Correlated displacement-T2 MRI by means of a Pulsed Field Gradient-Multi Spin Echo Method

An integrated magnetic resonance plant imager for mobile use in greenhouse and field

In this contribution we demonstrate a mobile, integrated MR plant imager that can be handled by one single person and used in the field. Key to the construction of it was a small and lightweight gradient amplifier, specifically tailored to our combination of magnet, gradient coils and the requirements of the desired pulse sequences. To allow imaging of branches and stems, an open C-shaped permanent magnet was used. In the design of the magnet, pole gap width, low weight and robustness were prioritized over homogeneity and field strength. To overcome the adverse effects of short T₂*, multi-spin echo imaging was employed, using short echo times and high spectral widths. To achieve microscopic resolution under these constraints requires fast switching field gradients, driven by strong and fast gradient amplifiers. While small-scale spectrometers and RF amplifiers are readily available, appropriate small-scale gradient amplifiers or designs thereof currently are not. We thus constructed a small, 3-channel gradient amplifier on the basis of a conventional current-controlled AB amplifier design, using cheap and well-known parts. The finished device weighs 5 kg and is capable of delivering 40 A gradient pulses of >6 ms in duration. With all components built onto an aluminum hand trolley, the imaging setup weighs 45 kg and is small enough to fit into a car. We demonstrate the mobility and utility of the device imaging quantitative water content and T₂, first of an apple tree in an orchard; second, of a beech tree during spring leaf flushing in a greenhouse. The latter experiment ran for a continuous period of 62 days, acquiring more than 6000 images.

A Technological Understanding of Biofilm Detection Techniques: A Review

Biofouling is a persistent problem in almost any water-based application in several industries. To eradicate biofouling-related problems in bioreactors, the detection of biofilms is necessary. The current literature does not provide clear supportive information on selecting biofilm detection techniques that can be applied to detect biofouling within bioreactors. Therefore, this research aims to review all available biofilm detection techniques and analyze their characteristic properties to provide a comparative assessment that researchers can use to find a suitable biofilm detection technique to investigate their biofilms. In addition, it discusses the confluence of common bioreactor fabrication materials in biofilm formation.

A small-scale MRI scanner and complementary imaging method to visualize and quantify xylem embolism formation

Magnetic resonance imaging (MRI) is a useful tool to image xylem embolism formation in plants. MRI scanners configured to accept intact plants are rare and expensive. Here, we investigate if affordable small-scale, custom-built low-field MRI scanners would suffice for the purpose. A small-scale, C-shaped permanent magnet was paired with open, plane parallel imaging gradients. The setup was small enough to fit between leaves or branches and offered open access for plant stems of arbitrary length. To counter the two main drawbacks of the system, low signal to noise and reduced magnetic field homogeneity, a multi-spin echo (MSE) pulse sequence was implemented, allowing efficient signal acquisition and quantitative imaging of water content and T₂ signal relaxation. The system was tested visualizing embolism formation in Fagus sylvatica during bench dehydration. High-quality images of water content and T₂ were readily obtained, which could be utilized to detect the cavitation of vessels smaller than could be spatially resolved. A multiplication of both map types yielded images in which filled xylem appeared with even greater contrast. T₂ imaging with small-scale MRI devices allows straightforward visualization of the spatial and temporal dynamics of embolism formation and the derivation of vulnerability curves.

In vivo pressure gradient heterogeneity increases flow contribution of small diameter vessels in grapevine

Leaves lose approximately 400 H₂O molecules for every 1 CO₂ gained during photosynthesis. Most long-distance water transport in plants, or xylem sap flow, serves to replace this water to prevent desiccation. Theory predicts that the largest vessels contribute disproportionately to overall sap flow because flow in pipe-like systems scales with the fourth power of radius. Here, we confront these theoretical flow predictions for a vessel network reconstructed from X-ray μCT imagery with in vivo flow MRI observations from the same sample of a first-year grapevine stem. Theoretical flow rate predictions based on vessel diameters are not supported. The heterogeneity of the vessel network gives rise to transverse pressure gradients that redirect flow from wide to narrow vessels, reducing the contribution of wide vessels to sap flow by 15% of the total. Our results call for an update of the current working model of the xylem to account for its heterogeneity.

Plants require long-distance water transport to avoid desiccation. Here, via μCT and MRI of grapevine stem, Bouda et al. show evidence of pressure gradient heterogeneity and flow redirection from wide to narrow vessels that suggests narrow vessels contribute more to xylem sap flow than previously appreciated.

Acquisition of spatially-resolved displacement propagators using compressed sensing APGSTE-RARE MRI

A method is presented for accelerating the acquisition of spatially-resolved displacement propagators via under-sampling of an Alternating Pulsed Gradient Stimulated Echo - Rapid Acquisition with Relaxation Enhancement (APGSTE-RARE) data acquisition with compressed sensing image reconstruction. The method was demonstrated with respect to the acquisition of 2D spatially-resolved displacement propagators of water flowing through a packed bed of hollow cylinders. The q,k-space was under-sampled according to variable-density pseudo-random sampling patterns. The quality of compressed sensing reconstructions of spatially-resolved propagators at a range of sampling fractions was assessed using the peak signal-to-noise ratio (PSNR) as a quality metric. Propagators of good quality (PSNR 33.2 dB) were reconstructed from only 6.25% of all data points in q,k-space, resulting in a reduction in the data acquisition time from 4 h to 14 min. The spatially-resolved propagators were reconstructed using both the total variation and nuclear norm sparsifying transforms; use of total variation resulted in a slightly higher quality of the reconstructed image in most cases. To illustrate the power of this method to characterise heterogeneous flow in porous media, the method is applied to the characterisation of flow in a vuggy carbonate rock.

Heat girdling does not affect xylem integrity: an in vivo magnetic resonance imaging study in the tomato peduncle

Heat girdling is a method to estimate the relative contribution of phloem vs xylem water flow to fruit growth. The heat girdling process is assumed to destroy all living tissues, including the phloem, without affecting xylem conductivity. However, to date, the assumption that xylem is not affected by heat girdling remains unproven. In this study, we used in vivo magnetic resonance imaging (MRI) velocimetry to test if heat girdling can cause xylem vessels to embolize or affect xylem water flow characteristics in the peduncle of tomato (Solanum lycopersicum cv Dirk). Anatomical and MRI data indicated that, at the site of girdling, all living tissues were disrupted, but that the functionality of the xylem remained unchanged. MRI velocimetry showed that the volume flow through the secondary xylem was not impeded by heat girdling in either the short or the long term (up to 91 h after girdling). This study provides support for the hypothesis that in the tomato peduncle the integrity and functionality of the xylem remain unaffected by heat girdling. It therefore confirms the validity of the heat girdling technique as a means to estimate relative contributions of xylem and phloem water flow to fruit growth.

Visualization of water transport into soybean nodules by Tof-SIMS cryo system

This paper examined the route of water supply into soybean nodules through the new visualization technique of time of flight secondary ion mass spectrometry (Tof-SIMS) cryo system, and obtained circumstantial evidence for the water inflow route. The maximum resolution of the Tof-SIMS imaging used by this study was 1.8 μm (defined as the three pixel step length), which allowed us to detect water movement at the cellular level. Deuterium-labeled water was supplied to soybean plants for 4h and the presence of deuterium in soybean nodules was analyzed by the Tof-SIMS cryo system. Deuterium ions were found only in the endodermis tissue surrounding the central cylinder in soybean nodules. Neither xylem vessels nor phloem complex itself did not indicate any deuterium accumulation. Deuterium-ion counts in the endodermis tissue were not changed by girdling treatment, which restricted water movement through the phloem complex. The results strongly indicated that nodule tissues did not receive water directly from the phloem complex, but received water through root cortex apoplastic pathway from the root axis.

Low-field nuclear magnetic resonance for the in vivo study of water content in trees

Nuclear magnetic resonance (NMR) and magnetic resonance imaging have long been used to study water content in plants. Approaches have been primarily based on systems using large magnetic fields (~1 T) to obtain NMR signals with good signal-to-noise. This is because the NMR signal scales approximately with the magnetic field strength squared. However, there are also limits to this approach in terms of realistic physiological configuration or those imposed by the size and cost of the magnet. Here we have taken a different approach--keeping the magnetic field low to produce a very light and inexpensive system, suitable for bulk water measurements on trees less than 5 cm in diameter, which could easily be duplicated to measure on many trees or from multiple parts of the same tree. Using this system we have shown sensitivity to water content in trees and their cuttings and observed a diurnal signal variation in tree water content in a greenhouse. We also demonstrate that, with calibration and modeling of the thermal polarization, the system is reliable under significant temperature variation.

T₂ distribution mapping profiles with phase-encode MRI

Two 1-D phase-encode sequences for T₂ mapping, namely CPMG-prepared SPRITE and spin-echo SPI, are presented and compared in terms of image quality, accuracy of T₂ measurements and the measurement time. The sequences implement two different approaches to acquiring T₂-weighted images: in the CPMG-prepared SPRITE, the T₂-weighting of magnetization precedes the spatial encoding, while in the spin-echo SPI, the T₂-weighting follows the spatial encoding. The sequences are intended primarily for T₂ mapping of fluids in porous solids, where using frequency encode techniques may be problematic either due to local gradient distortions or too short T₂. Their possible applications include monitoring fluid-flow processes in rocks, cement paste hydration, curing of rubber, filtering paramagnetic impurities and other processes accomplished by changing site-specific T₂.

Visualization of lateral water transport pathways in soybean by a time of flight-secondary ion mass spectrometry cryo-system

Water movement between cells in a plant body is the basic phenomenon of plant solute transport; however, it has not been well documented due to limitations in observational techniques. This paper reports a visualization technique to observe water movement among plant cells in different tissues using a time of flight-secondary ion mass spectrometry (Tof-SIMS) cryo-system. The specific purpose of this study is to examine the route of water supply from xylem to stem tissues. The maximum resolution of Tof-SIMS imaging was 1.8 μm (defined as the three pixel step length), which allowed detection of water movement at the cellular level. Deuterium-labelled water was found in xylem vessels in the stem 2.5 min after the uptake of labelled water by soybean plants. The water moved from the xylem to the phloem, cambium, and cortex tissues within 30-60 min after water absorption. Deuterium ion counts in the phloem complex were slightly higher than those in the cortex and cambium tissue seen in enlarged images of stem cell tissue during high transpiration. However, deuterium ion counts in the phloem were lower than those in the cambium at night with no evaporative demand. These results indicate that the stem tissues do not receive water directly from the xylem, but rather from the phloem, during high evaporative demand. In contrast, xylem water would be directly supplied to the growing sink during the night without evaporative demand.

A portable Halbach magnet that can be opened and closed without force: the NMR-CUFF

Portable equipment for nuclear magnetic resonance (NMR) is becoming increasingly attractive for use in a variety of applications. One of the main scientific challenges in making NMR portable is the design of light-weight magnets that possess a strong and homogeneous field. Existing NMR magnets can provide such magnetic fields, but only for small samples or in small regions, or are rather heavy. Here we show a simple yet elegant concept for a Halbach-type permanent magnet ring, which can be opened and closed with minimal mechanical force. An analytical solution for an ideal Halbach magnet shows that the magnetic forces cancel if the structure is opened at an angle of 35.3° relative to its poles. A first prototype weighed only 3.1 kg, and provided a flux density of 0.57 T with a homogeneity better than 200 ppm over a spherical volume of 5mm in diameter without shimming. The force needed to close it was found to be about 20 N. As a demonstration, intact plants were imaged and water (xylem) flow measured. Magnets of this type (NMR-CUFF = Cut-open, Uniform, Force Free) are ideal for portable use and are eminently suited to investigate small or slender objects that are part of a larger or immobile whole, such as branches on a tree, growing fruit on a plant, or non-metallic tubing in industrial installations. This new concept in permanent-magnet design enables the construction of openable, yet strong and homogeneous magnets, which aside from use in NMR or MRI could also be of interest for applications in accelerators, motors, or magnetic bearings.

Flow characteristics and exchange in complex biological systems as observed by pulsed-field-gradient magnetic-resonance imaging

Water flow through model porous media was studied in the presence of surface relaxation, internal magnetic field inhomogeneities and exchange with stagnant water pools with different relaxation behavior, demonstrating how the apparent flow parameters average velocity, volume flow and flow conducting area in these situations depend on the observation time. To investigate the water exchange process a two component biological model system consisting of water flowing through a biofilm reactor (column packed with methanogenic granular sludge beads) was used, before and after a heat treatment to introduce exchange. We show that correction of the stagnant fluid signal amplitude for relaxation at increasing observation time using the observed relaxation times reveals exchange between the two fractions in the system. Further it is demonstrated how this exchange can be quantified.

MRI of intact plants

Nuclear magnetic resonance imaging (MRI) is a non-destructive and non-invasive technique that can be used to acquire two- or even three-dimensional images of intact plants. The information within the images can be manipulated and used to study the dynamics of plant water relations and water transport in the stem, e.g., as a function of environmental (stress) conditions. Non-spatially resolved portable NMR is becoming available to study leaf water content and distribution of water in different (sub-cellular) compartments. These parameters directly relate to stomatal water conductance, CO(2) uptake, and photosynthesis. MRI applied on plants is not a straight forward extension of the methods discussed for (bio)medical MRI. This educational review explains the basic physical principles of plant MRI, with a focus on the spatial resolution, factors that determine the spatial resolution, and its unique information for applications in plant water relations that directly relate to plant photosynthetic activity.

Most water in the tomato truss is imported through the xylem, not the phloem: a nuclear magnetic resonance flow imaging study

In this study, we demonstrate nuclear magnetic resonance flow imaging of xylem and phloem transport toward a developing tomato (Solanum lycopersicum) truss. During an 8-week period of growth, we measured phloem and xylem fluxes in the truss stalk, aiming to distinguish the contributions of the two transport tissues and draw up a balance between influx and efflux. It is commonly estimated that about 90% of the water reaches the fruit by the phloem and the remaining 10% by the xylem. The xylem is thought to become dysfunctional at an early stage of fruit development. However, our results do not corroborate these findings. On the contrary, we found that xylem transport into the truss remained functional throughout the 8 weeks of growth. During that time, at least 75% of the net influx into the fruit occurred through the external xylem and about 25% via the perimedullary region, which contains both phloem and xylem. About one-half of the net influx was lost due to evaporation. Halfway through truss development, a xylem backflow appeared. As the truss matured, the percentage of xylem water that circulated into the truss and out again increased in comparison with the net uptake, but no net loss of water from the truss was observed. The circulation of xylem water continued even after the fruits and pedicels were removed. This indicates that neither of them was involved in generating or conducting the circulation of sap. Only when the main axis of the peduncle was cut back did the circulation stop.

Determining NMR flow propagator moments in porous rocks without the influence of relaxation

Flow propagators, used for the study of advective motion of brine solution in porous carbonate and sandstone rocks, have been obtained without the influence of Nuclear Magnetic Resonance (NMR) relaxation times, T1 and T2. These spin relaxation mechanisms normally result in a loss of signal that varies depending on the displacement zeta of the flowing spins, thereby preventing the acquisition of quantitative propagator data. The full relaxation behaviour of the system under flow needs to be characterised to enable the implementation of a true quantitative measurement. Two-dimensional NMR correlations of zeta-T2 and T1-T2 are used in combination to provide the flow propagators without relaxation weighting. T1-zeta correlations cannot be used due to the loss of T1 information during the displacement observation time Delta. Here the moments of the propagators are extracted by statistical analysis of the full propagator shape. The measured displacements (first moments) are seen to correlate with the expected mean displacements for long observation times Delta. The higher order moments of the propagators determined by this method indicate those obtained previously using a correction were overestimated.