Bioenergy sorghum stem growth regulation: intercalary meristem localization, development, and gene regulatory network analysis.

Bioenergy sorghum is a highly productive drought tolerant C4 grass that accumulates 80% of its harvestable biomass in approximately 4 m length stems. Stem internode growth is regulated by development, shading, and hormones that modulate cell proliferation in intercalary meristems (IMs). In this study, sorghum stem IMs were localized above the pulvinus at the base of elongating internodes using magnetic resonance imaging, microscopy, and transcriptome analysis. A change in cell morphology/organization occurred at the junction between the pulvinus and internode where LATERAL ORGAN BOUNDARIES (SbLOB), a boundary layer gene, was expressed. Inactivation of an AGCVIII kinase in DDYM (dw2) resulted in decreased SbLOB expression, disrupted IM localization, and reduced internode cell proliferation. Transcriptome analysis identified approximately 1000 genes involved in cell proliferation, hormone signaling, and other functions selectively upregulated in the IM compared with a non-meristematic stem tissue. This cohort of genes is expressed in apical dome stem tissues before localization of the IM at the base of elongating internodes. Gene regulatory network analysis identified connections between genes involved in hormone signaling and cell proliferation. The results indicate that gibberellic acid induces accumulation of growth regulatory factors (GRFs) known to interact with ANGUSTIFOLIA (SbAN3), a master regulator of cell proliferation. GRF:AN3 was predicted to induce SbARF3/ETT expression and regulate SbAN3 expression in an auxin-dependent manner. GRFs and ARFs regulate genes involved in cytokinin and brassinosteroid signaling and cell proliferation. The results provide a molecular framework for understanding how hormone signaling regulates the expression of genes involved in cell proliferation in the stem IM.

Low-field magnetic resonance imaging of roots in intact clayey and silty soils.

The development of a robust method to non-invasively visualize root morphology in natural soils has been hampered by the opaque, physical, and structural properties of soils. In this work we describe a novel technology, low field magnetic resonance imaging (LF-MRI), for imaging energy sorghum (Sorghum bicolor (L.) Moench) root morphology and architecture in intact soils. The use of magnetic fields much weaker than those used with traditional MRI experiments reduces the distortion due to magnetic material naturally present in agricultural soils. A laboratory based LF-MRI operating at 47 mT magnetic field strength was evaluated using two sets of soil cores: 1) soil/root cores of Weswood silt loam (Udifluventic Haplustept) and a Belk clay (Entic Hapluderts) from a conventionally tilled field, and 2) soil/root cores from rhizotrons filled with either a Houston Black (Udic Haplusterts) clay or a sandy loam purchased from a turf company. The maximum soil water nuclear magnetic resonance (NMR) relaxation time T2 (4 ms) and the typical root water relaxation time T2 (100 ms) are far enough apart to provide a unique contrast mechanism such that the soil water signal has decayed to the point of no longer being detectable during the data collection time period. 2-D MRI projection images were produced of roots with a diameter range of 1.5-2.0 mm using an image acquisition time of 15 min with a pixel resolution of 1.74 mm in four soil types. Additionally, we demonstrate the use of a data-driven machine learning reconstruction approach, Automated Transform by Manifold Approximation (AUTOMAP) to reconstruct raw data and improve the quality of the final images. The application of AUTOMAP showed a SNR (Signal to Noise Ratio) improvement of two fold on average. The use of low field MRI presented here demonstrates the possibility of applying low field MRI through intact soils to root phenotyping and agronomy to aid in understanding of root morphology and the spatial arrangement of roots in situ.

What makes a good pediatric transplant lung: Insights from in vivo lung morphometry with hyperpolarized 3 He magnetic resonance imaging.

Obtaining information on transplanted lung microstructure is an important part of the current care for monitoring transplant recipients. However, until now this information was only available from invasive lung biopsy. The objective of this study was to evaluate the use of an innovative non-invasive technique, in vivo lung morphometry with hyperpolarized ³He MRI-to characterize lung microstructure in the pediatric lung transplant population. This technique yields quantitative measurements of acinar airways' (alveolar ducts and sacs) parameters, such as acinar airway radii and alveolar depth. Six pediatric lung transplant recipients with cystic fibrosis underwent in vivo lung morphometry MRI, pulmonary function testing, and quantitative CT. We found a strong correlation between lung lifespan and alveolar depth-patients with more shallow alveoli were likely to have a negative outcome sooner than those with larger alveolar depth. Combining morphometric results with CT, we also determined mean alveolar wall thickness and found substantial increases in this parameter in some patients that negatively correlated with DLCO. In vivo lung morphometry uniquely provides previously unavailable information on lung microstructure that may be predictive of a negative outcome and has a potential to aid in lung selection for transplantation.

A Molecular Rotor Possessing an H-M-H "Spoke" on a P-M-P "Axle": A Platinum(II) trans-Dihydride Spins Rapidly Even at 75 K.

A new class of low-barrier molecular rotors, metal trans-dihydrides, is suggested here. To test whether rapid rotation can be achieved, the known complex trans-H2Pt(P(t)Bu3)2 was experimentally studied by (2)H and (195)Pt solid-state NMR spectroscopy (powder pattern changes with temperature) and computationally modeled as a (t)Bu3P-Pt-P(t)Bu3 stator with a spinning H-Pt-H rotator. Whereas the related chloro-hydride complex, trans-H(Cl)Pt(P(t)Bu3)2, does not show rotational behavior at room temperature, the dihydride trans-H2Pt(P(t)Bu3)2 rotates fast on the NMR time scale, even at low temperatures down to at least 75 K. The highest barrier to rotation is estimated to be ∼3 kcal mol(-1), for the roughly 3 Šlong rotator in trans-H2Pt(P(t)Bu3)2.

Determining pH at elevated pressure and temperature using in situ ¹³C NMR.

We have developed an approach for determining pH at elevated pressures and temperatures by using (13)C NMR measurements of inorganic carbon species together with a geochemical equilibrium model. The approach can determine in situ pH with precision better than 0.1 pH units at pressures, temperatures, and ionic strengths typical of geologic carbon sequestration systems. A custom-built high pressure NMR probe was used to collect (13)C NMR spectra of (13)C-labeled CO2 reactions with NaOH solutions and Mg(OH)2 suspensions at pressures up to 107 bar and temperatures of 80 °C. The quantitative nature of NMR spectroscopy allows the concentration ratio [CO2]/[HCO3(-)] to be experimentally determined. This ratio is then used with equilibrium constants calculated for the specific pressure and temperature conditions and appropriate activity coefficients for the solutes to calculate the in situ pH. The experimentally determined [CO2]/[HCO3(-)] ratios agree well with the predicted values for experiments performed with three different concentrations of NaOH and equilibration with multiple pressures of CO2. The approach was then applied to experiments with Mg(OH)2 slurries in which the change in pH could track the dissolution of CO2 into solution, rapid initial Mg(OH)2 dissolution, and onset of magnesium carbonate precipitation.

Characterization of a Mixture of CO2 Adsorption Products in Hyperbranched Aminosilica Adsorbents by (13)C Solid-State NMR.

Hyperbranched amine polymers (HAS) grown from the mesoporous silica SBA-15 (hereafter "SBA-15-HAS") exhibit large capacities for CO2 adsorption. We have used static in situ and magic-angle spinning (MAS) ex situ (13)C nuclear magnetic resonance (NMR) to examine the adsorption of CO2 by SBA-15-HAS. (13)C NMR distinguishes the signal of gas-phase (13)CO2 from that of the chemisorbed species. HAS polymers possess primary, secondary, and tertiary amines, leading to multiple chemisorption reaction outcomes, including carbamate (RnNCOO(-)), carbamic acid (RnNCOOH), and bicarbonate (HCO3(-)) moieties. Carbamates and bicarbonate fall within a small (13)C chemical shift range (162-166 ppm), and a mixture was observed including carbamic acid and carbamate, the former disappearing upon evacuation of the sample. By examining the (13)C-(14)N dipolar coupling through low-field (B0 = 3 T) (13)C{(1)H} cross-polarization MAS NMR, carbamate is confirmed through splitting of the (13)C resonance. A third species that is either bicarbonate or a second carbamate is evident from bimodal T2 decay times of the ∼163 ppm peak, indicating the presence of two species comprising that single resonance. The mixture of products suggests that (1) the presence of amines and water leads to bicarbonate being present and/or (2) the multiple types of amine sites in HAS permit formation of chemically distinct carbamates.

Quantitative identification of metastable magnesium carbonate minerals by solid-state 13C NMR spectroscopy.

In the conversion of CO2 to mineral carbonates for the permanent geosequestration of CO2, there are multiple magnesium carbonate phases that are potential reaction products. Solid-state (13)C NMR is demonstrated as an effective tool for distinguishing magnesium carbonate phases and quantitatively characterizing magnesium carbonate mixtures. Several of these mineral phases include magnesite, hydromagnesite, dypingite, and nesquehonite, which differ in composition by the number of waters of hydration or the number of crystallographic hydroxyl groups. These carbonates often form in mixtures with nearly overlapping (13)C NMR resonances which makes their identification and analysis difficult. In this study, these phases have been investigated with solid-state (13)C NMR spectroscopy, including both static and magic-angle spinning (MAS) experiments. Static spectra yield chemical shift anisotropy (CSA) lineshapes that are indicative of the site-symmetry variations of the carbon environments. MAS spectra yield isotropic chemical shifts for each crystallographically inequivalent carbon and spin-lattice relaxation times, T1, yield characteristic information that assist in species discrimination. These detailed parameters, and the combination of static and MAS analyses, can aid investigations of mixed carbonates by (13)C NMR.

Development and performance of a 129-GHz dynamic nuclear polarizer in an ultra-wide bore superconducting magnet.

OBJECTIVE: We sought to build a dynamic nuclear polarization system for operation at 4.6 T (129 GHz) and evaluate its efficiency in terms of (13)C polarization levels using free radicals that span a range of ESR linewidths. MATERIALS AND METHODS: A liquid helium cryostat was placed in a 4.6 T superconducting magnet with a 150-mm warm bore diameter. A 129-GHz microwave source was used to irradiate (13)C enriched samples. Temperatures close to 1 K were achieved using a vacuum pump with a 453-m(3)/h roots blower. A hyperpolarized (13)C nuclear magnetic resonance (NMR) signal was detected using a saddle coil and a Varian VNMRS console operating at 49.208 MHz. Samples doped with free radicals BDPA (1,3-bisdiphenylene-2-phenylallyl), trityl OX063 (tris{8-carboxyl-2,2,6,6-benzo(1,2-d:4,5-d)-bis(1,3)dithiole-4-yl}methyl sodium salt), galvinoxyl ((2,6-di-tert-butyl-α-(3,5-di-tert-butyl-4-oxo-2,5-cyclohexadien-1-ylidene)-p-tolyloxy), 2,2-diphenylpicrylhydrazyl (DPPH) and 4-oxo-TEMPO (4-Oxo-2,2,6,6-tetramethyl-1-piperidinyloxy) were assayed. Microwave dynamic nuclear polarization (DNP) spectra and solid-state (13)C polarization levels for these samples were determined. RESULTS: (13)C polarization levels close to 50 % were achieved for [1-(13)C]pyruvic acid at 1.15 K using the narrow electron spin resonance (ESR) linewidth free radicals trityl OX063 and BDPA, while 10-20 % (13)C polarizations were achieved using galvinoxyl, DPPH and 4-oxo-TEMPO. CONCLUSION: At this field strength free radicals with smaller ESR linewidths are still superior for DNP of (13)C as opposed to those with linewidths that exceed that of the (1)H Larmor frequency.

Probing lung microstructure with hyperpolarized noble gas diffusion MRI: theoretical models and experimental results.

The introduction of hyperpolarized gases ((3)He and (129)Xe) has opened the door to applications for which gaseous agents are uniquely suited-lung MRI. One of the pulmonary applications, diffusion MRI, relies on measuring Brownian motion of inhaled hyperpolarized gas atoms diffusing in lung airspaces. In this article we provide an overview of the theoretical ideas behind hyperpolarized gas diffusion MRI and the results obtained over the decade-long research. We describe a simple technique based on measuring gas apparent diffusion coefficient (ADC) and an advanced technique, in vivo lung morphometry, that quantifies lung microstructure both in terms of Weibel parameters (acinar airways radii and alveolar depth) and standard metrics (mean linear intercept, surface-to-volume ratio, and alveolar density) that are widely used by lung researchers but were previously available only from invasive lung biopsy. This technique has the ability to provide unique three-dimensional tomographic information on lung microstructure from a less than 15 s MRI scan with results that are in good agreement with direct histological measurements. These safe and sensitive diffusion measurements improve our understanding of lung structure and functioning in health and disease, providing a platform for monitoring the efficacy of therapeutic interventions in clinical trials.

Impacts of diffusive transport on carbonate mineral formation from magnesium silicate-CO2-water reactions.

Reactions of CO2 with magnesium silicate minerals to precipitate magnesium carbonates can result in stable carbon sequestration. This process can be employed in ex situ reactors or during geologic carbon sequestration in magnesium-rich formations. The reaction of aqueous CO2 with the magnesium silicate mineral forsterite was studied in systems with transport controlled by diffusion. The approach integrated bench-scale experiments, an in situ spectroscopic technique, and reactive transport modeling. Experiments were performed using a tube packed with forsterite and open at one end to a CO2-rich solution. The location and amounts of carbonate minerals that formed were determined by postexperiment characterization of the solids. Complementing this ex situ characterization, (13)C NMR spectroscopy tracked the inorganic carbon transport and speciation in situ. The data were compared with the output of reactive transport simulations that accounted for diffusive transport processes, aqueous speciation, and the forsterite dissolution rate. All three approaches found that the onset of magnesium carbonate precipitation was spatially localized about 1 cm from the opening of the forsterite bed. Magnesite was the dominant reaction product. Geochemical gradients that developed in the diffusion-limited zones led to locally supersaturated conditions at specific locations even while the volume-averaged properties of the system remained undersaturated.

In situ measurement of magnesium carbonate formation from CO2 using static high-pressure and -temperature 13C NMR.

We explore a new in situ NMR spectroscopy method that possesses the ability to monitor the chemical evolution of supercritical CO(2) in relevant conditions for geological CO(2) sequestration. As a model, we use the fast reaction of the mineral brucite, Mg(OH)(2), with supercritical CO(2) (88 bar) in aqueous conditions at 80 °C. The in situ conversion of CO(2) into metastable and stable carbonates is observed throughout the reaction. After more than 58 h of reaction, the sample was depressurized and analyzed using in situ Raman spectroscopy, where the laser was focused on the undisturbed products through the glass reaction tube. Postreaction, ex situ analysis was performed on the extracted and dried products using Raman spectroscopy, powder X-ray diffraction, and magic-angle spinning (1)H-decoupled (13)C NMR. These separate methods of analysis confirmed a spatial dependence of products, possibly caused by a gradient of reactant availability, pH, and/or a reaction mechanism that involves first forming hydroxy-hydrated (basic, hydrated) carbonates that convert to the end-product, anhydrous magnesite. This carbonation reaction illustrates the importance of static (unmixed) reaction systems at sequestration-like conditions.

Low-cost gradient amplifiers for small MRI systems.

We describe low-cost gradient amplifiers for small MRI systems, such as those based on small/medium permanent magnets. The requirements for MRI gradient amplifiers are quite similar to those of modestly priced audio stereo power amplifiers. Such amplifiers for sound service can be modified to be DC coupled, extending their response down to zero frequency, as needed for MRI gradient service. We describe such modifications to one unit (Samson Servo 600) and mention a commercially available modification of another. The 600 is capable of an output greater than ±8 A and ±60 V, much greater than our needs for a greenhouse MRI. Audio amplifiers can be used this way as controlled voltage (CV) gradient amplifiers, with acceptable performance because the gradient coils typically have short L/R time constants. Superior performance can be had by using a controlled current (CC) "front end"; the circuit of our simple front end is included. The complete 3-axis CC system costs about $1200.

Simple through-plane spatial filter for 2D MRI projections.

A simple spatial filter for 2D projection MR imaging is introduced. It works in the third (unresolved) direction to eliminate uniform or slowly varying interfering background signals. A constant amplitude gradient pulse in the unresolved direction is applied at the same time as the usual phase encode gradient during 2D acquisition. The filter is demonstrated for root imaging in soil, where background soil water signals can be troublesome. The filter suppresses the soil water signal while preserving the desired signal of plant roots. Fundamental to the operation of the filter is that the roots are sparse in the image domain, meaning there are relatively few pixels with multiple roots present. The performance of the through-plane filter is demonstrated and compares favorably to more conventional in-plane spatial filtering.

In vivo detection of acinar microstructural changes in early emphysema with (3)He lung morphometry.

PURPOSE: To quantitatively characterize early emphysematous changes in the lung microstructure of current and former smokers with noninvasive helium 3 ((3)He) lung morphometry and to compare these results with the clinical standards, pulmonary function testing (PFT) and low-dose computed tomography (CT). MATERIALS AND METHODS: This study was approved by the local institutional review board, and all subjects provided informed consent. Thirty current and former smokers, each with a minimum 30-pack-year smoking history and mild or no abnormalities at PFT, underwent (3)He lung morphometry. This technique is based on diffusion MR imaging with hyperpolarized (3)He gas and yields quantitative localized in vivo measurements of acinar airway geometric parameters, such as airway radii, alveolar depth, and number of alveoli per unit lung volume. These measurements enable calculation of standard morphometric characteristics, such as mean linear intercept and surface-to-volume ratio. RESULTS: Noninvasive (3)He lung morphometry was used to detect alterations in acinar structure in smokers with normal PFT findings. When compared with smokers with the largest forced expiratory volume in 1 second (FEV(1)) to forced vital capacity (FVC) ratio, those with chronic obstructive pulmonary disease had significantly reduced alveolar depth (0.07 mm vs 0.13 mm) and enlarged acinar ducts (0.36 mm vs 0.3 mm). The mean alveolar geometry measurements in the healthiest subjects were in excellent quantitative agreement with literature values obtained by using invasive techniques (acinar duct radius, 0.3 mm; alveolar depth, 0.14 mm at 1 L above functional residual capacity). (3)He lung morphometry depicted greater abnormalities than did PFT and CT. No adverse events were associated with inhalation of (3)He gas. CONCLUSION: (3)He lung morphometry yields valuable noninvasive insight into early emphysematous changes in alveolar geometry with increased sensitivity compared with conventional techniques.

Imaging lung microstructure in mice with hyperpolarized 3He diffusion MRI.

Quantitative measurement of lung microstructure is of great significance in assessment of pulmonary disease, particularly in the earliest stages. The technique for MRI-based 3He lung morphometry was previously developed and validated for human lungs, and was recently extended to ex vivo mouse lungs. The technique yields accurate, quantitative information about the microstructure and geometry of acinar airways. In this study, the 3He lung morphometry technique is successfully implemented for in vivo studies of mice. Results indicate excellent agreement between in vivo morphometry via 3He MRI and microscopic morphometry after sacrifice. This opens up new avenues for application of the technique as a precise, noninvasive, in vivo biomarker of changes in lung microstructure, within various mouse models of lung disease.

NMR spectroscopy of coin cell batteries with metal casings.

Battery cells with metal casings are commonly considered incompatible with nuclear magnetic resonance (NMR) spectroscopy because the oscillating radio-frequency magnetic fields ("rf fields") responsible for excitation and detection of NMR active nuclei do not penetrate metals. Here, we show that rf fields can still efficiently penetrate nonmetallic layers of coin cells with metal casings provided "B1 damming" configurations are avoided. With this understanding, we demonstrate noninvasive high-field in situ 7Li and 19F NMR of coin cells with metal casings using a traditional external NMR coil. This includes the first NMR measurements of an unmodified commercial off-the-shelf rechargeable battery in operando, from which we detect, resolve, and separate 7Li NMR signals from elemental Li, anodic ß-LiAl, and cathodic LixMnO2 compounds. Real-time changes of ß-LiAl lithium diffusion rates and variable ß-LiAl 7Li NMR Knight shifts are observed and tied to electrochemically driven changes of the ß-LiAl defect structure.

Emphysema quantification in inflation-fixed lungs using low-dose computed tomography and 3He magnetic resonance imaging.

OBJECTIVE: To evaluate the use of inflation-fixed lung tissue for emphysema quantification with computed tomography (CT) and He magnetic resonance (MR) diffusion imaging. METHODS: Fourteen subjects representing a range of chronic obstructive pulmonary disease severity who underwent complete or lobar lung resection were studied. Computed tomographic measurements of lung attenuation and MR measurements of the hyperpolarized 3He apparent diffusion coefficient (ADC) in resected specimens fixed in inflation with heated formalin vapor were compared with measurements obtained before fixation. RESULTS: The mean (SD) CT emphysema indices were 56% (17%) before and 58% (19%) after fixation (P = 0.77; R = 0.76). Index differences correlated with differences in lung volume (R = 0.47). The mean (SD) 3He ADCs were 0.40 (0.15) cm/s before and 0.39 (0.14) cm/s after fixation (P = 0.03, R = 0.98). The CT emphysema index and the 3He ADC were correlated before (R = 0.89) and after fixation (R = 0.79). CONCLUSIONS: Concordance of CT and 3He MR imaging measurements in unfixed and inflation-fixed lungs supports the use of inflation-fixed lungs for quantitative imaging studies in emphysema.

Precision current regulator for NMR electromagnets.

When using electromagnets or non-persistent superconducting magnets, the field stability can be directly proportional to the current stability. We present here a simple design for a current regulator based upon a high-precision, dc-dc fluxgate transformer. The output current and NMR frequency are stabilized by about a factor of 50, over times of order one hour. The method can be applied to essentially any current supply.

NMR of petrochemical-type chemical reactions.

A simple technique is presented for NMR of chemically reacting systems at conditions of high temperature and pressure. The method can follow reactions that are typical of refinery operations - hydrogenation, transfer dehydrogenation, methanol synthesis, and isomerization. All of the reacting materials are flame-sealed into a glass capillary. Gaseous agents such as O2 and CO are loaded into the capillary by condensation at liquid N2 temperature. H2 is provided by loading LiAlH4. The capillary holds the high pressure, up to 7 MPa, so the NMR probe can be a simple design with hot air flowing over the sample tube, up to 350 °C. Example reaction results are presented, including hydrogenation of benzene, hydrogenation/dehydrogenation of cyclohexene to benzene and cyclohexane (a disproportionation), and synthesis of methane, methanol and dimethyl ether from CO and H2. In this work we present a simple, inexpensive method with rapid temperature response for tracking chemical reactions in real-time at high temperature and high pressure.

Calibration of RF transmitter voltages for hyperpolarized gas MRI.

MRI with hyperpolarized gases, (3)He, (129)Xe, (13)C, and others, has the potential to become an important diagnostic technique for clinical imaging. Due to the nonreversible loss of magnetization in hyperpolarized gas imaging, the choice of the flip angle is a major factor that influences the signal intensity, and hence, the signal-to-noise ratio. Conventional automated radiofrequency (RF) calibration procedures for (1)H imaging are not suitable for hyperpolarized gas imaging. Herein, we have demonstrated a simple procedure for RF calibration for magnetic resonance imaging (MRI) with hyperpolarized gases that is easily adaptable to clinical settings. We have demonstrated that there exists a linear relationship between the RF transmitter voltages required to obtain the same nutation angle for protons (V(1H)) and hyperpolarized gas nuclei (V(3He)). For our (1)H and (3)He coils we found that V(3He) = 1.937 . V(1H) with correlation coefficient r(2) = 0.97. This calibration can be done as a one-time procedure during the routine quality assurance (QA) protocol. The proposed procedure was found to be extremely robust in routine scanning and provided an efficient method to achieve a desired flip angle, thus allowing optimum image quality.