Image Analysis of Microorganisms

Lawrence, John R.; Korber, Darren R.; Wolfaardt, Gideon

doi:10.1002/0471263397.env042

Cited by 8 publications

(8 citation statements)

References 61 publications

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“…The preponderance of empirical D e values that are available in the scientific literature are only 0- or 1-dimensional (that is, volume-averaged or surface-averaged). The primary techniques used to measure D e are fluorescence recovery after photobleaching with scanning confocal laser microscopy 48-50 ; porosity determination using microtomed slices 51 ; injected dyes or tagged molecules 52 ; and microelectrodes 53 . Regardless of the specific technique used, researchers generally measure D e in distinct cell clusters (0-dimensional) or as depth profiles through the biofilm layers (1-dimensional), without monitoring how the values change with biofilm age.…”

Section: Introductionmentioning

confidence: 99%

Diffusion in biofilms respiring on electrodes

Renslow

Babauta

Majors

et al. 2013

Energy Environ. Sci.

100

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The goal of this study was to measure spatially and temporally resolved effective diffusion coefficients (De) in biofilms respiring on electrodes. Two model electrochemically active biofilms, Geobacter sulfurreducens PCA and Shewanella oneidensis MR-1, were investigated. A novel nuclear magnetic resonance microimaging perfusion probe capable of simultaneous electrochemical and pulsed-field gradient nuclear magnetic resonance (PFG-NMR) techniques was used. PFG-NMR allowed noninvasive, nondestructive, high spatial resolution in situ De measurements in living biofilms respiring on electrodes. The electrodes were polarized so that they would act as the sole terminal electron acceptor for microbial metabolism. We present our results as both two-dimensional De heat maps and surface-averaged relative effective diffusion coefficient (Drs) depth profiles. We found that 1) Drs decreases with depth in G. sulfurreducens biofilms, following a sigmoid shape; 2) Drs at a given location decreases with G. sulfurreducens biofilm age; 3) average De and Drs profiles in G. sulfurreducens biofilms are lower than those in S. oneidensis biofilms—the G. sulfurreducens biofilms studied here were on average 10 times denser than the S. oneidensis biofilms; and 4) halting the respiration of a G. sulfurreducens biofilm decreases the De values. Density, reflected by De, plays a major role in the extracellular electron transfer strategies of electrochemically active biofilms.

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Section: Introductionmentioning

confidence: 99%

Diffusion in biofilms respiring on electrodes

Renslow

Babauta

Majors

et al. 2013

Energy Environ. Sci.

100

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“…The individual particles of the chemical populations are then allowed to undergo unbiased random walks by jumping from one compartment to the next, i.e., each particle has an equal probability per unit time, or transition rate, of jumping to one of the neighboring boxes. We are interested in diffusion as it is a fundamental mechanism of transport that underpins a large number of biological processes [31][32][33]. We approach the biological system through a chemical master-equation formalism and use white-noise expansions to derive Fokker-Planck equations that allow us to characterize the properties of the noise [6].…”

Section: Introductionmentioning

confidence: 99%

Power spectra methods for a stochastic description of diffusion on deterministically growing domains

et al. 2011

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A central challenge in developmental biology is understanding the creation of robust spatiotemporal heterogeneity. Generally, the mathematical treatments of biological systems have used continuum, mean-field hypotheses for their constituent parts, which ignores any sources of intrinsic stochastic effects. In this paper we consider a stochastic space-jump process as a description of diffusion, i.e., particles are able to undergo a random walk on a discretized domain. By developing analytical Fourier methods we are able to probe this probabilistic framework, which gives us insight into the patterning potential of diffusive systems. Further, an alternative description of domain growth is introduced, with which we are able to rigorously link the mean-field and stochastic descriptions. Finally, through combining these ideas, it is shown that such stochastic descriptions of diffusion on a deterministically growing domain are able to support the nucleation of states that are far removed from the deterministic mean-field steady state.

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“…A plethora of researchers have investigated diffusion phenomena within biofilms using various experimental techniques such as microelectrodes [7,8], fiberoptic microsensors [9], nuclear magnetic resonance spectroscopy [10,11], infrared spectroscopy combined with Raman microscopy [12], and confocal laser scanning microscopy [13][14][15]. Although some of the experimental results were well explained using the hindered diffusion concept, effects of physical and chemical hindrances are somewhat ambiguously combined into a single quantity, i.e., diffusive tortuosity factor.…”

Section: Introductionmentioning

confidence: 99%