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PubMed2002

Disruption of a DNA topoisomerase I gene affects morphogenesis in Arabidopsis.

The genesis of phyllotaxis, which often is associated with the Fibonacci series of numbers, is an old unsolved puzzle in plant morphogenesis. Here, we show that disruption of an Arabidopsis topoisomerase (topo) I gene named TOP1alpha affects phyllotaxis and plant architecture. The divergence angles and internode lengths between two successive flowers were more random in the top1alpha mutant than in the wild type. The top1alpha plants sporadically produced multiple flowers from one node, and the number of floral organ primordia often was different. The mutation also caused the twisting of inflorescences and individual flowers and the serration of leaf margins. These morphological abnormalities indicate that TOP1alpha may play a critical role in the maintenance of a regular pattern of organ initiation. The top1alpha mutant transformed with the RNA interference construct for TOP1beta, another topo I gene arrayed tandemly with TOP1alpha, was found to be lethal at young seedling stages, suggesting that topo I activity is essential in plants.

Amino Acid Sequence↗

PubMed1974

Potassium flux and leaf movement in Samanea saman. II. Phytochrome controlled movement.

Phytochrome, a membrane-localized biliprotein whose conformation is shifted reversibly by brief red or far-red light treatments, interacts with the rhythmic oscillator to regulate leaflet movement and potassium flux in pulvinal motor cells of Samanea. Darkened pinnae exposed briefly to red light (high P(fr) level) have less potassium in motor cells in the extensor region, more potassium in motor cells in the flexor region, and smaller angles than those exposed to far-red light (low P(fr) level). Increase in temperature from 24 degrees to 37 degrees increases the differential effect of the light treatments during opening (the energetic phase) but not during closure, implying that phytochrome controls an energetic process. It seems likely that phytochrome interacts with rhythmically controlled potassium pumps in flexor and extensor cells. During nyctinastic closure of white-illuminated pinnae, exposure to far-red light before darkening results in larger angles than does exposure to red. As in rhythmic opening, the angles of all pinnae and the differential effect of the light treatments increases with increasing temperature.

Bile Pigments↗

PubMed1981

Estimation of protein turnover in soybean leaves using magic angle double cross-polarization nitrogen 15 nuclear magnetic resonance.

Magic angle cross-polarization 15N nuclear magnetic resonance spectra of intact lyophilized soybean leaves have been obtained at 9.12 MHz. The leaves were harvested over a 6-week period from 15N-uniformly labeled plants exposed to 13CO2 for 1 to 7 days. The concentration of 13C-15N double labels in the main chains of leaf protein was determined nondestructively by double cross-polarization techniques. Both incorporation and turnover rates of these double labels were estimated and together lead to the conclusion that the protein of a mature, fully expanded soybean leaf is fairly long lived, with a half-life of about 30 days.

Kinetics↗

PubMed2004

MRI-based treatment planning for radiotherapy: dosimetric verification for prostate IMRT.

PURPOSE: Magnetic resonance (MR) and computed tomography (CT) image fusion with CT-based dose calculation is the gold standard for prostate treatment planning. MR and CT fusion with CT-based dose calculation has become a routine procedure for intensity-modulated radiation therapy (IMRT) treatment planning at Fox Chase Cancer Center. The use of MRI alone for treatment planning (or MRI simulation) will remove any errors associated with image fusion. Furthermore, it will reduce treatment cost by avoiding redundant CT scans and save patient, staff, and machine time. The purpose of this study is to investigate the dosimetric accuracy of MRI-based treatment planning for prostate IMRT. METHODS AND MATERIALS: A total of 30 IMRT plans for 15 patients were generated using both MRI and CT data. The MRI distortion was corrected using gradient distortion correction (GDC) software provided by the vendor (Philips Medical System, Cleveland, OH). The same internal contours were used for the paired plans. The external contours were drawn separately between CT-based and MR imaging-based plans to evaluate the effect of any residual distortions on dosimetric accuracy. The same energy, beam angles, dose constrains, and optimization parameters were used for dose calculations for each paired plans using a treatment optimization system. The resulting plans were compared in terms of isodose distributions and dose-volume histograms (DVHs). Hybrid phantom plans were generated for both the CT-based plans and the MR-based plans using the same leaf sequences and associated monitor units (MU). The physical phantom was then irradiated using the same leaf sequences to verify the dosimetry accuracy of the treatment plans. RESULTS: Our results show that dose distributions between CT-based and MRI-based plans were equally acceptable based on our clinical criteria. The absolute dose agreement for the planning target volume was within 2% between CT-based and MR-based plans and 3% between measured dose and dose predicted by the planning system in the physical phantom. CONCLUSIONS: Magnetic resonance imaging is a useful tool for radiotherapy simulation. Compared with CT-based treatment planning, MR imaging-based treatment planning meets the accuracy for dose calculation and provides consistent treatment plans for prostate IMRT. Because MR imaging-based digitally reconstructed radiographs do not provide adequate bony structure information, a technique is suggested for producing a wire-frame image that is intended to replace the traditional digitally reconstructed radiographs that are made from CT information.

Humans↗

PubMed1984

Analysis and significance of gravity-induced asymmetric growth in the grass leaf-sheath pulvinus.

The negative gravitropic response in the grass leaf-sheath pulvinus is a consequence of cell elongation involving all cells except those of the uppermost region of the upper flank of an horizontally oriented pulvinus. The lowermost layer of cells elongate maximally, and the regions in between elongate to intermediate extents. The resulting curvatures of a responding pulvinus can be expressed mathematically by relating the angle of curvature (theta) to the original length (L0) and the maximal length of the lower surface (L1) and the diameter of the organ (D), using the equation, theta = (L1-L0)/D, where theta is in radians. The elongation response (S) of any individual cells within the pulvinus can be expressed by the equation, S = 0.5 - r cos theta, where r is the radius of the pulvinus and theta is in degrees. Microscopic measurement of cell lengths in different regions of the pulvinus supports the mathematical predictions. Indirect support is also obtained from the use of colchicine, coumarin, dichlorobenzonitrile (DCBN) and isopropyl N-chlorophenyl carbamate which exaggerate the inherent asymmetry during gravitropic response. Coumarin and DCBN also induce thickenings in the radial walls which appear first in the statenchyma, and later, in cells located towards the outer periphery of the pulvinus. The distribution patterns of these thickenings suggest that the asymmetric growth response of the pulvinus may be due to a differential and radial, centrifugal transport of growth promotors from the central statenchyma region.

Avena↗

PubMed2005

Doppler-shift compensation in the Taiwanese leaf-nosed bat (Hipposideros terasensis) recorded with a telemetry microphone system during flight.

Biosonar behavior was examined in Taiwanese leaf-nosed bats (Hipposideros terasensis; CF-FM bats) during flight. Echolocation sounds were recorded using a telemetry microphone mounted on the bat's head. Flight speed and three-dimensional trajectory of the bat were reconstructed from images taken with a dual high-speed video camera system. Bats were observed to change the intensity and emission rate of pulses depending on the distance from the landing site. Frequencies of the dominant second harmonic constant frequency component (CF2) of calls estimated from the bats' flight speed agreed strongly with observed values. Taiwanese leaf-nosed bats changed CF2 frequencies depending on flight speed, which caused the CF2 frequencies of the Doppler-shifted echoes to remain constant. Pulse frequencies were also estimated using echoes returning directly ahead of the bat and from its sides for two different flight conditions: landing and U-turn. Bats in flight may periodically alter their attended angles from the front to the side when emitting echolocation pulses.

Acoustics↗

PubMed1988

Diameters and dry weights of tree shoots: effects of Young's modulus, taper, deflection and angle.

The structural theory for cantilever beams was used to calculate the diameters and dry weights of wood that unbranched shoots must produce to support their own weights. The study was done on Picea sitchensis (Bong.) Carr., Pinus contorta Dougl., Larix decidua Mill. and Betula pendula Roth. syn. verrucosa Ehrh. The weights of wood increased in a non-linear fashion with increase in shoot length. A large investment in wood (as measured by diameter and dry weight) was required to maintain a small endpoint deflection (1-5% of the length). By contrast, the degree of linear taper had only a small effect on support costs, as did the Young's modulus of the wood (over the range 1-4 GPa) and the angle of the shoot from the horizontal (over the range 0-45 degrees ). Current year's shoots on young trees of P. sitchensis and P. contorta incur a high support cost in order to maintain small (1-5%) deflections throughout the year: similar shoots of L. decidua and B. pendula have smaller support costs because they deflect by about 20% after leaf expansion in spring.

Journal Article↗

PubMed2003

Evidence for cross-linking in tomato cutin using HR-MAS NMR spectroscopy.

Cutin is a polyester biopolymer component of plant leaf and fruit cuticles, most often associated with waxes and cuticular polysaccharides, and sometimes with another aliphatic biopolymer called cutan. Insolubility of these cuticular biopolymers has made it difficult to apply traditional analytical techniques for structure determination, because most techniques providing molecular level details require solubility. By using the relatively new technique of one and two-dimensional high-resolution magic angle spinning (HR-MAS) NMR spectroscopy, with added information from solid-state 13C NMR spectroscopy, detailed through-bond connectivities and assignments are made for cutin from Lycopersicon esculentum (tomato) fruit. Based on the data obtained, tomato cutin is found to be predominantly an aliphatic polyester with some olefinic and aromatic moieties, consistent with previous studies that employed various degradative approaches. Aside from esters, there are free primary and secondary alcohol groups, as well as free fatty acids. A significant finding is the presence of alpha-branched fatty acids/esters. Mid-chain hydroxyls appear to be generally unesterified, but esters of mid-chain hydroxyls have been identified. The alpha-branched fatty acids/esters and esters of mid-chain hydroxyls could point towards cross-linking.

Biopolymers↗

PubMed2000

The computation of forest leaf area index on slope using fish-eye sensors.

Leaf area index (LAI) measured with fish-eye sensors is inevitably affected by slope. In order to quantify this effect, LAIs measured in contrasted forests were corrected for slope. Digitised hemispherical photographs were analysed to compute LAI according to azimuth and as a function of slope. The topographic mask (part of hemisphere obstructed by slope) and the path length of a ray of light at a given zenith angle (longer upslope and shorter downslope) were taken into account. Results indicate a strong slope effect, both in temperate conifer forest plantation and in tropical rain forest. On regular slope, this effect is easily corrected, although the topographic mask affects data. On irregular topography, corrected and uncorrected LAIs strongly differ, suggesting a need for reference measurements; corrected figures appear nevertheless realistic and normality is reached only for corrected values. LAIs should systematically be corrected for slope above 15-20 degrees, more so if topography is irregular or the forest cover heterogeneous.

Cycadopsida↗

PubMed2006

Application of a new leaf area index algorithm to China's landmass using MODIS data for carbon cycle research.

An operational system was developed for mapping the leaf area index (LAI) for carbon cycle models from the moderate resolution imaging spectroradiometer (MODIS) data. The LAI retrieval algorithm is based on Deng et al. [2006. Algorithm for global leaf area index retrieval using satellite imagery. IEEE Transactions on Geoscience and Remote Sensing, 44, 2219-2229], which uses the 4-scale radiative transfer model [Chen, J.M., Leblancs, 1997. A 4-scale bidirectional reflection model based on canopy architecture. IEEE Transactions on Geoscience and Remote Sensing, 35, 1316-1337] to simulate the relationship of LAI with vegetated surface reflectance measured from space for various spectral bands and solar and view angles. This algorithm has been integrated to the MODISoft platform, a software system designed for processing MODIS data, to generate 250 m, 500 m and 1 km resolution LAI products covering all of China from MODIS MOD02 or MOD09 products. The multi-temporal interpolation method was implemented to remove the residual cloud and other noise in the final LAI product so that it can be directly used in carbon models without further processing. The retrieval uncertainties from land cover data were evaluated using five different data sets available in China. The results showed that mean LAI discrepancies can reach 27%. The current product was also compared with the NASA MODIS MOD15 LAI product to determine the agreement and disagreement of two different product series. LAI values in the MODIS product were found to be 21% larger than those in the new product. These LAI products were compared against ground TRAC measurements in forests in Qilian Mountain and Changbaishan. On average, the new LAI product agrees with the field measurement in Changbaishan within 2%, but the MODIS product is positively biased by about 20%. In Qilian Mountain, where forests are sparse, the new product is lower than field measurements by about 38%, while the MODIS product is larger by about 65%.

Algorithms↗

PubMed1979

Ultrastructural observations on collagen and proteoglycans in the annulus fibrosus of the intervertebral disc.

Replicas of freeze-fractured collagen fibrils of peripheral and central parts of the annulus fibrosus of bovine intervertebral discs show microfibrils which run either arranged in parallel or in a helix with an inclination-angle ranging from 4 degrees to 8 degrees. According to results of freeze-fracutred tissues, thin sections of specimens treated with 4M guanidinium chloride show collagen fibrils with a parallel or a slightly wavy microfibrillar packing. Thin sections of specimens treated with alcian blue diluted in MgCl2 critical electrolyte solutions reveal interfibrillar proteoglycan particles with a filamentous shape in the peripheral zones of the annulus fibrosus and a predominant leaf-like appearance in the inner ones. These observations are discussed with reference to previous data concerning the variation in composition from the peripheral to the inner parts of the annulus fibrosus.

Animals↗

PubMed1986

Plasticity in shoot development: a biophysical view.

The construction and spacing of leaves can be analysed in terms of the direction of reinforcement in the walls of the organ surface. In general, growth is at right angles to the reinforcement. When, however, tissues are actively stretched by adjacent organs they apparently take on, by cell activity, reinforcement which lies in the direction of stretch. Thus reinforcement can dictate extension direction; extension direction, when imposed on a tissue, may dictate reinforcement direction. This proposed two-way relationship has been used to model the activity of shoot meristems. It produces biophysically plausible schemes for the progressive development of various leaf structures and for the cyclical revision of apical structure seen in various types of phyllotaxis.

Models, Biological↗

PubMed1998

Conversion of total leaf area to projected leaf area in lodgepole pine and Douglas-fir.

Three definitions of leaf area index (LAI) in the literature have no predictable relationship with each other. Factors were derived for converting total LAI to projected LAI of horizontal leaves and to projected LAI for inclined leaves of lodgepole pine (Pinus contorta Dougl. var. latifolia Engelm.) and coastal Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) to allow comparison of results from different studies. An algorithm was derived to allow determination of these factors based on twig angles and the angles that the foliage subtends with the twig. Allowances were made for both the vertical and horizontal components of projection. The value of the factor for converting total LAI to projected LAI for inclined leaves was 0.229 + 0.0032 for lodgepole pine and 0.230 + 0.0037 for Douglas-fir. Sensitivity analysis established that this conversion factor was more sensitive to differences in vertical angles of the twigs than to twig rotation or foliar arrangement on the twig.

Journal Article↗

PubMed2003

Convolution/superposition using the Monte Carlo method.

The convolution/superposition calculations for radiotherapy dose distributions are traditionally performed by convolving polyenergetic energy deposition kernels with TERMA (total energy released per unit mass) precomputed in each voxel of the irradiated phantom. We propose an alternative method in which the TERMA calculation is replaced by random sampling of photon energy, direction and interaction point. Then, a direction is randomly sampled from the angular distribution of the monoenergetic kernel corresponding to the photon energy. The kernel ray is propagated across the phantom, and energy is deposited in each voxel traversed. An important advantage of the explicit sampling of energy is that spectral changes with depth are automatically accounted for. No spectral or kernel hardening corrections are needed. Furthermore, the continuous sampling of photon direction allows us to model sharp changes in fluence, such as those due to collimator tongue-and-groove. The use of explicit photon direction also facilitates modelling of situations where a given voxel is traversed by photons from many directions. Extra-focal radiation, for instance, can therefore be modelled accurately. Our method also allows efficient calculation of a multi-segment/multi-beam IMRT plan by sampling of beam angles and field segments according to their relative weights. For instance, an IMRT plan consisting of seven 14 x 12 cm2 beams with a total of 300 field segments can be computed in 15 min on a single CPU, with 2% statistical fluctuations at the isocentre of the patient's CT phantom divided into 4 x 4 x 4 mm3 voxels. The calculation contains all aperture-specific effects, such as tongue and groove, leaf curvature and head scatter. This contrasts with deterministic methods in which each segment is given equal importance, and the time taken scales with the number of segments. Thus, the Monte Carlo superposition provides a simple, accurate and efficient method for complex radiotherapy dose calculations.

Algorithms↗

PubMed2001

Independent dose calculations for the PEACOCK System.

An independent dose calculation method has been developed to validate intensity-modulated radiation therapy (IMRT) plans from the NOMOS PEACOCK System. After the plan is generated on the CORVUS planning system, the beam parameters are imported into an independent workstation. The beam parameters consist of intensity maps at each gantry angle and each arc position. In addition, CT scans of the patient are imported into the independent workstation to obtain the external contour of the patient. The coordinate system is defined relative to the alignment point chosen in the CORVUS plan. The independent calculation uses the pencil beam data viz tissue maximum ratio (TMR) and beam profiles for a single 1 x 0.8-cm beamlet formed by the NOMOS multileaf intensity-modulating collimator (MIMiC) leaf. The pencil beam data were measured for the 6-MV photon beam from Siemens PRIMUS linear accelerator using film dosimetry. The dose at a point is calculated using the depth and off-axis distance from a given pencil beam, corrected for its beam intensity. Isodose distributions are generated using the independent dose calculations and compared to the CORVUS plans. Isodose distributions show good agreement with the CORVUS plans for a number of clinical cases. The independent dose calculation algorithm is described in this paper.

Algorithms↗

PubMed1982

Analysis of strain-induced EPR-line shapes and anisotropic spin-lattice relaxation in a [2Fe-2S] ferredoxin.

The electron paramagnetic resonance spectrum of the [2Fe-2S]1+(2+;1+) cluster in spinach-leaf ferredoxin has been measured at four microwave frequencies from 1 to 35 GHz. Using a modified g-strain formula, the asymmetrical spectrum has been simulated in detail without the assumption of signal multiplicity. In all but the lowest frequency bands the line width is dominated by an extremely anisotropic g-shift distribution, caused by a statistical distribution in dislocation strains. The crossover point of domination by unresolved proton splittings is around 2 GHz. The angle-dependent elasticity of the cluster can be related to an anisotropy in the spin-lattice relaxation rate. Intensity behaviour under continuous saturation, at temperatures in the two-phonon region, is in qualitative agreement with elementary theory. On the basis of these results it is argued that biochemists should be aware of the questionable nature of some ad hoc assumptions commonly made to interpret EPR of metalloproteins. Specifically, a physically meaningful determination of the number and stoicheiometry of distinguishable compounds, represented in a complex spectrum, may well require more advanced theoretical tools than the frequently employed deconvolution in symmetrical Gaussians with associated unique relaxation times.

Electron Spin Resonance Spectroscopy↗

PubMed2006

Scion-rootstock interaction affects the physiology and fruit quality of sweet cherry.

Water relations, leaf gas exchange, chlorophyll a fluorescence, light canopy transmittance, leaf photosynthetic pigments and metabolites and fruit quality indices of cherry cultivars 'Burlat', 'Summit' and 'Van' growing on five rootstocks with differing size-controlling potentials that decrease in the order: Prunus avium L. > CAB 11E > Maxma 14 > Gisela 5 > Edabriz, were studied during 2002 and 2003. Rootstock genotype affected all physiological parameters. Cherry cultivars grafted on invigorating rootstocks had higher values of midday stem water potential (Psi(MD)), net CO(2) assimilation rate (A), stomatal conductance (g(s)), intercellular CO(2) concentration (C(i)) and maximum photochemical efficiency of photosystem II (PSII) (F(v)/F(m)) than cultivars grafted on dwarfing rootstocks. The Psi(MD) was positively correlated with A, g(s) and C(i). Moreover, A was positively correlated with g(s), and the slopes of the linear regression increased from invigorating to dwarfing rootstocks, indicating a stronger regulation of photosynthesis by stomatal aperture in trees on dwarfing Edabriz and Gisela 5. The effect of rootstock genotype was also statistically significant for leaf photosynthetic pigments, whereas metabolite concentrations and fruit physicochemical characteristics were more dependent on cultivar genotype. Among cultivars, 'Burlat' leaves had the lowest concentrations of photosynthetic pigments, but were richest in total soluble sugars, starch and total phenols. Compared with the other cultivars, 'Summit' had heavier fruits, independent of the rootstock. 'Burlat' cherries were less firm and had lower concentrations of soluble sugars and a lower titratable acidity than 'Van' cherries. Nevertheless, 'Van' cherries had lower lightness, chroma and hue angle, representing redder and darker cherries, compared with 'Summit' fruits. In general, Psi(MD) was positively correlated with fruit mass and A was negatively correlated with lightness and chroma. These results demonstrate that: (1) water relations and photosynthesis of sweet cherry tree are mainly influenced by the rootstock genotype; (2) different physicochemical characteristics observed in cherries of the three cultivars suggest that regulation of fruit quality was mainly dependent on the cultivar genotype, although the different size-controlling rootstocks also had a significant effect.

Chlorophyll↗

PubMed2002

Discrimination of closed shapes by two species of bee, Apis mellifera and Megachile rotundata.

In the present study, the performance of two bee species, the honeybee Apis mellifera and the leaf-cutter bee Megachile rotundata, in discriminating among various closed (convex) shapes was examined systematically for the first time. Bees were trained to each of five different shapes, a disc, a square, a diamond and two different triangles, all of the same area, using fresh bees in each experiment. In subsequent tests, the trained bees were given a choice between the learned shape and each of the other four shapes. Two sets of experiments were conducted with both species. In the first, solid black shapes were presented against a white background, thus providing a high luminance contrast. In the second, the shapes carried a random black-and-white pattern and were presented 5 cm in front of a similar pattern, thus producing motion contrast, rather than luminance contrast, against the background. The results obtained with the solid shapes reveal that both bee species accomplish the discrimination, although the performance of the honeybee is significantly better than that of the leaf-cutter bee. Furthermore, the effectiveness of the various shapes differs between the two species. However, in neither species is the discrimination performance correlated with the amount of overlap of the black areas contained in the various pairs of shapes, suggesting that, in our experiments, shape discrimination is not based on a template-matching process. We propose that it is based on the use of local parameters situated at the outline of the shape, such as the position of angles or acute points and, in particular, the position and orientation of edges. This conclusion is supported by the finding that bees of both species accomplish the discrimination even with the patterned shapes. These shapes are visible only because of the discontinuity of the speed of image motion perceived at the edge between the shape and the background.

Animals↗