scholarly journals Plant root PET: visualization of photosynthate translocation to roots in rice plant

2021 ◽  
Vol 16 (12) ◽  
pp. C12018
Author(s):  
Y. Miyoshi ◽  
Y. Nagao ◽  
M. Yamaguchi ◽  
N. Suzui ◽  
Y.-G. Yin ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
High Throughput ◽  
Crop Production ◽  
Structural Information ◽  
Plant Root ◽  
Peripheral Region ◽  
Test Plant ◽  
Positron Emission ◽  
Ct System ◽  
Photosynthate Translocation

Abstract Roots are essential to plants for uptake of water and nutrients. For the improvement of crop production, it is necessary to understand the elucidation of the root development and its function under the ground. Especially, photosynthate translocation from plant leaves to roots is an important physiological function that affects the root elongation, adaptation to the soil environment and nutrients uptake. To evaluate the translocation dynamics to roots, positron emission tomography (PET) and 11C tracer have been used. However, the spatial resolution is degraded at roots that develop around the peripheral area of field of view (FOV) due to parallax errors. In this study, to overcome this problem, we developed a small OpenPET prototype applying four-layer depth-of-interaction detectors. We demonstrated the imaging capability of 11C-photosynthate translocation to rice roots that develop throughout the entire PET field. We also tried to obtain structural information of roots by high-throughput X-ray computerized tomography (CT) system using the same test plant. As a result, we succeeded in visualizing the root structure that developed around the peripheral region of FOV and imaging the accumulation of 11C-photosynthate to the roots in those areas without degrading the spatial resolution. From obtained images, we also succeeded in evaluating the translocation dynamics varied by roots. The combined use of the high-throughput CT system and the OpenPET prototype was demonstrated to be appropriate for structural and functional analysis of roots.

scholarly journals Determination of Spatial Resolution of Positron Emission Tomograph of Clear PET-XPAD3/CT System

2017 ◽  
Vol 11 (4) ◽  
pp. 97-101
Author(s):  
H. Olaya Dávila ◽  
S. A. Martínez Ovalle ◽  
H. Pérez ◽  
H. Castro
Keyword(s):  
Spatial Resolution ◽  
Positron Emission Tomograph ◽  
Positron Emission ◽  
Ct System

scholarly journals Imaging Salt Uptake Dynamics in Plants Using PET

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Gerard Ariño-Estrada ◽  
Gregory S. Mitchell ◽  
Prasenjit Saha ◽  
Ahmad Arzani ◽  
Simon R. Cherry ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Sodium Transport ◽  
Crop Production ◽  
Small Animal ◽  
Region Of Interest ◽  
Salt Transport ◽  
Small Animal Pet ◽  
Transport Dynamics ◽  
Positron Emission ◽  
Over Time

AbstractSoil salinity is a global environmental challenge for crop production. Understanding the uptake and transport properties of salt in plants is crucial to evaluate their potential for growth in high salinity soils and as a basis for engineering varieties with increased salt tolerance. Positron emission tomography (PET), traditionally used in medical and animal imaging applications for assessing and quantifying the dynamic bio-distribution of molecular species, has the potential to provide useful measurements of salt transport dynamics in an intact plant. Here we report on the feasibility of studying the dynamic transport of 22Na in millet using PET. Twenty-four green foxtail (Setaria viridis L. Beauv.) plants, 12 of each of two different accessions, were incubated in a growth solution containing 22Na+ ions and imaged at 5 time points over a 2-week period using a high-resolution small animal PET scanner. The reconstructed PET images showed clear evidence of sodium transport throughout the whole plant over time. Quantitative region-of-interest analysis of the PET data confirmed a strong correlation between total 22Na activity in the plants and time. Our results showed consistent salt transport dynamics within plants of the same variety and important differences between the accessions. These differences were corroborated by independent measurement of Na+ content and expression of the NHX transcript, a gene implicated in sodium transport. Our results demonstrate that PET can be used to quantitatively evaluate the transport of sodium in plants over time and, potentially, to discern differing salt-tolerance properties between plant varieties. In this paper, we also address the practical radiation safety aspects of working with 22Na in the context of plant imaging and describe a robust pipeline for handling and incubating plants. We conclude that PET is a promising and practical candidate technology to complement more traditional salt analysis methods and provide insights into systems-level salt transport mechanisms in intact plants.

Evaluation of Spatial Resolution for Heavy Ion CT System Based on the Measurement of Residual Range Distribution With HIMAC

2009 ◽  
Vol 56 (5) ◽  
pp. 2714-2721 ◽  
Author(s):  
H. Muraishi ◽  
K. Nishimura ◽  
S. Abe ◽  
H. Satoh ◽  
S. Hara ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Heavy Ion ◽  
Range Distribution ◽  
Residual Range ◽  
Ct System

scholarly journals Mito Hacker: a set of tools to enable high-throughput analysis of mitochondrial network morphology

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ali Rohani ◽  
Jennifer A. Kashatus ◽  
Dane T. Sessions ◽  
Salma Sharmin ◽  
David F. Kashatus
Keyword(s):  
Single Cell ◽  
High Throughput ◽  
Data Science ◽  
Structural Information ◽  
Morphological Changes ◽  
Mitochondrial Morphology ◽  
Single Cell Level ◽  
Mitochondrial Network ◽  
Cell Level ◽  
Wide Range

Abstract Mitochondria are highly dynamic organelles that can exhibit a wide range of morphologies. Mitochondrial morphology can differ significantly across cell types, reflecting different physiological needs, but can also change rapidly in response to stress or the activation of signaling pathways. Understanding both the cause and consequences of these morphological changes is critical to fully understanding how mitochondrial function contributes to both normal and pathological physiology. However, while robust and quantitative analysis of mitochondrial morphology has become increasingly accessible, there is a need for new tools to generate and analyze large data sets of mitochondrial images in high throughput. The generation of such datasets is critical to fully benefit from rapidly evolving methods in data science, such as neural networks, that have shown tremendous value in extracting novel biological insights and generating new hypotheses. Here we describe a set of three computational tools, Cell Catcher, Mito Catcher and MiA, that we have developed to extract extensive mitochondrial network data on a single-cell level from multi-cell fluorescence images. Cell Catcher automatically separates and isolates individual cells from multi-cell images; Mito Catcher uses the statistical distribution of pixel intensities across the mitochondrial network to detect and remove background noise from the cell and segment the mitochondrial network; MiA uses the binarized mitochondrial network to perform more than 100 mitochondria-level and cell-level morphometric measurements. To validate the utility of this set of tools, we generated a database of morphological features for 630 individual cells that encode 0, 1 or 2 alleles of the mitochondrial fission GTPase Drp1 and demonstrate that these mitochondrial data could be used to predict Drp1 genotype with 87% accuracy. Together, this suite of tools enables the high-throughput and automated collection of detailed and quantitative mitochondrial structural information at a single-cell level. Furthermore, the data generated with these tools, when combined with advanced data science approaches, can be used to generate novel biological insights.

scholarly journals SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes

2013 ◽  
Vol 21 (1) ◽  
pp. 203-208 ◽  
Author(s):  
Yannick G. Spill ◽  
Seung Joong Kim ◽  
Dina Schneidman-Duhovny ◽  
Daniel Russel ◽  
Ben Webb ◽  
...  
Keyword(s):  
Statistical Method ◽  
High Throughput ◽  
Gaussian Processes ◽  
Small Angle ◽  
Structural Information ◽  
Linear Interpolation ◽  
High Quality ◽  
X Ray ◽  
X Ray Scattering ◽  
Specific Order

Small-angle X-ray scattering (SAXS) is an experimental technique that allows structural information on biomolecules in solution to be gathered. High-quality SAXS profiles have typically been obtained by manual merging of scattering profiles from different concentrations and exposure times. This procedure is very subjective and results vary from user to user. Up to now, no robust automatic procedure has been published to perform this step, preventing the application of SAXS to high-throughput projects. Here,SAXS Merge, a fully automated statistical method for merging SAXS profiles using Gaussian processes, is presented. This method requires only the buffer-subtracted SAXS profiles in a specific order. At the heart of its formulation is non-linear interpolation using Gaussian processes, which provides a statement of the problem that accounts for correlation in the data.

scholarly journals NEMA NU4-2008 Performance Evaluation of Albira: A Two-Ring Small-Animal PET System Using Continuous LYSO Crystals

2016 ◽  
Vol 3 (1) ◽  
pp. 12-26 ◽  
Author(s):  
Malgorzata Z. Pajak ◽  
David Volgyes ◽  
Sally L. Pimlott ◽  
Carlos C. Salvador ◽  
Antonio S. Asensi ◽  
...  
Keyword(s):  
Spatial Resolution ◽  
Small Animal Imaging ◽  
Small Animal ◽  
Axial Direction ◽  
Small Animal Pet ◽  
Performance Review ◽  
Good Spatial Resolution ◽  
Positron Emission ◽  
Animal Images ◽  
Pet System

Goals:This paper presents the performance review based on a dual-ring Positron Emission Tomography (PET) scanner being a part of Bruker Albira: a multi-modal small-animal imaging platform. Each ring of Albira PET contains eight detectors arranged as octagon, and each detector is built using a single continuous lutetium-yttrium oxyorthosilicate crystal and multi-anode photo multiplier tube. In two-ring configuration, the scanner covers 94.4 mm in axial- and 80´80 mm in trans-axial direction, which is sufficient to acquire images of small animals (e.g.mice) without the need of moving the animal bed during the scan.Methods:All measurements and majority of data processing were performed according to the NEMA NU4-2008 standard with one exception. Due to the scanner geometry, the spatial resolution test was reconstructed using iterative algorithm instead of the analytical one. The main performance characteristics were compared with those of the other PET sub-systems of tri-modal small-animal scanners.Results:The measured spatial resolution at the centre of the axial field of view in radial, tangential and axial directions was 1.72, 1.70 and 2.45 mm, respectively. The scatter fraction for the mouse-like phantom was 9.8% and for the rat-like phantom, 21.8%. The maximum absolute sensitivity was 5.30%. Finally, the recovery co-efficients for 5, 4, 3, 2, 1 mm diameter rods in image quality phantom were: 0.90, 0.77, 0.66, 0.30 and 0.05, respectively.Conclusion:The Bruker Albira is a versatile small-animal multi-modal device that can be used for variety of studies. Overall the PET sub-system provides a good spatial resolution coupled with better-than average sensitivity and the ability to produce good quality animal images when administering low activities.

scholarly journals Influence of Spatial Resolution on Remote Sensing-Based Irrigation Performance Assessment Using WaPOR Data

2020 ◽  
Vol 12 (18) ◽  
pp. 2949
Author(s):  
Megan Blatchford ◽  
Chris M. Mannaerts ◽  
Yijian Zeng ◽  
Hamideh Nouri ◽  
Poolad Karimi
Keyword(s):  
Remote Sensing ◽  
Open Access ◽  
Performance Assessment ◽  
Spatial Resolution ◽  
Performance Indicators ◽  
Crop Production ◽  
Water Productivity ◽  
Temporal Trends ◽  
Irrigation Performance ◽  
Crop Water

This paper analyses the effect of the spatial assessment scale on irrigation performance indicators in small and medium-scale agriculture. Three performance indicators—adequacy (i.e., sufficiency of water use to meet the crop water requirement), equity (i.e., fairness of irrigation distribution), and productivity (i.e., unit of physical crop production/yield per unit water consumption)—are evaluated in five irrigation schemes for three spatial resolutions—250 m, 100 m, and 30 m. Each scheme has varying plot sizes and distributions, with average plot sizes ranging from 0.2 ha to 13 ha. The datasets are derived from the United Nations Food and Agricultural Organization (FAO) water productivity through open access of remotely sensed–derived data (the Water Productivity Open Access Portal—WaPOR) database. Irrigation indicators performed differently in different aspects; for adequacy, all three resolutions show similar spatial trends for relative evapotranspiration (ET) across levels for all years. However, the estimation of relative ET is often higher at higher resolution. In terms of equity, all resolutions show similar inter-annual trends in the coefficient of variation (CV); higher resolutions usually have a higher CV of the annual evapotranspiration and interception (ETIa) while capturing more spatial variability. For productivity, higher resolutions show lower crop water productivity (CWP) due to higher aboveground biomass productivity (AGBP) estimations in lower resolutions; they always have a higher CV of CWP. We find all resolutions of 250 m, 100 m, and 30 m suitable for inter-annual and inter-scheme assessments regardless of plot size. While each resolution shows consistent temporal trends, the magnitude of the trend in both space and time is smoothed by the 100 m and 250 m resolution datasets. This frequently results in substantial differences in the irrigation performance assessment criteria for inter-plot comparisons; therefore, 250 m and 100 m are not recommended for inter-plot comparison for all plot sizes, particularly small plots (<2 ha). Our findings highlight the importance of selecting the spatial resolution appropriate to scheme characteristics when undertaking irrigation performance assessment using remote sensing.

scholarly journals Technological advancements and their importance for nematode identification

SOIL ◽  
2016 ◽  
Vol 2 (2) ◽  
pp. 257-270 ◽  
Author(s):  
Mohammed Ahmed ◽  
Melanie Sapp ◽  
Thomas Prior ◽  
Gerrit Karssen ◽  
Matthew Alan Back
Keyword(s):  
High Throughput ◽  
Crop Production ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Biological Indicators ◽  
Rapid Identification ◽  
Community Studies ◽  
Terrestrial Environments ◽  
Traditional Taxonomy ◽  
Sequencing Platforms

Abstract. Nematodes represent a species-rich and morphologically diverse group of metazoans known to inhabit both aquatic and terrestrial environments. Their role as biological indicators and as key players in nutrient cycling has been well documented. Some plant-parasitic species are also known to cause significant losses to crop production. In spite of this, there still exists a huge gap in our knowledge of their diversity due to the enormity of time and expertise often involved in characterising species using phenotypic features. Molecular methodology provides useful means of complementing the limited number of reliable diagnostic characters available for morphology-based identification. We discuss herein some of the limitations of traditional taxonomy and how molecular methodologies, especially the use of high-throughput sequencing, have assisted in carrying out large-scale nematode community studies and characterisation of phytonematodes through rapid identification of multiple taxa. We also provide brief descriptions of some the current and almost-outdated high-throughput sequencing platforms and their applications in both plant nematology and soil ecology.

scholarly journals Bacterial Community Members Increase Bacillus subtilis Maintenance on the Roots of Arabidopsis thaliana

2020 ◽  
Vol 4 (4) ◽  
pp. 303-313
Author(s):  
Noam Eckshtain-Levi ◽  
Susanna Leigh Harris ◽  
Reizo Quilat Roscios ◽  
Elizabeth Anne Shank
Keyword(s):  
Arabidopsis Thaliana ◽  
Bacillus Subtilis ◽  
Crop Production ◽  
Crop Yields ◽  
Plant Root ◽  
Plant Roots ◽  
Plant Growth Promoting Bacteria ◽  
Bacterial Strains ◽  
Root Microbiome ◽  
Over Time

Plant-growth-promoting bacteria (PGPB) are used to improve plant health and promote crop production. However, because some PGPB (including Bacillus subtilis) do not maintain substantial colonization on plant roots over time, it is unclear how effective PGPB are throughout the plant growing cycle. A better understanding of the dynamics of plant root community assembly is needed to develop and harness the potential of PGPB. Although B. subtilis is often a member of the root microbiome, it does not efficiently monoassociate with plant roots. We hypothesized that B. subtilis may require other primary colonizers to efficiently associate with plant roots. We utilized a previously designed hydroponic system to add bacteria to Arabidopsis thaliana roots and monitor their attachment over time. We inoculated seedlings with B. subtilis and individual bacterial isolates from the native A. thaliana root microbiome either alone or together. We then measured how the coinoculum affected the ability of B. subtilis to colonize and maintain on A. thaliana roots. We screened 96 fully genome-sequenced strains and identified five bacterial strains that were able to significantly improve the maintenance of B. subtilis. Three of these rhizobacteria also increased the maintenance of two strains of B. amyloliquefaciens commonly used in commercially available bioadditives. These results not only illustrate the utility of this model system to address questions about plant–microbe interactions and how other bacteria affect the ability of PGPB to maintain their relationships with plant roots but also may help inform future agricultural interventions to increase crop yields. [Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Sign in / Sign up

Export Citation Format

Share Document