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At least 217 records · Page 12

Statistical and linguistic features of DNA sequences

We present evidence supporting the idea that the DNA sequence in genes containing noncoding regions is correlated, and that the correlation is remarkably long range--indeed, base pairs thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationary" feature of the sequence of base pairs by applying a new algorithm called Detrended Fluctuation Analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and noncoding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to all eukaryotic DNA sequences (33 301 coding and 29 453 noncoding) in the entire GenBank database. We describe a simple model to account for the presence of long-range power-law correlations which is based upon a generalization of the classic Levy walk. Finally, we describe briefly some recent work showing that the noncoding sequences have certain statistical features in common with natural languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts, and the Shannon approach to quantifying the "redundancy" of a linguistic text in terms of a measurable entropy function. We suggest that noncoding regions in plants and invertebrates may display a smaller entropy and larger redundancy than coding regions, further supporting the possibility that noncoding regions of DNA may carry biological information.

Non-NASA Center↗

Bioregenerative life-support systems

Long-duration future habitation of space involving great distances from Earth and/or large crew sizes (eg, lunar outpost, Mars base) will require a controlled ecological life-support system (CELSS) to simultaneously revitalize atmosphere (liberate oxygen and fix carbon dioxide), purify water (via transpiration), and generate human food (for a vegetarian diet). Photosynthetic higher plants and algae will provide the essential functions of biomass productivity in a CELSS, and a combination of physicochemical and bioregenerative processes will be used to regenerate renewable resources from waste materials. Crop selection criteria for a CELSS include nutritional use characteristics as well as horticultural characteristics. Cereals, legumes, and oilseed crops are used to provide the major macronutrients for the CELSS diet. A National Aeronautics and Space Administration (NASA) Specialized Center of Research and Training (NSCORT) was established at Purdue University to establish proof of the concept of the sustainability of a CELSS. The Biosphere 2 project in Arizona is providing a model for predicted and unpredicted situations that arise as a result of closure in a complex natural ecosystem.

NASA Discipline Life Support Systems↗

The gravitational plant physiology facility-Description of equipment developed for biological research in spacelab

In January 1992, the NASA Suttle mission STS 42 carried a facility designed to perform experiments on plant gravi- and photo-tropic responses. This equipment, the Gravitational Plant Physiology Facility (GPPF) was made up of a number of interconnected units mounted within a Spacelab double rack. The details of these units and the plant growth containers designed for use in GPPF are described. The equipment functioned well during the mission and returned a substantial body of time-lapse video data on plant responses to tropistic stimuli under conditions of orbital microgravity. GPPF is maintained by NASA Ames Research Center, and is flight qualifiable for future spacelab missions.

Heathcote, D. G.↗

Heat dissipation in controlled environment enclosures through the application of water screens

The use of plate glass-water thermal barriers in controlled environment facilities effectively reduces the thermal load within the plant growth chamber. This allows high PPFs to be provided for plant growth and development studies, adequate simulation of daily light integrals, and simulation of peak PPF's. Further, substantial amounts of incandescent lamp supplementation can be used to achieve simulation of daylight R:FR ratios which are needed to ensure adequate stem development in some species. While the focus in this paper is on the use of entire thermal barriers which separate the lighting enclosure from the plant growth chamber, the same principles apply to the use of water jackets for cooling individual lamps (such as can occur with xenon-arc lamps). In this instance, the barrier separating the lamps from the plant chamber can be much simpler (e.g., plexiglass) as the main function of the barrier is to separate the air ventilation of the lamp enclosure from the air system within the plant growth chamber. The main advantage of water as a thermal barrier is the negligible absorption of radiation in the photosynthetically-active and near infrared wavebands. Consequently, plate glass-water barriers typically allow transmission of approximately 90% of radiation in these regions. While ventilated double and triple glazing systems appear to be attractive alternative to water barriers from an operating standpoint, their significant absorption in the biologically-important wavebands (7 - 12%) with each glass layer and longer-wave cut-offs (typically 2500 - 4000 nm) makes them a much less attractive alternative. The data presented here demonstrate clearly that measurement of PPF alone is not an adequate representation of the radiation environment being used in a controlled environment study. The amounts and proportions of long-wave and short-wave radiation in a plant growth chamber are dependent on lamp type, lamp combination, presence of a thermal barrier, the type of thermal barrier between the lamps and the plant growing area and the overall construction and design of the chamber. It is important, therefore, in reporting results of controlled environment studies, to adequately describe both the details of the lighting system used and the characteristics of the radiation produced by that system, so results of different studies can be adequately evaluated and compared.

Warrington, I. J.↗

Assessing Vegetation Function with Imaging Spectroscopy

Healthy vegetation function supports diverse biological communities and ecosystem processes, and provides crops, forest products, forage, and countless other benefits. Vegetation function can be assessed by examining dynamic processes and by evaluating plant traits, which themselves are dynamic. Using both trait-based and process-based approaches, spectroscopy can assess vegetation function at multiple scales using a variety of sensors and platforms ranging from proximal to airborne and satellite measurements. Since spectroscopic data are defined by the instruments and platforms available, along with their corresponding spatial, temporal and spectral scales, and since these scales may not always match those of the function of interest, consideration of scale is a necessary focus. For a full understanding of vegetation processes, combined (multi-scale) sampling methodsusing empirical and theoretical approaches are required, along with improved informatics.

Gamon, J. A.↗

Parameterization of albedo, thermal inertia, and surface roughness of desert scrub/sandy soil surface

Spectral albedo, A sub n, for the direct solar beam is defined as A sub n (r sub i,s, theta sub 0) = r sub i exp(-s tan theta sub 0)1-I(s) where I(s) is the integral over all reflection angles describing the interception by the absorbing plants of the flux reflected from the soil, r sub i soil reflectance, assumed Lambertian, S the projection on a vertical plane of plants per unit surface area, and theta sub 0 is the solar zenith angle. Hemispheric reflectance for the direct solar beam equals 1-I(s) times the reflectance to the zenith. The values of s of 0.1, 0.2, and 0.3 respectively quantify sparse, moderately dense, and very dense desert scrub. Thin plants are assumed to be of negligible thermal inertia, and thus directly yield the absorbed insolation to the atmosphere. Surface thermal inertia is therefore effectively reduced. The ratio of surface roughness height to plant height is parameterized for sparse, moderately dense, and very dense desert-scrub as a function of s based on data expressing the dependence of this ratio on plant silhouette.

Otterman, J.↗

Gravitational studies in cellular and developmental biology

The paucity of data on the role of gravity in cellular and developmental biology has been examined, and a hypothesis has been generated that unifies potential gravity sensitivity in both plant and animal systems. This hypothesis considers the macromolecular order and functional importance of the extracellular matrix compartment, the intracellular cytoskeleton compartment, and the connecting plasma membrane-signal transduction compartment of plant and animal systems as potentially sensitive to alterations in the unit gravity environment in which they evolved.

NASA Discipline Developmental Biology↗

The Total Synthesis Problem of linear multivariable control. II - Unity feedback and the design morphism

Zames (1981) has observed that there is, in general, no 'separation principle' to guarantee optimality of a division between control law design and filtering of plant uncertainty. Peczkowski and Sain (1978) have solved a model matching problem using transfer functions. Taking into consideration this investigation, Peczkowski et al. (1979) proposed the Total Synthesis Problem (TSP), wherein both the command/output-response and command/control-response are to be synthesized, subject to the plant constraint. The TSP concept can be subdivided into a Nominal Design Problem (NDP), which is not dependent upon specific controller structures, and a Feedback Synthesis Problem (FSP), which is. Gejji (1980) found that NDP was characterized in terms of the plant structural matrices and a single, 'good' transfer function matrix. Sain et al. (1981) have extended this NDP work. The present investigation is concerned with a study of FSP for the unity feedback case. NDP, together with feedback synthesis, is understood as a Total Synthesis Problem.

Sain, M. K.↗

Experimental test of plant canopy reflectance models on cotton

Spectroradiometric data on the bidirectional reflectance function was collected for a cotton canopy as a function of observer zenith angle, observer angle, and solar zenith angle. The area under study was about 40 miles from the Gulf of Mexico and the prevailing winds blew inland such that cloud formation increased during the day. The standard reflectance panel was constructed of plywood that had been spray painted with a flat white latex paint. Physical and optical plant parameters were measured. A time lapse mechanism was constructed to operate a 16 mm movie camera such that single frames could be exposed at intervals of one per second up to one per hour. Data were digitized from a strip chart recorder and reflectance panel measurements.

Lemaster, E. W.↗

Immunological and biochemical evidence for nuclear localization of annexin in peas

Immunofluorescent localization of annexins using an anti-pea annexin polyclonal antibody (anti-p35) in pea (Pisum sativum) leaf and stem epidermal peels showed staining of the nuclei and the cell periphery. Nuclear staining was also seen in cell teases prepared from pea plumules. The amount of nuclear stain was reduced both by fixation time and by dehydration and organic solvent treatment. Observation with confocal microscopy demonstrated that the anti-p35 stain was diffusely distributed throughout the nuclear structure. Immunoblots of purified nuclei, nuclear envelope matrix, nucleolar, and chromatin fractions showed a cross-reactive protein band of 35 kDa. These data are the first to show annexins localized in plant cell nuclei where they may play a role in nuclear function.

Non-NASA Center↗

The dynamics and control of large flexible space structures, 8

A development of the in plane open loop rotational equations of motion for the proposed Spacecraft Control Laboratory Experiment (SCOLE) in orbit configuration is presented based on an Eulerian formulation. The mast is considered to be a flexible beam connected to the (rigid) shuttle and the reflector. Frequencies and mode shapes are obtained for the mast vibrational appendage modes (assumed to be decoupled) for different boundary conditions based on continuum approaches and also preliminary results are obtained using a finite element representation of the mast reflector system. The linearized rotational in plane equation is characterized by periodic coefficients and open loop system stability can be examined with an application of the Floquet theorem. Numerical results are presented to illustrate the potential instability associated with actuator time delays even for delays which represent only a small fraction of the natural period of oscillation of the modes contained in the open loop model of the system. When plant and measurement noise effects are added to the previously designed deterministic model of the hoop column system, it is seen that both the system transient and steady state performance are degraded. Mission requirements can be satisfied by appropriate assignment of cost function weighting elements and changes in the ratio of plant noise to measurement noise.

Bainum, P. M.↗

Hydrogen peroxide homeostasis: activation of plant catalase by calcium/calmodulin

Environmental stimuli such as UV, pathogen attack, and gravity can induce rapid changes in hydrogen peroxide (H(2)O(2)) levels, leading to a variety of physiological responses in plants. Catalase, which is involved in the degradation of H(2)O(2) into water and oxygen, is the major H(2)O(2)-scavenging enzyme in all aerobic organisms. A close interaction exists between intracellular H(2)O(2) and cytosolic calcium in response to biotic and abiotic stresses. Studies indicate that an increase in cytosolic calcium boosts the generation of H(2)O(2). Here we report that calmodulin (CaM), a ubiquitous calcium-binding protein, binds to and activates some plant catalases in the presence of calcium, but calcium/CaM does not have any effect on bacterial, fungal, bovine, or human catalase. These results document that calcium/CaM can down-regulate H(2)O(2) levels in plants by stimulating the catalytic activity of plant catalase. Furthermore, these results provide evidence indicating that calcium has dual functions in regulating H(2)O(2) homeostasis, which in turn influences redox signaling in response to environmental signals in plants.

NASA Discipline Plant Biology↗

Spaceflight exposure effects on transcription, activity, and localization of alcohol dehydrogenase in the roots of Arabidopsis thaliana

Although considerable research and speculation have been directed toward understanding a plant's perception of gravity and the resulting gravitropic responses, little is known about the role of gravity-dependent physical processes in normal physiological function. These studies were conducted to determine whether the roots of plants exposed to spaceflight conditions may be experiencing hypoxia. Arabidopsis thaliana (L.) Heynh. plants were grown in agar medium during 6 or 11 d of spaceflight exposure on shuttle missions STS-54 (CHROMEX-03) and STS-68 (CHROMEX-05), respectively. The analysis included measurement of agar redox potential and root alcohol dehydrogenase (ADH) activity, localization, and expression. ADH activity increased by 89% as a result of spaceflight exposure for both CHROMEX-03 and -05 experiments, and ADH RNase protection assays revealed a 136% increase in ADH mRNA. The increase in ADH activity associated with the spaceflight roots was realized by a 28% decrease in oxygen availability in a ground-based study; however, no reduction in redox potential was observed in measurements of the spaceflight bulk agar. Spaceflight exposure appears to effect a hypoxic response in the roots of agar-grown plants that may be caused by changes in gravity-mediated fluid and/or gas behavior.

STS-68 Shuttle Project↗

New genes and new biological roles for expansins

Expansins are extracellular proteins that loosen plant cell walls in novel ways. They are thought to function in cell enlargement, pollen tube invasion of the stigma (in grasses), wall disassembly during fruit ripening, abscission and other cell separation events. Expansins are encoded by two multigene families and each gene is often expressed in highly specific locations and cell types. Structural analysis indicates that one expansin region resembles the catalytic domain of family-45 endoglucanases but glucanase activity has not been detected. The genome projects have revealed numerous expansin-related sequences but their putative wall-loosening functions remain to be assessed.

NASA Program Fundamental Space Biology↗

Device for Automated Cutting and Transfer of Plant Shoots

A device that enables the automated cutting and transfer of plant shoots is undergoing development for use in the propagation of plants in a nursery or laboratory. At present, it is standard practice for a human technician to use a knife and forceps to cut, separate, and grasp a plant shoot. The great advantage offered by the present device is that its design and operation are simpler than would be those of a device based on the manual cutting/separation/grasping procedure. [The present device should not be confused with a prior device developed for partly the same purpose and described in Compliant Gripper for a Robotic Manipulator (NPO-21104), NASA Tech Briefs, Vol. 27, No. 3 (March 2003), page 59.]. The device (see figure) includes a circular tube sharpened at its open (lower) end and mounted on a robotic manipulator at its closed (upper) end. The robotic manipulator simply pushes the sharpened open end of the tube down onto a bed of plants and rotates a few degrees clockwise then counterclockwise about the vertical axis, causing the tube to cut a cylindrical plug of plant material. Exploiting the natural friction between the tube and plug, the tube retains the plug, without need for a gripping mechanism and control. The robotic manipulator then retracts the tube, translates it to a new location over a plant-growth tray, and inserts the tube part way into the growth medium at this location in the tray. A short burst of compressed air is admitted to the upper end of the tube to eject the plug of plant material and drive it into the growth medium. A prototype has been tested and verified to function substantially as intended. It is projected that in the fully developed robotic plant-propagation system, the robot control system would include a machine- vision subsystem that would automatically guide the robotic manipulator in choosing the positions from which to cut plugs of plant material. Planned further development efforts also include more testing and refinement of the design and operation described above.

Cipra, Raymond↗

Estimation of X-band scattering properties of tree components

An X-band FM-CW very fine range resolution scatterometer was used to acquire backscattering data for a number of tree species. Using a model to describe the scattering source function and an experimental procedure for selected removal of plant parts allows the estimation of the volume backscatter coefficient and the volume extinction coefficient. It is found that: (1) leaves are strong attenuators as well as scatterers; (2) the albedo at a given angle of incidence is nearly independent of the tree type; (3) the tree limbs are good attenuators but rather poor scatterers; and (4) the albedo changes as a function of the angle of incidence and for deciduous trees is also a function of the season.

Pitts, D. E.↗

A separation theorem for the stochastic sampled-data LQG problem

This paper considers the control of a continuous linear plant disturbed by white plant noise when the control is constrained to be a piecewise constant function of time; i.e. a stochastic sampled-data system. The cost function is the integral of quadratic error terms in the state and control, thus penalizing errors at every instant of time while the plant noise disturbs the system continuously. The problem is solved by reducing the constrained continuous problem to an unconstrained discrete one. It is shown that the separation principle for estimation and control still holds for this problem when the plant disturbance and measurement noise are Gaussian.

Halyo, N.↗

Functional relation among subpixel canopy cover, ground shadow, and illuminated ground at large sampling scales

The functional relation among subpixel canopy cover, illuminated soil, and shadowed soil, which progressively develops with increasing pixel size, is investigated for Poisson distributed plants using a geometric canopy simulation model. An analytical relation among cover components is shown to be applicable when the scale of the pixel is much larger than the scale of the plant and ground shadow. The analysis is facilitated through the use of a nondimensional solar-geometric similarity parameter, eta, equal to the ratio of the area of one plant canopy to its associated ground shadow area, as viewed from nadir. A sampling scale ratio, defined as the ratio of the area of the pixel to the mean area of a single plant shadow, is tested as a quantitative criterion to evaluate when the functional relation among subpixel components occurs. The results of a remote sensing experiment over a natural conifer landscape provide preliminary confirmation of the theoretical analysis.

Jasinski, Michael F.↗