scholarly journals Methods of In Situ Quantitative Root Biology

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2399
Author(s):  
Taras Pasternak ◽  
José Manuel Pérez-Pérez
Keyword(s):  
Quantitative Methods ◽  
Three Dimensional ◽  
Root Apical Meristem ◽  
Volume Distribution ◽  
3D Analysis ◽  
Root Structure ◽  
Coarse Root ◽  
Nicotiana Tabacum L

When dealing with plant roots, a multiscale description of the functional root structure is needed. Since the beginning of 21st century, new devices such as laser confocal microscopes have been accessible for coarse root structure measurements, including three-dimensional (3D) reconstruction. Most researchers are familiar with using simple 2D geometry visualization that does not allow quantitative determination of key morphological features from an organ-like perspective. We provide here a detailed description of the quantitative methods available for 3D analysis of root features at single-cell resolution, including root asymmetry, lateral root analysis, cell size and nuclear organization, cell-cycle kinetics, and chromatin structure analysis. Quantitative maps of the root apical meristem (RAM) are shown for different species, including Arabidopsis thaliana (L.), Heynh, Nicotiana tabacum L., Medicago sativa L., and Setaria italica (L.) P. Beauv. The 3D analysis of the RAM in these species showed divergence in chromatin organization and cell volume distribution that might be used to study root zonation for each root tissue. Detailed protocols and possible pitfalls in the usage of the marker lines are discussed. Therefore, researchers who need to improve their quantitative root biology portfolio can use them as a reference.

scholarly journals Methods for in situ quantitative root biology

2021 ◽  
Author(s):  
Taras Pasternak ◽  
Jose Manuel Perez-Perez
Keyword(s):  
Quantitative Methods ◽  
Primary Root ◽  
Three Dimensional ◽  
Cell Types ◽  
Root Tip ◽  
Volume Distribution ◽  
3D Analysis ◽  
Root Structure ◽  
Coarse Root ◽  
Phloem Structure

When dealing with plant roots, a multi-scale description of the functional root structure is needed. Since the beginning of XXI century, new devices like laser confocal microscopes have been accessible for coarse root structure measurements, including 3D reconstruction. Most re-searchers are familiar with using simple 2D geometry visualization that does not allow quantitatively determination of key morphological features from an organ-like perspective. We provide here a detailed description of the quantitative methods available for three-dimensional (3D) analysis of root features at single cell resolution, including root asymmetry, lateral root analysis, xylem and phloem structure, cell cycle kinetics, and chromatin determination. Quantitative maps of the distal and proximal root meristems are shown for different species, including Arabidopsis thaliana, Nicotiana tabacum and Medicago sativa. A 3D analysis of the primary root tip showed divergence in chromatin organization and cell volume distribution between cell types and precisely mapped root zonation for each cell file. Detailed protocols are also provided. Possible pitfalls in the usage of the marker lines are discussed. Therefore, researchers who need to improve their quantitative root biology portfolio can use them as a reference.

scholarly journals Three-dimensional in situ morphometrics of Mycobacterium tuberculosis infection within lesions by optical mesoscopy and novel acid-fast staining

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Robert J. Francis ◽  
Gillian Robb ◽  
Lee McCann ◽  
Bhagwati Khatri ◽  
James Keeble ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Three Dimensional ◽  
Large Field ◽  
Staining Procedure ◽  
3D Analysis ◽  
Mycobacterium Tuberculosis Infection ◽  
In Vivo Models ◽  
Novel Approach

AbstractTuberculosis (TB) preclinical testing relies on in vivo models including the mouse aerosol challenge model. The only method of determining colony morphometrics of TB infection in a tissue in situ is two-dimensional (2D) histopathology. 2D measurements consider heterogeneity within a single observable section but not above and below, which could contain critical information. Here we describe a novel approach, using optical clearing and a novel staining procedure with confocal microscopy and mesoscopy, for three-dimensional (3D) measurement of TB infection within lesions at sub-cellular resolution over a large field of view. We show TB morphometrics can be determined within lesion pathology, and differences in infection with different strains of Mycobacterium tuberculosis. Mesoscopy combined with the novel CUBIC Acid-Fast (CAF) staining procedure enables a quantitative approach to measure TB infection and allows 3D analysis of infection, providing a framework which could be used in the analysis of TB infection in situ.

scholarly journals High Rates of Conjugation in Bacterial Biofilms as Determined by Quantitative In Situ Analysis

1999 ◽  
Vol 65 (8) ◽  
pp. 3710-3713 ◽  
Author(s):  
Martina Hausner ◽  
Stefan Wuertz
Keyword(s):  
Laser Scanning ◽  
Nutrient Concentration ◽  
Three Dimensional ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Bacterial Biofilms ◽  
Conjugative Gene Transfer ◽  
Biofilm Structure

ABSTRACT Quantitative in situ determination of conjugative gene transfer in defined bacterial biofilms using automated confocal laser scanning microscopy followed by three-dimensional analysis of cellular biovolumes revealed conjugation rates 1,000-fold higher than those determined by classical plating techniques. Conjugation events were not affected by nutrient concentration alone but were influenced by time and biofilm structure.

Determination of three-dimensional directions of in situ stress from core discing

Rock Stress ◽  
2020 ◽  
pp. 237-243
Author(s):  
K. Matsuki ◽  
N. Kaga ◽  
T. Yokoyama ◽  
N. Tsuda
Keyword(s):  
Three Dimensional ◽  
In Situ Stress ◽  
Core Discing

scholarly journals Design and Validation of a Holographic Particle Counter

Sensors ◽  
2019 ◽  
Vol 19 (22) ◽  
pp. 4899 ◽  
Author(s):  
Georg Brunnhofer ◽  
Alexander Bergmann ◽  
Andreas Klug ◽  
Martin Kraft
Keyword(s):  
Particle Number ◽  
State Of The Art ◽  
Three Dimensional ◽  
Particle Counter ◽  
Detection And Counting ◽  
Sampling Volume ◽  
Processing Techniques ◽  
The Impact

An in-line holographic particle counter concept is presented and validated where multiple micrometer sized particles are detected in a three dimensional sampling volume, all at once. The proposed PIU is capable of detecting holograms of particles which sizes are in the lower μ m- range. The detection and counting principle is based on common image processing techniques using a customized HT with a result directly relating to the particle number concentration in the recorded sampling volume. The proposed counting unit is mounted ontop of a CNM for comparison with a commercial TSI-3775 CPC. The concept does not only allow for a precise in-situ determination of low particle number concentrations but also enables easy upscaling to higher particle densities (e.g., > 30 . 000 # c c m ) through its linear expandability and option of cascading. The impact of coincidence at higher particle densities is shown and two coincidence correction approaches are presented where, at last, its analogy to the coincidence correction methods used in state-of-the-art CPCs is identified.

scholarly journals Determination of three dimensional in-situ stress by double fracturing method.

1992 ◽  
pp. 9-18 ◽  
Author(s):  
Shozo SAKUMA ◽  
Shinji KIKUCHI ◽  
Tetsuya NAKAMURA ◽  
Yoshiaki MIZUTA
Keyword(s):  
Three Dimensional ◽  
In Situ Stress
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