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.

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.

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.

Coil extensions improve line shapes by removing field distortions.

The static magnetic susceptibility of the rf coil can substantially distort the field B0 and be a dominant source of line broadening. A scaling argument shows that this may be a particular problem in microcoil NMR. We propose coil extensions to reduce the distortion. The actual rf coil is extended to a much longer overall length by abutted coil segments that do not carry rf current. The result is a long and nearly uniform sheath of copper wire, in terms of the static susceptibility. The line shape improvement is demonstrated at 43.9 MHz and in simulation calculations.

Earth's field NMR detection of oil under arctic ice-water suppression.

Earth's field NMR has been developed to detect oil trapped under or in Arctic sea-ice. A large challenge, addressed here, is the suppression of the water signal that dominates the oil signal. Selective suppression of water is based on relaxation time T1 because of the negligible chemical shifts in the weak earth's magnetic field, making all proton signals overlap spectroscopically. The first approach is inversion-null recovery, modified for use with pre-polarization. The requirements for efficient inversion over a wide range of B1 and subsequent adiabatic reorientation of the magnetization to align with the static field are stressed. The second method acquires FIDs at two durations of pre-polarization and cancels the water component of the signal after the data are acquired. While less elegant, this technique imposes no stringent requirements. Similar water suppression is found in simulations for the two methods. Oil detection in the presence of water is demonstrated experimentally with both techniques.

Adiabatic sweep pulses for earth's field NMR with a surface coil.

Adiabatic NMR sweep pulses are described for inversion and excitation in very low magnetic fields B0 and with broad distribution of excitation field amplitude B1. Two aspects distinguish the low field case: (1) when B1 is comparable to or greater than B0, the rotating field approximation fails and (2) inversion sweeps cannot extend to values well below the Larmor frequency because they would approach or pass through zero frequency. Three approaches to inversion are described. The first is a conventional tangent frequency sweep down to the Larmor frequency, a 180° phase shift, and a sweep back up to the starting frequency. The other two are combined frequency and amplitude sweeps covering a narrower frequency range; one is a symmetric sweep from above to below the Larmor frequency and the other uses a smooth decrease of B1 immediately before and after the 180° phase shift. These two AM/FM sweeps show excellent inversion efficiencies over a wide range of B1, a factor of 30 or more. We also demonstrate an excitation sweep that works well in the presence of the same wide range of B1. We show that the primary effect of the counter-rotating field (i.e., at low B0) is that the magnetization suffers large, periodic deviations from where it would be at large B0. Thus, successful sweep pulses must avoid any sharp features in the amplitude, phase, or frequency.

Failure of Rhodiola rosea to alter skeletal muscle phosphate kinetics in trained men.

Rhodiola rosea is an herbal supplement purported to improve resistance to stressors and to enhance physical performance, potentially by improving adenosine triphosphate (ATP) turnover. Phosphocreatine (PCr) kinetics serves as a reflection of ATP turnover. The purpose of this investigation was to examine the effect of R rosea ingestion on human skeletal muscle PCr recovery after exhaustive exercise. Twelve resistance-trained men, aged 19 to 39 years, completed incremental forearm wrist flexion exercise to volitional fatigue, once after ingesting 1500 mg R rosea per day for 4 days, and once after ingesting an equivalent placebo dose. During exercise and recovery from exercise, muscle phosphates were examined using phosphorus 31 nuclear magnetic resonance spectroscopy. [PCr] during recovery was fit with a monoexponential function, and the resulting rate constants (k) were compared between groups. Rating of perceived exertion per stage and time to exhaustion were also compared between groups. For R rosea, k=0.3744+/-0.1532, whereas for placebo, k=0.3956+/-0.2238. Although rating of perceived exertion significantly increased within groups as workload increased, it did not differ between conditions, nor did time to exhaustion (R rosea, 10.71+/-0.54 minutes; placebo, 10.48+/-0.68 minutes). Estimates of [PCr] at time 0, 5, 10, 15, and 20 minutes of recovery were nearly identical between groups. In summary, there were no significant differences between groups for any of theparameters measured. Based on these results, we conclude that R rosea ingestion does not improve ATP turnover during or immediately after exercise.

Pre-polarization fields for earth's field NMR: Fast discharge for use with short T1 and large coils.

The sensitivity of earth's field NMR is greatly increased by the use of a pre-polarizing field Bp. When used with short T1 samples, the field must be decreased rapidly to avoid loss of the pre-polarized magnetization by relaxation. Such a rapid decrease in the field requires rapid discharge (∼10ms) of a large stored magnetic field energy (∼700J). In addition, in order that the full pre-polarized magnetization be available for the subsequent pulse sequence, the field discharge should be adiabatic. This requirement is difficult to fulfill in cases where Bp is not everywhere parallel to the earth's field, such as with a large surface coil. Circuitry for rapid and controlled discharge is presented. Simulations and experiments confirm the importance of both of these conditions.

Validation of a two-compartment model of ventilation/perfusion distribution.

Ventilation (V (A)) to perfusion (Q ) heterogeneity (V (A)/Q ) analyses by a two-compartment lung model (2C), utilizing routine gas exchange measurements and a computer solution to account for O(2) and CO(2) measurements, were compared with multiple inert gas elimination technique (MIGET) analyses and a multi-compartment (MC) model. The 2C and MC estimates of V (A)/Q mismatch were obtained in 10 healthy subjects, 43 patients having chronic obstructive pulmonary disease (COPD) and in 14 dog experiments where hemodynamics and acid-base status were manipulated with gas mixtures, fluid loading and tilt-table stressors. MIGET comparisons with 2C were made on 6 patients and 32 measurements in healthy subjects before and after exercise at normoxia and altitude hypoxia. Statistically significant correlations for logarithmic standard deviations of V (A)/Q distributions (SD(V (A)/Q )) were obtained for all 2C comparisons, with similar values between 2C and both other methods in the 1.1-1.5 range, compatible with mild to moderate COPD. 2C tended to overestimate MC and MIGET values at low and underestimate them at high SD(V (A)/Q ) values. SD(V (A)/Q ) weighted by Q agreed better with MC and MIGET estimates in the normal range, whereas SD(V (A)/Q ) weighted by V (A) was closer to MC at higher values because the V (A)-weighted SD(V (A)/Q ) is related to blood-to-gas PCO(2) differences that are elevated in disease, thereby allowing better discrimination. The 2C model accurately described functional V (A)/Q characteristics in 26 normal and bronchoconstricted dogs during non-steady state rebreathing and could be used to quantify the effect of reduced O(2) diffusing capacity in diseased lungs. These comparisons indicate that 2C adequately describes V (A)/Q mismatch and can be useful in clinical or experimental situations where other techniques are not feasible.

Chemically selective NMR imaging of a 3-component (solid-solid-liquid) sedimenting system.

A novel magnetic resonance imaging (MRI) technique which resolves the separate components of the evolving vertical concentration profiles of 3-component non-colloidal suspensions is described. This method exploits the sensitivity of MRI to chemical differences between the three phases to directly image the fluid phase and one of the solid phases, with the third phase obtained by subtraction. 19F spin-echo imaging of a polytetrafluoroethylene (PTFE) oil was interlaced with 1H SPRITE imaging of low-density polyethylene (LDPE) particles. The third phase was comprised of borosilicate glass spheres, which were not visible while imaging the PTFE or LDPE phases. The method is demonstrated by performing measurements on 2-phase materials containing only the floating (LDPE) particles, with the results contrasted to the experimental behaviour of the individual phases in the full 3-phase system. All experiments were performed using nearly monodisperse particles, with initial suspension volume fractions, phi(i), of 0.1.

Velocity of mist droplets and suspending gas imaged separately.

Nuclear Magnetic Resonance Images (MRIs) of the velocity of water droplets and velocity of the suspending gas, hexafluoroethane, are presented for a vertical and horizontal mist pipe flow. In the vertical flow, the upward velocity of the droplets is clearly slower than the upward velocity of the gas. The average droplet size calculated from the average falling velocity in the upward flow is larger than the average droplet size of mist drawn from the top of the pipe measured with a multi-stage aerosol impactor. Vertical flow concentrates larger particles because they have a longer transit time through the pipe. In the horizontal flow there is a gravity-driven circulation with high-velocity mist in the lower portion of the pipe and low-velocity gas in the upper portion. MRI has the advantages that it can image both phases and that it is unperturbed by optical opacity. A drawback is that the droplet phase of mist is difficult to image because of low average spin density and because the signal from water coalesced on the pipe walls is high. To our knowledge these are the first NMR images of mist.

Imaging of Her2-targeted magnetic nanoparticles for breast cancer detection: comparison of SQUID-detected magnetic relaxometry and MRI.

Both magnetic relaxometry and magnetic resonance imaging (MRI) can be used to detect and locate targeted magnetic nanoparticles, noninvasively and without ionizing radiation. Magnetic relaxometry offers advantages in terms of its specificity (only nanoparticles are detected) and the linear dependence of the relaxometry signal on the number of nanoparticles present. In this study, detection of single-core iron oxide nanoparticles by superconducting quantum interference device (SQUID)-detected magnetic relaxometry and standard 4.7 T MRI are compared. The nanoparticles were conjugated to a Her2 monoclonal antibody and targeted to Her2-expressing MCF7/Her2-18 (breast cancer cells); binding of the nanoparticles to the cells was assessed by magnetic relaxometry and iron assay. The same nanoparticle-labeled cells, serially diluted, were used to assess the detection limits and MR relaxivities. The detection limit of magnetic relaxometry was 125 000 nanoparticle-labeled cells at 3 cm from the SQUID sensors. T(2)-weighted MRI yielded a detection limit of 15 600 cells in a 150 µl volume, with r(1) = 1.1 mm(-1) s(-1) and r(2) = 166 mm(-1) s(-1). Her2-targeted nanoparticles were directly injected into xenograft MCF7/Her2-18 tumors in nude mice, and magnetic relaxometry imaging and 4.7 T MRI were performed, enabling direct comparison of the two techniques. Co-registration of relaxometry images and MRI of mice resulted in good agreement. A method for obtaining accurate quantification of microgram quantities of iron in the tumors and liver by relaxometry was also demonstrated. These results demonstrate the potential of SQUID-detected magnetic relaxometry imaging for the specific detection of breast cancer and the monitoring of magnetic nanoparticle-based therapies.

CO2 rebreathing model in COPD: blood-to-gas equilibration.

Rebreathing in a closed system can be used to estimate mixed venous PCO2 (PvCO2) and cardiac output, but these estimates are affected by VA/Q heterogeneity. The purpose of this study was to validate a mathematical model of CO2 exchange during CO2 rebreathing in 29 patients with chronic obstructive pulmonary disease (COPD), with baseline arterial PCO2 (PaCO2) ranging from 28 to 60 mmHg. Rebreathing increased end-tidal PCO2 (PETCO2) by 20 mmHg over 2.2 min. This model employed baseline values for inspired (bag) PCO2, estimated PvCO2, distribution of ventilation and blood flow in one high VA/Q and one low VA/Q compartment, the ventilation increase and conservation of mass equations to simulate time courses of PICO2, PETCO2, PvCO2, and PaCO2. Measured PICO2 and PETCO2 during rebreathing differed by an average (SEM) of 1.4 (0.4) mmHg from simulated values. By end of rebreathing, predicted PvCO2 was lower than measured and predicted PaCO2, indicating gas to blood CO2 flux. Estimates of the ventilatory response to CO2, quantified as the slope (S) of the ventilation increase versus PETCO2, were inversely related to gas-to-blood PCO2 disequilibria due to VA/Q heterogeneity and buffer capacity (BC), but not airflow limitation. S may be corrected for these artifacts to restore S as a more valid noninvasive index of central CO2 responsiveness. We conclude that a rebreathing model incorporating baseline VA/Q heterogeneity and BC can simulate gas and blood PCO2 in patients with COPD, where VA/Q variations are large and variable.