Reconstruction and computation of microscale biovolumes using geographical information systems: potential difficulties.

doi:10.1016/J.RESMIC.2004.02.008

Home
/
Papers
/
Reconstruction and computation of microscale biovolumes using geographical information systems: potential difficulties.

Journal Article•DOI•

Reconstruction and computation of microscale biovolumes using geographical information systems: potential difficulties.

Alexandru I. Petrisor¹, Adrian Cuc¹, Alan W. Decho¹•Institutions (1)

University of South Carolina¹

01 Jul 2004-Research in Microbiology (Elsevier Masson)-Vol. 155, Iss: 6, pp 447-454

TL;DR: Two approaches are used, the program COMSTAT and a Geographical Information Systems-based method, to reconstitute three-dimensional structures and estimate biovolumes of biofilms, and results indicate that the Geographical information Systems approach produced results consistent with the existing COMSTAT approach, and close to theoretical values.

read less

About: This article is published in Research in Microbiology.The article was published on 2004-07-01. It has received 10 citations till now.

...read moreread less

Citations

PDF

Open Access

More filters

Journal Article•DOI•

Morphology and bacterial colonisation of tooth/ceramic restoration interface after different cement excess removal techniques

[...]

Lilian Costa Anami¹, Cristiane Aparecida Pereira¹, Elen Guerra¹, Rodrigo Othávio de Assunção e Souza², Antonio Olavo Cardoso Jorge¹, Marco Antonio Bottino¹ - Show less +2 more•Institutions (2)

Sao Paulo State University¹, Federal University of Paraíba²

01 Sep 2012-Journal of Dentistry

TL;DR: The brush technique seems to be a good option for removing the excess resin cement after adhesive cementation in clinical practice, as indicated by its better results with lower bacterial colonisation.

...read moreread less

45 citations

Cites background or methods from "Reconstruction and computation of m..."

...thickness values are calculated using the COMSTAT software, since the obtained images indicate biofilm adaptation and maturation on different surfaces.(19,23,27) Higher mean values obtained in three-dimensional images represent higher biofilm accumulation on the respective substrates....
[...]
...On the other hand, CLSM is considered a noninvasive and nondestructive observation method and, therefore, has been widely used for biofilm evaluation.(19,23,27) In the CLSM analysis, biofilm biovolume and average...
[...]
...Higher mean values obtained in three-dimensional images represent higher biofilm accumulation on the respective substrates.(19,27) As the quantification of these properties is performed from images obtained under microscopy, the choice of area to obtain these images is a critical factor....
[...]

Journal Article•DOI•

Confocal Laser Microscopic Analysis of Biofilm on Newer Feldspar Ceramic

[...]

Aline Scalone Brentel¹, Karla Zanini Kantorski, Luiz Felipe Valandro, Suzana Beatriz Portugal de Fucio, Regina Maria Puppin-Rontani, Marco Antonio Bottino - Show less +2 more•Institutions (1)

Sao Paulo State University¹

01 Jan 2011-Operative Dentistry

TL;DR: Polishing with rubber points followed by felt disks impregnated with a fine-aluminum oxide particle resulted in biofilm formation similar to that present with a glazed ceramic surface, even though the surface is still rougher and more hydrophobic.

...read moreread less

Abstract: Clinical Relevance When the glazed surface of glass ceramics is submitted to chairside preparation, polishing with rubber points followed by felt disks impregnated with a fine-aluminum oxide particle appears be a good option to polish the surface of the glass ceramic, since this finishing-polishing method results in biofilm formation similar to the glazed ceramic surface.

...read moreread less

25 citations

Journal Article•DOI•

Determining the influence of active cells and conditioning layer on early stage biofilm formation using cellulose acetate ultrafiltration membranes

[...]

Amr M. Zaky¹, Isabel C. Escobar¹, Amir Mohaghegh Motlagh¹, Cyndee L. Gruden¹•Institutions (1)

University of Toledo¹

01 Feb 2012-Desalination

TL;DR: While biofilm surface area coverage could not effectively distinguish membranes being filtered with active and inactive cells, permeate flux data indicated that the presence of active cells resulted in significantly more flux decline, suggesting abiotic and biotic fouling are not independent.

...read moreread less

22 citations

Journal Article•DOI•

Biofilm formation on different materials for tooth restoration: analysis of surface characteristics

[...]

Juliana Silvério Flausino¹, Priscilla Barbosa Ferreira Soares¹, Valessa Florindo Carvalho¹, Denildo de Magalhães¹, Washington Martins da Silva¹, H.L. Costa¹, Carlos José Soares¹ - Show less +3 more•Institutions (1)

Federal University of Uberlandia¹

27 Jun 2014-Journal of Materials Science

TL;DR: Evaluating the effect of roughness parameters and hydrophobicity of restorative material used to restore non-carious cervical lesions on the biofilm formation found material with nanoparticles presented better performance-related topography parameters andBiofilm formation.

...read moreread less

Abstract: The purpose of this study was to evaluate the effect of roughness parameters and hydrophobicity of restorative material used to restore non-carious cervical lesions on the biofilm formation. Four restorative materials were investigated: conventional glass ionomer cement (KF, Ketac Fill Plus, 3M ESPE), resin-modified glass ionomer cement (VT, Vitremer, 3M ESPE), nanofilled resin-modified glass ionomer cement (KN, Ketac Nano, 3M ESPE), and nanofilled resin composite (FZ, Filtek Z350 XT, 3M ESPE). Forty disk specimens were prepared from each material, dived in four groups. Five samples were used for topography parameters analysis using a 3D profilometry. The amplitude parameters (Sa and Sq), spatial parameter (Sds), and hybrid parameter (Ssc) were extracted in area using cut-off of 0.25 mm. Hydrophobicity was determined by the contact angle measurement of deionized water on the surface. The biofilm collected from a 24-year-old subject was grown on modified brain–heart infusion agar under aerobic conditions at 37 °C for 24 h. Each test disk was immersed in 200 µL of biofilm suspension (n = 10) and incubated for 24 h at 37 °C. Biofilm was evaluated after 24 h formation on each disk after stained with 1 % fluorescein using confocal laser-scanning microscopy. Data were analyzed using one-way ANOVA and Tukey test (α = 0.05), Pearson correlation was used to compare topography parameters with biofilm formation. Significant differences were found in related amplitude parameters (Sa and Sq, FZ = KN > VT > KF). KN presented the highest hydrophobicity. FZ and KN presented the lowest thickness and biovolume of biofilm when compared with VT and KF. All topography parameters were significantly correlated with biofilm formation. FZ and KN, material with nanoparticles presented better performance-related topography parameters and biofilm formation. Clinical relevance: The incorporation of nanotechnology into restorative materials promotes better surface topography with lower biofilm formation.

...read moreread less

14 citations

Cites background or methods from "Reconstruction and computation of m..."

...Biofilm structures can be quantified and subsequently analyzed statistically using an analysis of variance model [15, 18, 19]....
[...]
...Despite the many attempts to quantify biofilms, the reproducibility of experiments is difficult to address [19]....
[...]
...biofilms according to the literature [15, 18, 19], biofilm...
[...]

Journal Article•DOI•

Application of atomic force microscopy for characterizing membrane biofouling in the micrometer and nanometer scales

[...]

Amr M. Zaky, Isabel C. Escobar, Cyndee L. Gruden

01 Oct 2013-Environmental Progress

TL;DR: It is suggested that AFM‐based biofilm characterization may provide the details needed to distinguish variations in cell deposition on a single membrane surface and/or between varied feed waters.

...read moreread less

Abstract: Despite the availability of new detection and monitoring methods, a complete understanding of biofouling is still lacking. Therefore, this study employed a combination of biofilm characterization protocols macro, micro, and nano (meter) scales to provide insight into the early stages of biofilm formation using cellulose acetate ultrafiltration membranes. Membranes were fouled during 53 hours of crossflow filtration using two distinct feed waters. Biofilm characterization techniques included flux decline, image analysis, and atomic force microscopy (AFM). The flux decline and image analysis (bulk biofilm surface area coverage) data could not be correlated with feed water characteristics. Using AFM, it was possible to provide feature height analyses on the nano- scale to verify distinct biofilm distribution and formation as function of feed water characteristics. These findings suggest that AFM-based biofilm characterization may provide the details needed to distinguish variations in cell deposition on a single membrane surface and/or between varied feed waters. © 2012 American Institute of Chemical Engineers Environ Prog, 32: 449–457, 2013

...read moreread less

13 citations

Cites background or methods from "Reconstruction and computation of m..."

...In addition, in microbiological imaging where spatial correlation is more important than signal intensity, histogram equalization provides better detection of microorganisms as it enhances their capability to separate from the background [53, 54]....
[...]
...Contrast stretching by histogram equalization was applied to all samples to eliminate noise and enhance contrast [53]....
[...]

References

PDF

Open Access

More filters

Journal Article•DOI•

Phylogenetic identification and in situ detection of individual microbial cells without cultivation.

[...]

Rudolf Amann¹, Wolfgang Ludwig¹, Karl-Heinz Schleifer¹•Institutions (1)

Technische Universität München¹

01 Mar 1995-Microbiological Research

TL;DR: Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts.

...read moreread less

9,017 citations

"Reconstruction and computation of m..." refers methods in this paper

...Previous approaches have utilized digital images of biofilms from CSLM in conjunction with fluorescent lectin probes [1,11,12,17,19,20] to develop a tool that will ideally determine or conservatively estimate the volume occupied by bacteria in a certain region of space [21]....
[...]

Book•

Introductory Digital Image Processing: A Remote Sensing Perspective

[...]

John R. Jensen

01 Dec 1995

TL;DR: Introductory Digital Image Processing: A Remote Sensing Perspective focuses on digital image processing of aircraft- and satellite-derived, remotely sensed data for Earth resource management applications.

...read moreread less

Abstract: For junior/graduate-level courses in Remote Sensing in Geography, Geology, Forestry, and Biology. Introductory Digital Image Processing: A Remote Sensing Perspective focuses on digital image processing of aircraft- and satellite-derived, remotely sensed data for Earth resource management applications. Extensively illustrated, it explains how to extract biophysical information from remote sensor data for almost all multidisciplinary land-based environmental projects. Part of the Pearson Series Geographic Information Science. Now in full color, the Fourth Edition provides up-to-date information on analytical methods used to analyze digital remote sensing data. Each chapter contains a substantive reference list that can be used by students and scientists as a starting place for their digital image processing project or research. A new appendix provides sources of imagery and other geospatial information.

...read moreread less

5,478 citations

"Reconstruction and computation of m..." refers background or methods in this paper

...In geography, or more precisely when satellite images are analyzed, a “ground truth” is typically obtained [8]....
[...]
...In the next step, a 3 × 3 high pass filter was applied to the enhanced images [8]....
[...]
...The concept of “image classification” is used in this paper as a synonym of the “traditional single-stage hard classification” to define the “hard partition of feature space and assignment of each pixel to one of m classes” [8]....
[...]
...The efficiency of different classification algorithms relies on the quality of the images, visual ability and experience of the researcher, and appropriateness of classification criteria in the second one [8]....
[...]
...Briefly, a first step was to enhance images through contrast stretching [8], in order to eliminate the noise and facilitate the separation of bacteria from the background....
[...]

Journal Article•DOI•

Biofilms as complex differentiated communities.

[...]

Paul Stoodley¹, Karin Sauer, David G. Davies, J. W. Costerton•Institutions (1)

Montana State University¹

01 Oct 2002-Annual Review of Microbiology

TL;DR: It is submitted that complex cell-cell interactions within prokaryotic communities are an ancient characteristic, the development of which was facilitated by the localization of cells at surfaces, which may have provided the protective niche in which attached cells could create a localized homeostatic environment.

...read moreread less

Abstract: Prokaryotic biofilms that predominate in a diverse range of ecosystems are often composed of highly structured multispecies communities. Within these communities metabolic activities are integrated, and developmental sequences, not unlike those of multicellular organisms, can be detected. These structural adaptations and interrelationships are made possible by the expression of sets of genes that result in phenotypes that differ profoundly from those of planktonically grown cells of the same species. Molecular and microscopic evidence suggest the existence of a succession of de facto biofilm phenotypes. We submit that complex cell-cell interactions within prokaryotic communities are an ancient characteristic, the development of which was facilitated by the localization of cells at surfaces. In addition to spatial localization, surfaces may have provided the protective niche in which attached cells could create a localized homeostatic environment. In a holistic sense both biofilm and planktonic phenotypes may be viewed as integrated components of prokaryote life.

...read moreread less

2,862 citations

"Reconstruction and computation of m..." refers background in this paper

...Natural biofilms likely exhibit great diversity of bacterial species, and also of sizes and shapes of their bacteria cells [14,24]....
[...]
...species may interact to form specialized “consortia” [16,24]....
[...]
...Biofilms consist of bacterial colonies encapsulated within a matrix of extracellular polymeric secretions (EPS), and form under a range of environmental conditions [24]....
[...]

Journal Article•DOI•

Quantification of biofilm structures by the novel computer program COMSTAT.

[...]

Arne Heydorn¹, Alex Toftgaard Nielsen¹, Morten Hentzer¹, Claus Sternberg¹, Michael Givskov¹, Bjarne Kjær Ersbøll¹, Søren Molin¹ - Show less +3 more•Institutions (1)

Technical University of Denmark¹

01 Oct 2000-Microbiology

TL;DR: Analysis of biofilms of P. aureofaciens growing on 0.03 mM, 0.1 mM or 0.5 mM citrate minimal media showed that mean biofilm thickness increased with increasing citrate concentration, whereas surface to volume ratio increased with higher citrate concentrations.

...read moreread less

Abstract: The structural organization of four microbial communities was analysed by a novel computer program, COMSTAT, which comprises ten features for quantifying three-dimensional biofilm image stacks. Monospecies biofilms of each of the four bacteria, Pseudomonas putida, P. aureofaciens, P. fluorescens and P. aeruginosa, tagged with the green fluorescent protein (GFP) were grown in flow chambers with a defined minimal medium as substrate. Analysis by the COMSTAT program of four variables describing biofilm structure ‐ mean thickness, roughness, substratum coverage and surface to volume ratio ‐ showed that the four Pseudomonas strains represent different modes of biofilm growth. P. putida had a unique developmental pattern starting with single cells on the substratum growing into micro-colonies, which were eventually succeeded by long filaments and elongated cell clusters. P. aeruginosa colonized the entire substratum, and formed flat, uniform biofilms. P. aureofaciens resembled P. aeruginosa, but had a stronger tendency to form micro-colonies. Finally, the biofilm structures of P. fluorescens had a phenotype intermediate between those of P. putida and P. aureofaciens. Analysis of biofilms of P. aureofaciens growing on 0<03 mM, 0< 1m M or 0< 5m M citrate minimal media showed that mean biofilm thickness increased with increasing citrate concentration. Moreover, biofilm roughness increased with lower citrate concentrations, whereas surface to volume ratio increased with higher citrate concentrations.

...read moreread less

1,952 citations

"Reconstruction and computation of m..." refers background or methods in this paper

...A special program named COMSTAT has been developed and has become very valuable for computing the area occupied by bacteria in each layer, thickness distribution and mean thickness, fractal dimension, roughness coefficient, distribution of diffusion distances, and surface to volume ratio [6]....
[...]
...Following GIS computations, COMSTAT [5,6] was used to estimate the biovolume in voxels....
[...]
...COMSTAT is very flexible and allows experienced researchers to use the appropriate value, allowing for very-fine tuning [5,6]....
[...]

Book•

Manual of environmental microbiology.

[...]

C. J. Hurst, R. L. Crawford, Jay L. Garland, David A. Lipson, Aaron L. Mills, L. D. Stetzenbach - Show less +2 more

01 Jan 2007

TL;DR: This book discusses water Microbiology in Public Health, soil, Rhizosphere and Phyllosphere, and the role of aerobiology in these environments.

...read moreread less

Abstract: Section I: Introduction to Environmental Microbiology Section II: General Methodology Section III: Water Microbiology in Public Health Section IV: Aquatic Environments Section V: Soil, Rhizosphere and Phyllosphere Section VI: Subsurface and Landfills Section VII: Aerobiology Section VIII: Biotransformation and Biodegradation

...read moreread less

1,489 citations