Three dimensional quantification of biological samples using micro-computer aided tomography (microCT)

Lilje, Osu; Lilje, Erna; Marano, Agostina V.; Gleason, Frank H.

doi:10.1016/j.mimet.2012.10.006

Cited by 13 publications

(7 citation statements)

References 32 publications

(43 reference statements)

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“…Unfortunately, the only experimental information available to us at this point, at the microscopic scale, about the growth pattern of fungal hyphae in soil pores has not evolved much in the last 30 years. Some progress has been made in the 3D visualization of the configuration of fungal hyphae in systems constituted of polystyrene beads (Lilje et al, 2013) or in wood. Recent advances in the visualization of root hairs of similar diameter as fungi in small samples using synchrotron X-ray CT does demonstrate that at least in very small samples visualizing fungi might be possible (Koebernick et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Pore-Scale Monitoring of the Effect of Microarchitecture on Fungal Growth in a Two-Dimensional Soil-Like Micromodel

Soufan

Delaunay

Gonod

et al. 2018

Front. Environ. Sci.

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In spite of the very significant role that fungi are called to play in agricultural production and climate change over the next two decades, very little is known at this point about the parameters that control the spread of fungal hyphae in the pore space of soils. Monitoring of this process in 3 dimensions is not technically feasible at the moment. The use of transparent micromodels simulating the internal geometry of real soils affords an opportunity to approach the problem in 2 dimensions, provided it is confirmed that fungi would actually want to propagate in such artificial systems. In this context, the key objectives of the research described in this article are to ascertain, first, that the fungus Rhizoctonia solani can indeed grow in a micromodel of a sandy loam soil, and, second, to identify and analyze in detail the pattern by which it spreads in the tortuous pores of the micromodel. Experimental observations show that hyphae penetrate easily inside the micromodel, where they bend frequently to adapt to the confinement to which they are subjected, and branch at irregular intervals, unlike in current computer models of the growth of hyphae, which tend to describe them as series of straight tubular segments. A portion of the time, hyphae in the micromodels also exhibit thigmotropism, i.e., tend to follow solid surfaces closely. Sub-apical branching, which in unconfined situations seems to be controlled by the fungus, appears to be closely connected with the bending of the hyphae, resulting from their interactions with surfaces. These different observations not only indicate different directions to follow to modify current mesoscopic models of fungal growth, so they can apply to soils, but they also suggest a wealth of further experiments using the same set-up, involving for example competing fungal hyphae, or the coexistence of fungi and bacteria in the same pore space.

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Section: Introductionmentioning

confidence: 99%

Pore-Scale Monitoring of the Effect of Microarchitecture on Fungal Growth in a Two-Dimensional Soil-Like Micromodel

Soufan

Delaunay

Gonod

et al. 2018

Front. Environ. Sci.

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“…Lilje et al (2013) describe the development of a culture system and staining protocol they have used to obtain 3D quantitative data of filamentous and zoosporic soil fungi in an artificial matrix that was “developed to simulate the particulate nature of soil.” This artificial matrix consists of 500–900 μm diameter X-ray translucent polystyrene beads, which might be morphologically similar, to some extent, to coarse sand particles, but would likely have very different surface and hydration properties than typically highly heterogeneous soils. In many ways, the same comment pertains to the use of nuclear resonance imaging to detect “biofilms” in systems composed of polystyrene beads (Vogt et al, 2013).…”

Section: The Microbiological Scenementioning

confidence: 99%

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

et al. 2018

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Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

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“…The diffusion rate of PTA and OsO 4 was relatively slower and the stains failed to infuse inside of the samples; the iodine‐based contrast agent does not result in diminishing and shrinkage in sample structures and gave better enhancement. Staining methods and quantification of soft fungi tissues for CT applications were reported by Lilje, Lilje, Marano, and Gleason (). The group assessed the growth of filamentous and zoosporic soil fungi, including composition of the samples and vessels.…”

Section: Molecule‐based Contrast Agentsmentioning

confidence: 99%

“…The diffusion rate of PTA and OsO 4 was relatively slower and the stains failed to infuse inside of the samples; the iodine-based contrast agent does not result in diminishing and shrinkage in sample structures and gave better enhancement. Staining methods and quantification of soft fungi tissues for CT applications were reported byLilje, Lilje, Marano, and Gleason (2013). The group assessed the growth of filamentous and zoosporic soil fungi, including composition of the samples and vessels.Fungi and polystyrene beads were left overnight and washed in deionized water, fixed with 2.5% glutaraldehyde and 4% paraformaldehyde for 40 min at room temperature, and exposed to OsO 4 vapors;another application was staining polysaccharide-containing OsO 4 in the culture media.…”

mentioning

confidence: 99%

Evaluation of X‐ray tomography contrast agents: A review of production, protocols, and biological applications

Koç

Aslan

Kao

et al. 2019

Microscopy Res & Technique

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X‐ray computed tomography is a strong tool that finds many applications both in medical applications and in the investigation of biological and nonbiological samples. In the clinics, X‐ray tomography is widely used for diagnostic purposes whose three‐dimensional imaging in high resolution helps physicians to obtain detailed image of investigated regions. Researchers in biological sciences and engineering use X‐ray tomography because it is a nondestructive method to assess the structure of their samples. In both medical and biological applications, visualization of soft tissues and structures requires special treatment, in which special contrast agents are used. In this detailed report, molecule‐based and nanoparticle‐based contrast agents used in biological applications to enhance the image quality were compiled and reported. Special contrast agent applications and protocols to enhance the contrast for the biological applications and works to develop nanoparticle contrast agents to enhance the contrast for targeted drug delivery and general imaging applications were also assessed and listed.

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Three dimensional quantification of biological samples using micro-computer aided tomography (microCT)

Cited by 13 publications

References 32 publications

Pore-Scale Monitoring of the Effect of Microarchitecture on Fungal Growth in a Two-Dimensional Soil-Like Micromodel

Pore-Scale Monitoring of the Effect of Microarchitecture on Fungal Growth in a Two-Dimensional Soil-Like Micromodel

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

Evaluation of X‐ray tomography contrast agents: A review of production, protocols, and biological applications

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