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Time‐series multi‐omics analysis of micronutrient stress in Sorghum bicolor reveals iron and zinc crosstalk and regulatory network conservation

Micronutrient stress impacts growth, biomass production, and grain yield in crops. Multi-omics studies are valuable resources in identifying genes for functional studies and trait improvement, such as accumulation of Fe or Zn under deficient or excess conditions for bioenergy or grain agriculture. We conducted transcriptomics and ionomics analyses on Sorghum bicolor BTx623, grown under Fe and Zn limited and excess conditions over a 21-day period. To identify early and late transcriptional response in roots and leaves, 180 RNAseq libraries were sequenced for differential expression and co-expression network analyses. Fe and Zn accumulation was measured using ICP-MS at each time point, and a fluorometer was used to estimate chlorophyll content in leaves. Among the four treatments, Fe limitation and Zn excess resulted in the largest phenotypic effects and transcriptional response in roots and leaves. Several of the reduction (Strategy I) and chelation (Strategy II) strategy genes that improve bioavailability of Fe and Zn in plant roots often used by non-grass and grass species, respectively, were differentially expressed. Gene regulatory network (GRN) analysis of roots revealed enrichment of genes from Fe limiting and Zn excess which strongly connect to homologues of SbFIT, SbPYE, and SbBTS as hub genes. The GRN for leaf responses showed homologues of SbPYE and SbBTS as hubs connecting genes for chloroplast biosynthesis, Fe-S cluster assembly, photosynthesis, and ROS scavenging. Expression analyses suggest sorghum uses Strategy II genes for Fe and Zn uptake, as expected, but can also utilize Strategy I genes, which may be advantageous in variable moisture environments. We found strong overlap between Fe and Zn responsive GRNs, indicative of micronutrient crosstalk. We also found conservation of root and leaf GRNs, and known homologous genes suggest strong constraints on homeostasis networks in plants. These data will provide a resource for functional genetics to enhance micronutrient transport in sorghum, and opportunities to conduct further comparative GRN analysis across diverse crops species.

59 BASIC BIOLOGICAL SCIENCES↗

Fraunhofer line-dept sensing applied to water

An experimental Fraunhofer line discriminator is basically an airborne fluorometer, capable of quantitatively measuring the concentration of fluorescent substances dissolved in water. It must be calibrated against standards and supplemented by ground-truth data on turbidity and on approximate vertical distribution of the fluorescent substance. Quantitative use requires that it be known in advance what substance is the source of the luminescence emission; qualitative sensing, or detection of luminescence is also possible. The two approaches are fundamentally different, having different purposes, different applications, and different instruments. When used for sensing of Rhodamine WT dye in coastal waters and estuaries, the FLD is sensing in the spectral region permitting nearly maximum depth of light penetration.

Stoertz, G. E.↗

Laboratory studies of in vivo fluorescence of phytoplankton

A lidar system is developed that uses four selected excitation wavelengths to induce chlorophyll 'a' fluorescence which is indicative of both the concentration and diversity of phytoplankton. The operating principles of the system and the results of measurements of phytoplankton fluorescence in a controlled laboratory environment are presented. A comparative study of results from lidar fluorosensor laboratory tank tests using representative species of phytoplankton in single and multispecies cultures from each of four color groups reveals that (1) there is good correlation between the fluorescence of chlorophyll 'a' remotely simulated and detected by the lidar system and in-situ measurements using four similar excitation wavelengths in a flow-through fluorometer; (2) good correlation exists between the total chlorophyll 'a' calculated from lidar-fluorosensor data and measurements obtained by the Strickland-Parsons method; and (3) the lidar fluorosensor can provide an index of population diversity.

Brown, C. A., Jr.↗

Satellite detection of phytoplankton export from the mid-Atlantic Bight during the 1979 spring bloom

Analysis of Coastal Zone Color Scanner (CZCS) imagery confirms shipboard and in situ moored fluorometer observations of resuspension of near-bottom chlorophyll within surface waters (1 to 10 m) by northwesterly wind events in the mid-Atlantic Bight. As much as 8 to 16 micrograms chl/l are found during these wind events from March to May, with a seasonal increase of algal biomass until onset of stratification of the water column. Rapid sinking or downwelling apparently occurs after subsequent wind events, however, such that the predominant surface chlorophyll pattern is approx. 0.5 to 1.5 micrograms/l over the continental shelf during most of the spring bloom. Perhaps half of the chlorophyll increase observed by satellite during a wind resuspension event represents in-situ production during the 4 to 5 day interval, with the remainder attributed to accumulation of algal biomass previously produced and temporarily stored within near-bottom water. Present calculations suggest that about 10% of the primary production of the spring bloom may be exported as ungrazed phytoplankton carbon from mid-Atlantic shelf waters to those of the continental slope.

Walsh, J. J.↗

High frequency sampling of the 1984 spring bloom within the mid-Atlantic Bight: Synoptic shipboard, aircraft, and in situ perspectives of the SEEP-I experiment

Moorings of current meters, thermistors, transmissometers, and fluorometers on the mid-Atlantic shelf, south of Long Island, suggest a cumulative seaward export of perhaps 0.35 g C/sq m/day between the 80 and 120 m isobaths during February-April 1984. Such a horizontal loss of algal carbon over the lower third of the water column would be 23 to 78% of the March-April 1984 primary production. This physical carbon loss is similar to daily grazing losses from zooplankton of 32-40% of the algal fixation of carbon. Metabolic demands of the benthos could be met by just the estimated fecal pellet flux, without direct consumption of algal carbon, while bacterioplankton needs could be served by excretory release of dissolved organic matter during photosynthesis. Sediment traps tethered 10 m off the bottom at the 120 m isobath and 50 m above the 500 m isobath caught as much as 0.16 to 0.26 g C /sq m/day during March-April 1984, in reasonable agreement with the flux estimated from the other moored instruments.

Walsh, J. J.↗

Moorable spectroradiometers in the BIOWATT experiment

A new oceanographic instrument, the MER-2020, has been developed for the long term measurement of bio-optical properties. This instrument is a self-contained reflectance spectroradiometer with 40 megabytes of internal data storage and battery power permitting deployments for as long as 6 months. It can serve as the control and recording center for a variety of other sensors including fluorometers, transmissometers, temperature and conductivity probes. Instruments of this type were deployed at depths to 70 meters on a 5000 meter mooring during the BIOWATT experiment between February and November 1987. Measurements of the spectral diffuse attenuation coefficient and of the remote sensed reflectance from the ten month period in 1987 in the Northern Sargasso Sea are presented. In addition, the temperature, pressure, package orientation and sunlight stimulated natural fluorescence of phytoplankton are discussed. This instrument will be a key part of in situ optical calibration for future remote color sensors, and presently permits direct measurement of long term optical variability, important in visibility and communication problems.

Booth, C. R.↗

Bio-optical profile data report coastal transition zone program, R/V Point Sur, June 15-28, 1987

Twenty vertical profiles of the bio-optical properties of the ocean were made during a research cruise on the R/V Point Sur, June 15 to 28, 1987, as part of the Coastal Transition Zone Program off Point Arena, California. Extracted chlorophyll values were also measured at some stations to provide calibration data for the in situ fluorometer. This summary provides investigators with an overview of the data collected. The entire data set is available in digital form.

Davis, Curtiss O.↗

Simultaneous three-dimensional velocity and mixing measurements by use of laser Doppler velocimetry and fluorescence probes in a water tunnel

A water tunnel investigation was conducted to demonstrate the capabilities of a laser-based instrument that can measure velocity and fluorescence intensity simultaneously. Fluorescence intensity of an excited fluorescent dye is directly related to concentration level and is used to indicate the extent of mixing in flow. This instrument is a three-dimensional laser Doppler velocimeter (LDV) in combination with a fluorometer for measuring fluorescence intensity variations. This capability allows simultaneous flow measurements of the three orthogonal velocity components and mixing within the same region. Two different flows which were generated by two models were studied: a generic nonaxisymmetric nozzle propulsion simulation model with an auxiliary internal water source that generated a jet flow and an axisymmetric forebody model with a circular sector strake that generated a vortex flow. The off-body flow fields around these models were investigated in the Langley 16- by 24-Inch Water Tunnel. The experimental results were used to calculate 17 quantities that included mean and fluctuating velocities, Reynolds stresses, mean and fluctuating dye fluorescence intensities (proportional to concentration), and fluctuating velocity and dye concentration correlations. An uncertainty analysis was performed to establish confidence levels in the experimental results. In general, uncertainties in mean velocities varied between 1 and 7 percent of free-stream velocity; uncertainties in fluctuating velocities varied between 1 and 5 percent of reference values. The results show characteristics that are unique to each type of flow.

Neuhart, Dan H.↗

SeaWiFS technical report series. Volume 32: Level-3 SeaWiFS data products. Spatial and temporal binning algorithms

The level-3 data products from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) are statistical data sets derived from level-2 data. Each data set will be based on a fixed global grid of equal-area bins that are approximately 9 x 9 sq km. Statistics available for each bin include the sum and sum of squares of the natural logarithm of derived level-2 geophysical variables where sums are accumulated over a binning period. Operationally, products with binning periods of 1 day, 8 days, 1 month, and 1 year will be produced and archived. From these accumulated values and for each bin, estimates of the mean, standard deviation, median, and mode may be derived for each geophysical variable. This report contains two major parts: the first (Section 2) is intended as a users' guide for level-3 SeaWiFS data products. It contains an overview of level-0 to level-3 data processing, a discussion of important statistical considerations when using level-3 data, and details of how to use the level-3 data. The second part (Section 3) presents a comparative statistical study of several binning algorithms based on CZCS and moored fluorometer data. The operational binning algorithms were selected based on the results of this study.

Hooker, Stanford B.↗

[MODIS Investigation]

The objective of the last six months were: (1) Continue analysis of Hawaii Ocean Time-series (HOT) bio-optical mooring data, and Southern Ocean bio-optical drifter data; (2) Complete development of documentation of MOCEAN algorithms and software for use by MOCEAN team and GLI team; (3) Deploy instrumentation during JGOFS cruises in the Southern Ocean; (4) Participate in test cruise for Fast Repetition Rate (FRR) fluorometer; (5) Continue chemostat experiments on the relationship of fluorescence quantum yield to environmental factors; and (6) Continue to develop and expand browser-based information system for in situ bio-optical data. We are continuing to analyze bio-optical data collected at the Hawaii Ocean Time Series mooring as well as data from bio-optical drifters that were deployed in the Southern Ocean. A draft manuscript has now been prepared and is being revised. A second manuscript is also in preparation that explores the vector wind fields derived from NSCAT measurements. The HOT bio-optical mooring was recovered in December 1997. After retrieving the data, the sensor package was serviced and redeployed. We have begun preliminary analysis of these data, but we have only had the data for 3 weeks. However, all of the data were recovered, and there were no obvious anomalies. We will add second sensor package to the mooring when it is serviced next spring. In addition, Ricardo Letelier is funded as part of the SeaWiFS calibration/validation effort (through a subcontract from the University of Hawaii, Dr. John Porter), and he will be collecting bio-optical and fluorescence data as part of the HOT activity. This will provide additional in situ measurements for MODIS validation. As noted in the previous quarterly report, we have been analyzing data from three bio-optical drifters that were deployed in the Southern Ocean in September 1996. We presented results on chlorophyll and drifter speed. For the 1998 Ocean Sciences meeting, a paper will be presented on this data set, focusing on the diel variations in fluorescence quantum yield. Briefly, there are systematic patterns in the apparent quantum yield of fluorescence (defined as the slope of the line relating fluorescence/chlorophyll and incoming solar radiation). These systematic variations appear to be related to changes in the circulation of the Antarctic Polar Front which force nutrients into the upper ocean. A more complete analysis will be provided in the next Quarterly report.

Abbott, Mark R.↗

Oceanographic Research

The PNF-300 Natural Fluorometer is an optical instrument for oceanographic research developed under NASA contract by Biospherical Instruments, Inc. An important innovation for oceanographers, it measures photosynthetic productivity and estimates phytoplankton production less expensively, is non-intrusive and can be used on site - an improved way of estimating ocean productivity. Applications include environmental impact studies, monitoring plankton concentrations in a reservoir, and other research uses.

Source record↗

BENCAL Cruise Report

This report documents the scientific activities on board the South African Fisheries Research Ship (FRS) Africana during an ocean color calibration and validation cruise in the Benguela upwelling ecosystem (BEN-CAL), 4-17 October 2002. The cruise, denoted Afncana voyage 170, was staged in the southern Benguela between Cape Town and the Orange River within the region 14-18.5 deg E,29-34 deg S, with 15 scientists participat- ing from seven different international organizations. Uniquely in October 2002, four high-precision ocean color sensors were operational, and these included the Moderate Resolution Imaging Spectroradiometer (MODIS) instruments on the Aqua and Terra spacecraft, the Medium Resolution Imaging Spectrometer (MERIS), and the Sea-viewing Wide Field-of-view Sensor (SeaWiFS). SeaWiFS imagery was transmitted daily to the ship to assist in choosing the vessel's course and selecting stations for bio-optical deployments. There were four primary objectives of the cruise. The first was to conduct bio-optical measurements with above- and in-water optical instruments to vicariously calibrate the satellite sensors. The second was to interrelate diverse measurements of the apparent optical properties (AOPs) at satellite sensor wavelengths with inherent optical properties (IOPs) and bio-optically active constituents of seawater such as particles, pigments, and dissolved compounds. The third was to determine the interrelationships between optical properties, phytoplankton pigment composition, photosynthetic rates, and primary production, while the fourth objective was to collect samples for a second pigment round-robin intercalibration experiment. Weather conditions were generally very favorable, and a range of hyperspectral and fixed wavelength AOP instruments were deployed during daylight hours. Various IOP instruments were used to determine the absorption, attenuation, scattering, and backscattering properties of particulate matter and dissolved substances, while a Fast Repetition Rate Fluorometer (FRRF) was deployed to acquire data on phytoplankton photosynthetic activity. Hydrographic profiling was conducted routinely during the cruise, and seawater samples were collected for measurements of salinity, oxygen, inorganic nutrients, pigments, particulate organic carbon, suspended particulate material, and primary production. Location of stations and times of optical deployments were selected to coincide with satellite overpasses whenever possible, and to cover a large range in trophic conditions.

Hooker, Stanford B.↗

The Use of Chlorophyll Fluorescence Lifetime to Assess Phytoplankton Physiology within a River-Dominated Environment

Chlorophyll a fluorescence lifetime was measured for phytoplankton populations inhabiting the three physical zones surrounding the Mississippi River's terminus in the Gulf of Mexico. Observations of river discharge volume, nitrate + nitrite, silicate, phosphate, PAR (Photosynthetically Active Radiation) diffuse attenuation within the water column, salinity, temperature, SPM, and chl a concentration were used to characterize the distribution of chl fluorescence lifetime within a given region within restricted periods of time. 33 stations extending from the Mississippi River plume to the shelf break of the Louisiana coast were surveyed for analysis of chlorophyll fluorescence lifetime during two cruises conducted March 31 - April 6, 2000, and October 24 - November 1, 2000. At each station, two to three depths were chosen for fluorescence lifetime measurement to represent the vertical characteristics of the water column. Where possible, samples were taken from just below the surface and from just above and below the pycnocline. All samples collected were within the 1% light level of the water column (the euphotic zone). Upon collection, samples were transferred to amber Nalgene bottles and left in the dark for at least 15 minutes to reduce the effects of non-photochemical quenching and to insure that photosynthetic reaction centers were open. Before measurements within the phase fluorometer were begun, the instrument was allowed to warm up for no less than one hour.

Hall, Callie M.↗

Fluorogenic Cell-Based Biosensors for Monitoring Microbes

Fluorogenic cell-based sensor systems for detecting microbes (especially pathogenic ones) and some toxins and allergens are undergoing development. These systems harness the natural signaltransduction and amplification cascades that occur in mast cells upon activation with antigens. These systems include (1) fluidic biochips for automated containment of samples, reagents, and wastes and (2) sensitive, compact fluorometers for monitoring the fluorescent responses of mast cells engineered to contain fluorescent dyes. It should be possible to observe responses within minutes of adding immune complexes. The systems have been shown to work when utilizing either immunoglobulin E (IgE) antibodies or traditionally generated rat antibodies - a promising result in that it indicates that the systems could be developed to detect many target microbes. Chimeric IgE antibodies and rat immunoglobulin G (IgG) antibodies could be genetically engineered for recognizing biological and chemical warfare agents and airborne and food-borne allergens. Genetic engineering efforts thus far have yielded (1) CD14 chimeric antibodies that recognize both Grampositive and Gram-negative bacteria and bind to the surfaces of mast cells, eliciting a degranulation response and (2) rat IgG2a antibodies that act similarly in response to low levels of canine parvovirus.

Curtis, Theresa↗

NASA Tech Briefs, December 2007

Topics include: Ka-Band TWT High-Efficiency Power Combiner for High-Rate Data Transmission; Reusable, Extensible High-Level Data-Distribution Concept; Processing Satellite Imagery To Detect Waste Tire Piles; Monitoring by Use of Clusters of Sensor-Data Vectors; Circuit and Method for Communication Over DC Power Line; Switched Band-Pass Filters for Adaptive Transceivers; Noncoherent DTTLs for Symbol Synchronization; High-Voltage Power Supply With Fast Rise and Fall Times; Waveguide Calibrator for Multi-Element Probe Calibration; Four-Way Ka-Band Power Combiner; Loss-of-Control-Inhibitor Systems for Aircraft; Improved Underwater Excitation-Emission Matrix Fluorometer; Metrology Camera System Using Two-Color Interferometry; Design and Fabrication of High-Efficiency CMOS/CCD Imagers; Foam Core Shielding for Spacecraft CHEM-Based Self-Deploying Planetary Storage Tanks Sequestration of Single-Walled Carbon Nanotubes in a Polymer PPC750 Performance Monitor Application-Program-Installer Builder Using Visual Odometry to Estimate Position and Attitude Design and Data Management System Simple, Script-Based Science Processing Archive Automated Rocket Propulsion Test Management Online Remote Sensing Interface Fusing Image Data for Calculating Position of an Object Implementation of a Point Algorithm for Real-Time Convex Optimization Handling Input and Output for COAMPS Modeling and Grid Generation of Iced Airfoils Automated Identification of Nucleotide Sequences Balloon Design Software Rocket Science 101 Interactive Educational Program Creep Forming of Carbon-Reinforced Ceramic-Matrix Composites Dog-Bone Horns for Piezoelectric Ultrasonic/Sonic Actuators Benchtop Detection of Proteins Recombinant Collagenlike Proteins Remote Sensing of Parasitic Nematodes in Plants Direct Coupling From WGM Resonator Disks to Photodetectors Using Digital Radiography To Image Liquid Nitrogen in Voids Multiple-Parameter, Low-False-Alarm Fire-Detection Systems Mosaic-Detector-Based Fluorescence Spectral Imager Plasmoid Thruster for High Specific-Impulse Propulsion Analysis Method for Quantifying Vehicle Design Goals Improved Tracking of Targets by Cameras on a Mars Rover Sample Caching Subsystem Multistage Passive Cooler for Spaceborne Instruments GVIPS Models and Software Stowable Energy-Absorbing Rocker-Bogie Suspensions

Source record↗

Phytoplankton-Fluorescence-Lifetime Vertical Profiler

A battery-operated optoelectronic instrument is designed to be lowered into the ocean to measure the intensity and lifetime of fluorescence of chlorophyll A in marine phytoplankton as a function of depth from 0 to 300 m. Fluorescence lifetimes are especially useful as robust measures of photosynthetic productivity of phytoplankton and of physical and chemical mechanisms that affect photosynthesis. The knowledge of photosynthesis in phytoplankton gained by use of this and related instruments is expected to contribute to understanding of global processes that control the time-varying fluxes of carbon and associated biogenic elements in the ocean. The concentration of chlorophyll in the ocean presents a major detection challenge because in order to obtain accurate values of photosynthetic parameters, the intensity of light used to excite fluorescence must be kept very low so as not to disturb the photosynthetic system. Several innovations in fluorometric instrumentation were made in order to make it possible to reach the required low detection limit. These innovations include a highly efficient optical assembly with an integrated flow-through sample interface, and a high-gain, low-noise electronic detection subsystem. The instrument also incorporates means for self-calibration during operation, and electronic hardware and software for control, acquisition and analysis of data, and communications. The electronic circuitry is highly miniaturized and designed to minimize power demand. The instrument is housed in a package that can withstand the water pressure at the maximum depth of 300 m. A light-emitting diode excites fluorescence in the sample flow cell, which is placed at one focal point of an ellipsoidal reflector. A photomultiplier tube is placed at the other focal point. This optical arrangement enables highly efficient collection of fluorescence emitted over all polar directions. Fluorescence lifetime is measured indirectly, by use of a technique based on the same principle as the one described in "Fluorometer for Analysis of Photosynthesis in Phytoplankton" (SSC-00110), NASA Tech Briefs, Vol. 24, No. 1 (November 2000), page 79. The excitation is modulated at a frequency of 70 MHz, and the phase shift between the excitation light and the emitted fluorescence is measured by a detection method in which the 70 MHz signal is down-converted to a 400 Hz signal. The fluorescence lifetime can be computed from the known relationship among the fluorescence lifetime, phase shift, and modulation frequency

Fernandez, Salvador M.↗

Separation of Single-Walled Carbon Nanotubes with DEP-FFF

A process using a modified dielectrophoresis device separates single-walled carbon nanotubes (SWNTs) according to their polarizability in electric fields. This depends on the size and dielectric constant of individual nanotubes and easily separates metallic from semiconducting nanotubes. Separation by length has also been demonstrated. Partial separation (enrichment) according to bandgap (which is linked to polarizability) has also been shown and can be improved to full separation of individual types of semiconducting SWNTs with better control over operational parameters and the length of SWNT starting material. This process and device can be scaled affordably to generate useful amounts of semiconducting SWNTs for electronic device development and production. In this study, a flow injection dielectrophoresis technique was used with a modified dielectrophoresis device. The length, width, and height of the modified chamber were 28, 2.5, and 0.025 cm, respectively. On the bottom of the chamber, there are two arrays of 50-m-wide, 2-m-thick gold electrodes, which are connected to an AC voltage generator and are alternately arranged so that every electrode is adjacent to two electrodes of the opposite polar. There is an additional plate electrode on the top of the chamber that is negatively biased. During the experiment, a syringe pump constantly pumps in the mobile phase, 1-percent sodium dodecylbenzene sulfonate (SDBS) solution, into the chamber. The frequency and voltage are set to 1 MHz and 10 V peak-to-peak, respectively. About 150 micro-L of SWNTs in 1- percent SDBS decanted solution are injected to the mobile phase through a septum near the entrance of the chamber. The flow rate of the mobile phase is set to 0.02 cu cm/min. The injected SWNTs sample flows through the chamber before it is lead into a fluorescence flow-through cell and collected for further analysis. The flow-through cell has three windows, thus allowing the fluorometer to collect fluorescence spectrum and visible absorption spectrums simultaneously. Dielectrophoresis field-flow fractionation (DEP-FFF) generally depends on interaction of a sedimentation force and DEP force for particle separation, and SWNTs are neutrally buoyant in water. In this innovation, the third electrode was added to create a sedimentation force based on DC electrophoresis. This makes this particular device applicable to separations on any neutrally buoyant particles in solution and a more general process for a broad range of nanomaterials sorting and separations.

Schmidt, Howard K.↗

Spectral and Temporal Laser Fluorescence Analysis Such as for Natural Aquatic Environments

An Advanced Laser Fluorometer (ALF) can combine spectrally and temporally resolved measurements of laser-stimulated emission (LSE) for characterization of dissolved and particulate matter, including fluorescence constituents, in liquids. Spectral deconvolution (SDC) analysis of LSE spectral measurements can accurately retrieve information about individual fluorescent bands, such as can be attributed to chlorophyll-a (Chl-a), phycobiliprotein (PBP) pigments, or chromophoric dissolved organic matter (CDOM), among others. Improved physiological assessments of photosynthesizing organisms can use SDC analysis and temporal LSE measurements to assess variable fluorescence corrected for SDC-retrieved background fluorescence. Fluorescence assessments of Chl-a concentration based on LSE spectral measurements can be improved using photo-physiological information from temporal measurements. Quantitative assessments of PBP pigments, CDOM, and other fluorescent constituents, as well as basic structural characterizations of photosynthesizing populations, can be performed using SDC analysis of LSE spectral measurements.

Chekalyuk, Alexander↗