250 microseconds]) </p> <p>Column 5: CHC (number of tracked particles. A value < 1 gives the location of the biofilm, which was masked out)</p> <p> </p>
Source data for: Human monoclonal antibodies against Staphylococcus aureus surface antigens recognize in vitro biofilm and in vivo implant infections
<p class="CxSpFirst">Implant-associated <i>Staphylococcus aureus</i> infections are difficult to treat because of biofilm formation. Bacteria in a biofilm are often insensitive to antibiotics and host immunity. Monoclonal antibodies (mAbs) could provide an alternative approach to improve the diagnosis and potential treatment of biofilm-related infections. Here we show that mAbs targeting common surface components of <i>S. aureus</i> can recognize clinically relevant biofilm types. The mAbs were also shown to bind a collection of clinical isolates derived from different biofilm-associated infections (endocarditis, prosthetic joint, catheter). We identify two groups of antibodies: one group that uniquely binds <i>S. aureus </i>in biofilm state and one that recognizes <i>S. aureus </i>in both biofilm and planktonic state. Furthermore, we show that a mAb recognizing wall teichoic acid (WTA; clone 4497) specifically localizes to a subcutaneously implanted pre-colonized catheter in mice. In conclusion, we demonstrate the capacity of several human mAbs to detect <i>S. aureus</i> biofilms<i> in vitro</i> and <i>in vivo</i>.</p>
Surface Characterization and Anti-Biofilm Effectiveness of Hybrid Films of Polyurethane Functionalized with Saponite and Phloxine B
<p>The main objective of this work was to synthesize composites of polyurethane (PU) with organoclays (OC) exhibiting antimicrobial properties. Layered silicate (saponite) was modified with octadecyltrimethylammonium cations (ODTMA) and functionalized with phloxine B (PhB) and used as a filler in the composites. A unique property of composite materials is the increased concentration of modifier particles on the surface of the composite membranes. Materials of different compositions were tested and investigated using physico-chemical methods, such as infrared spectroscopy, X-ray diffraction, contact angle measurements, absorption, and fluorescence spectroscopy in the visible region. The composition of an optimal material was as follows: n<sub>ODTMA</sub>/m<sub>Sap</sub> = 0.8 mmol g<sup>−1</sup> and n<sub>PhB</sub>/m<sub>Sap</sub> = 0.1 mmol g<sup>−1</sup>. Only about 1.5% of present PhB was released in a cultivation medium for bacteria within 24 h, which proved good stability of the composite. Anti-biofilm properties of the composite membranes were proven in experiments with resistant Staphylococcus aureus. The composites without PhB reduced the biofilm growth 100-fold compared to the control sample (non-modified PU). The composite containing PhB in combination with the photodynamic inactivation (PDI) reduced cell growth by about 10,000-fold, thus proving the significant photosensitizing effect of the membranes. Cell damage was confirmed by scanning electron microscopy. A new method of the synthesis of composite materials presented in this work opens up new possibilities for targeted modification of polymers by focusing on their surfaces. Such composite materials retain the properties of the unmodified polymer inside the matrix and only the surface of the material is changed. Although these unique materials presented in this work are based on PU, the method of surface modification can also be applied to other polymers. Such modified polymers could be useful for various applications in which special surface properties are required, for example, for materials used in medical practice.</p>
Data for: Dark matters – contrasting responses of stream biofilm to browning and loss of riparian shading
<p><span>Concentrations of terrestrial-derived dissolved organic carbon (DOC) in freshwater ecosystems have increased consistently, causing freshwater browning. The mechanisms behind browning are complex, but in forestry-intensive regions browning is accelerated by land drainage. Forestry actions in streamside riparian forests alter canopy shading, which together with browning is expected to exert a complex and largely unpredictable control over key ecosystem functions. We conducted a stream mesocosm experiment with three levels of browning (ambient vs. moderate vs. high, with 2.7 and 5.5-fold increase, respectively, in absorbance) crossed with two levels of riparian shading (70% light reduction vs. open canopy) to explore the individual and combined effects of browning and loss of shading on the quantity (algal biomass) and nutritional quality (polyunsaturated fatty acid and sterol content) of the periphytic biofilm. We also conducted a field survey of differently colored (4.7 to 26.2 mg DOC L<sup>-1</sup>) streams to provide a 'reality check' for our experimental findings. Browning reduced greatly the algal biomass, suppressed the availability of essential polyunsaturated fatty acids, especially eicosapentaenoic acid (EPA), and sterols, but increased the availability of terrestrial-derived long-chain saturated fatty acids (LSAFA). In contrast, loss of shading increased primary productivity, which resulted in elevated sterol and EPA content of the biofilm. The field survey largely repeated the same pattern: biofilm nutritional quality decreased significantly with increasing DOC, as indicated particularly by a decrease of the </span><span><em><span><span>w</span></span></em>-3:</span><span><em><span><span>w</span></span></em>-6 ratio and increase in LSAFA content. Algal biomass, in contrast, was mainly controlled by dissolved inorganic nitrogen (DIN) concentration, while DOC concentration was of minor importance. The ongoing browning process is inducing a dramatic reduction in the nutritional quality of the stream biofilm. Such degradation of the major high-quality food source available for stream consumers may reduce the trophic transfer efficiency in stream ecosystems, potentially extending across the stream-forest ecotone. </span></p>
A high-throughput integrated biofilm-on-a-chip platform for the investigation of combinatory physicochemical responses to chemical and fluid shear stress
<p>Excel files for the data presented in the corresponding manuscript. </p>
Biofilm flow data from: Roughness effects of diatomaceous slime fouling on turbulent boundary layer hydrodynamics
<p>This dataset contains the instantaneous velocity vector fields as well as the time averaged velocity and turbulence fields from PIV data taken over a large acrylic plate fouled with a relatively uniform diatomaceous biofilm. </p> <p>See associated article, Roughness effects of diatomaceous slime fouling on turbulent boundary layer hydrodynamics, for methods description.</p> <p>Time averaged velocity and turbulence fields data are stored in the file velocity_fields.mat, which contains the following variables: </p> <p>X: The streamwise distance of each column in the velocity field matrices [mm]</p> <p>Y: The vertical distance (from the bottom of the frame) of each row in the velocity field matrices [mm]</p> <p>U: Time averaged streamwise velocity [m s^-1]</p> <p>V: Time averaged vertical velocity [m s^-1]</p> <p>tke: Time averaged turbulent kinetic energy [m^2 s^-2]</p> <p>u': Time averaged streamwise Reynolds stress [m^2 s^-2]</p> <p>v': Time averaged vertical Reynolds stress [m^2 s^-2]</p> <p>u'v': Time averaged Reynolds shear stress [m^2 s^-2]</p> <p>The zip file biofilm_vector_fields contains the 4,000 statistically independent velocity vector fields used to compute the time averaged velocity and turbulence fields. The vector field data is in the variable labeled matr. Size calibration: 2302 pixels/ inch (906.3 pixels/ cm). </p> <p>Column 1: X (streamwise distance in [pixels]) </p> <p>Column 2: Y (wall-normal distance from bottom of frame in [pixels])</p> <p>Column 3: U (streamwise velocity vector in [pixels / 250 microseconds]) </p> <p>Column 4: V (vertical velocity vector in [pixels / 250 microseconds]) </p> <p>Column 5: CHC (number of tracked particles. A value < 1 gives the location of the biofilm, which was masked out)</p> <p>Column 6: U2 </p> <p>Column 7: V2</p> <p>Column 8: U3</p> <p>Column 9: V3</p> <p>Column 10: U4</p> <p>Column 11: V4</p>
Live and dead cells in strong and weak biofilms of Klebsiella pneumoniae
<p>Video of CLSM Z-stack of strong and weak biofilm showing the arrangement of live and dead cells inside the biofilm matrix. </p>
Cavity Lasing Characteristics of Thioflavin T and Thioflavin X in Different Solvents and Their Interaction with DNA for the Controlled Reduction of a Light Amplification Threshold in Solid-State Biofilms
Open the record for dataset details and reuse information.
FIGURE 8 in New records of Cyanobacterial morphotypes with Leptolyngbya indica sp. nov. from terrestrial biofilms of the Lower Gangetic Plain, India
FIGURE 8. Phylogenetic relationships among Leptolyngbya strains based on NJ/ML analyses with 16S rRNA sequences (983 nt) representing the position of the sequence obtained in the present study. Bootstrap values (NJ/ML) for nodes>50% are shown in the tree. The 16S rRNA sequences of the cyanobacterial genus Gloeobacter [G. kilaueensis (Acc. no. NR121745) & G. violaceus (Acc. no. FR798924)] are used as out group.
FIGURE 2 in New records of Cyanobacterial morphotypes with Leptolyngbya indica sp. nov. from terrestrial biofilms of the Lower Gangetic Plain, India
FIGURE 2. Morphological features of Leptolyngbya indica sp. nov. A. Intermingled blue green unbranched filaments grown on agar plate with other cyanobacteria colonies. B. Filaments without heterocytes under LM. C. Transparent facultative sheath attached to the trichome revealed by FESEM. D. Trichome non-heterocytous, curved, bearing thin cells with constriction at cross walls under FESEM. E. Trichome without attenuation, apical cell round. F. Distribution of thylakoid in cell periphery towards the cell wall revealed by CLSM. Scale bars: A= 10 μm; B, D= 5 μm; C, E, F= 2 μm.
FIGURE 7 in New records of Cyanobacterial morphotypes with Leptolyngbya indica sp. nov. from terrestrial biofilms of the Lower Gangetic Plain, India
FIGURE 7. Phylogenetic tree (NJ/ML) of partial 16S rRNA sequences (1258 nt) of the family Leptolyngbyaceae (order Synechococcales) showing the phylogenetic position of the LBK isolate. Bootstrap values (NJ/ML) for nodes>50% are shown in the tree. The 16S rRNA sequences of the cyanobacterial genus Gloeobacter [G. kilaueensis (Acc. no. NR121745) & G. violaceus (Acc. no. FR798924)] are used as out group.
FIGURE 4 in New records of Cyanobacterial morphotypes with Leptolyngbya indica sp. nov. from terrestrial biofilms of the Lower Gangetic Plain, India
FIGURE 4. Morphological features of Geitlerinema cf. calcuttense in FESEM study. A. Trichome with ring like structure at cross walls. B. In actively growing young trichome zig zag ring at the apical trichal length upto 10 cells noted. C. In trichome active growth zone gradually restricted towards upper part (4–5 cell) in older trichomes and gradual bending of apical part. D. Sticky apical part of the mature trichome with fixed apical ring. E. Thickening present in mature trichome may be for fragmentation of whole trichomes into hormogonia insted of necridic cell formation. Scale bars: A–E= 5 μm.
FIGURE 6 in New records of Cyanobacterial morphotypes with Leptolyngbya indica sp. nov. from terrestrial biofilms of the Lower Gangetic Plain, India
FIGURE 6. Coleofasciculus cf. chthonoplastes filaments under LM and FESEM. A. Filaments with dark blue green trichomes. B. Sheath moderately thick, not intensely lamellated, colorless with many (10–15) trichomes. C. Trichomes outside sheath. D. Trichomes cylindrical, less constricted, apical part attenuated, without calyptra. Scale bars: A–D= 10 μm.
FIGURE 5 in New records of Cyanobacterial morphotypes with Leptolyngbya indica sp. nov. from terrestrial biofilms of the Lower Gangetic Plain, India
FIGURE 5. Morphological features of Geitlerinema cf. jasorvense in FESEM study A. Trichome curved or straight. B. Trichome straight with blunt round apical cell. C. Mature trichome gradually attenuated and bent, slightly constricted at the crosswalls. D. Trichome with straight conical apical cell but without calyptra. E. Trichome with bent apical cell. F. Apical trichal part hook like. G. Variation of apical trichal part in the morphologically similar filament. Scale bars: A= 15 μm;B, D–E= 5 μm; C, F, G=10 μm.
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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.