Three members of a novel small gene-family from Arabidopsis thaliana able to complement functionally an Escherichia coli mutant defective in PAPS reductase activity encode proteins with a thioredoxin-like domain and “APS reductase” activity

Three different cDNAs, Prh-19, Prh-26, and Prh-43 [3′-phosphoadenosine-5′-phosphosulfate (PAPS) reductase homolog], have been isolated by complementation of an Escherichia coli cysH mutant, defective in PAPS reductase activity, to prototrophy with an Arabidopsis thaliana cDNA library in the expression vector λYES. Sequence analysis of the cDNAs revealed continuous open reading frames encoding polypeptides of 465, 458, and 453 amino acids, with calculated molecular masses of 51.3, 50.5, and 50.4 kDa, respectively, that have strong homology with fungal, yeast, and bacterial PAPS reductases. However, unlike microbial PAPS reductases, each PRH protein has an N-terminal extension, characteristic of a plastid transit peptide, and a C-terminal extension that has amino acid and deduced three-dimensional homology to thioredoxin proteins. Adenosine 5′-phosphosulfate (APS) was shown to be a much more efficient substrate than PAPS when the activity of the PRH proteins was tested by their ability to convert 35S-labeled substrate to acid-volatile 35S-sulfite. We speculate that the thioredoxin-like domain is involved in catalytic function, and that the PRH proteins may function as novel “APS reductase” enzymes. Southern hybridization analysis showed the presence of a small multigene family in the Arabidopsis genome. RNA blot hybridization with gene-specific probes revealed for each gene the presence of a transcript of ≈1.85 kb in leaves, stems, and roots that increased on sulfate starvation. To our knowledge, this is the first report of the cloning and characterization of plant genes that encode proteins with APS reductase activity and supports the suggestion that APS can be utilized directly, without activation to PAPS, as an intermediary substrate in reductive sulfate assimilation.

A numerical strategy for efficient modeling of the equatorial wave guide

Convection in the tropics is observed to involve a wide-ranging hierarchy of scales from a few kilometers to the planetary scales and also has a profound impact on short-term climate. The mechanisms responsible for this behavior present a major unsolved problem. A promising emerging approach to address these issues is cloud-resolving modeling. Here a family of numerical models is introduced specifically to model the feedback of small-scale deep convection on tropical planetary waves and tropical circulation in a highly efficient manner compatible with the approach through cloud-resolving modeling. Such a procedure is also useful for theoretical purposes. The basic idea in the approach is to use low-order truncation in the meriodonal direction through Gauss–Hermite quadrature projected onto a simple discrete radiation condition. In this fashion, the cloud-resolving modeling of equatorially trapped planetary waves reduces to the solution of a small number of purely zonal two-dimensional wave systems along a few judiciously chosen meriodonal layers that are coupled only by some additional source terms. The approach is analyzed in detail with full mathematical rigor for linearized equatorial primitive equations with source terms.

A New Model for Nuclear Envelope BreakdownV⃞

Nuclear envelope breakdown was investigated during meiotic maturation of starfish oocytes. Fluorescent 70-kDa dextran entry, as monitored by confocal microscopy, consists of two phases, a slow uniform increase and then a massive wave. From quantitative analysis of the first phase of dextran entry, and from imaging of green fluorescent protein chimeras, we conclude that nuclear pore disassembly begins several minutes before nuclear envelope breakdown. The best fit for the second phase of entry is with a spreading disruption of the membrane permeability barrier determined by three-dimensional computer simulations of diffusion. We propose a new model for the mechanism of nuclear envelope breakdown in which disassembly of the nuclear pores leads to a fenestration of the nuclear envelope double membrane.

Signals and signs in the nervous system: The dynamic anatomy of electrical activity is probably information-rich

The dichotomy between two groups of workers on neuroelectrical activity is retarding progress. To study the interrelations between neuronal unit spike activity and compound field potentials of cell populations is both unfashionable and technically challenging. Neither of the mutual disparagements is justified: that spikes are to higher functions as the alphabet is to Shakespeare and that slow field potentials are irrelevant epiphenomena. Spikes are not the basis of the neural code but of multiple codes that coexist with nonspike codes. Field potentials are mainly information-rich signs of underlying processes, but sometimes they are also signals for neighboring cells, that is, they exert influence. This paper concerns opportunities for new research with many channels of wide-band (spike and slow wave) recording. A wealth of structure in time and three-dimensional space is different at each scale—micro-, meso-, and macroactivity. The depth of our ignorance is emphasized to underline the opportunities for uncovering new principles. We cannot currently estimate the relative importance of spikes and synaptic communication vs. extrasynaptic graded signals. In spite of a preponderance of literature on the former, we must consider the latter as probably important. We are in a primitive stage of looking at the time series of wide-band voltages in the compound, local field, potentials and of choosing descriptors that discriminate appropriately among brain loci, states (functions), stages (ontogeny, senescence), and taxa (evolution). This is not surprising, since the brains in higher species are surely the most complex systems known. They must be the greatest reservoir of new discoveries in nature. The complexity should not deter us, but a dose of humility can stimulate the flow of imaginative juices.

Mapping the universe in three dimensions

The determination of the three-dimensional layout of galaxies is critical to our understanding of the evolution of galaxies and the structures in which they lie, to our determination of the fundamental parameters of cosmology, and to our understanding of both the past and future histories of the universe at large. The mapping of the large scale structure in the universe via the determination of galaxy red shifts (Doppler shifts) is a rapidly growing industry thanks to technological developments in detectors and spectrometers at radio and optical wavelengths. First-order application of the red shift-distance relation (Hubble’s law) allows the analysis of the large-scale distribution of galaxies on scales of hundreds of megaparsecs. Locally, the large-scale structure is very complex but the overall topology is not yet clear. Comparison of the observed red shifts with ones expected on the basis of other distance estimates allows mapping of the gravitational field and the underlying total density distribution. The next decade holds great promise for our understanding of the character of large-scale structure and its origin.

Corneal collagen fibril structure in three dimensions: Structural insights into fibril assembly, mechanical properties, and tissue organization

The ability of the cornea to transmit light while being mechanically resilient is directly attributable to the formation of an extracellular matrix containing orthogonal sheets of collagen fibrils. The detailed structure of the fibrils and how this structure underpins the mechanical properties and organization of the cornea is understood poorly. In this study, we used automated electron tomography to study the three-dimensional organization of molecules in corneal collagen fibrils. The reconstructions show that the collagen molecules in the 36-nm diameter collagen fibrils are organized into microfibrils (≈4-nm diameter) that are tilted by ≈15° to the fibril long axis in a right-handed helix. An unexpected finding was that the microfibrils exhibit a constant-tilt angle independent of radial position within the fibril. This feature suggests that microfibrils in concentric layers are not always parallel to each other and cannot retain the same neighbors between layers. Analysis of the lateral structure shows that the microfibrils exhibit regions of order and disorder within the 67-nm axial repeat of collagen fibrils. Furthermore, the microfibrils are ordered at three specific regions of the axial repeat of collagen fibrils that correspond to the N- and C-telopeptides and the d-band of the gap zone. The reconstructions also show macromolecules binding to the fibril surface at sites that correspond precisely to where the microfibrils are most orderly.

A numerical model for predicting shoreline changes /

A mathematical model for long-term, three-dimensional shoreline evolution is developed. The combined effects of variations of sea level; wave refraction and diffraction; loss of sand by density currents during storms, by rip currents, and by wind; bluff erosion and berm accretion; effects of manmade structures such as long groin or navigational structures; and beach nourishment are all taken into account. A computer program is developed with various subroutines which permit modification as the state-of-the-art progresses. The program is applied to a test case at Holland Harbor, Michigan. (Author).

A novel phantom and method for comprehensive 3-dimensional measurement and correction of geometric distortion in magnetic resonance imaging

A phantom that can be used for mapping geometric distortion in magnetic resonance imaging (MRI) is described. This phantom provides an array of densely distributed control points in three-dimensional (3D) space. These points form the basis of a comprehensive measurement method to correct for geometric distortion in MR images arising principally from gradient field non-linearity and magnet field inhomogeneity. The phantom was designed based on the concept that a point in space can be defined using three orthogonal planes. This novel design approach allows for as many control points as desired. Employing this novel design, a highly accurate method has been developed that enables the positions of the control points to be measured to sub-voxel accuracy. The phantom described in this paper was constructed to fit into a body coil of a MRI scanner, (external dimensions of the phantom were: 310 mm x 310 mm x 310 mm), and it contained 10,830 control points. With this phantom, the mean errors in the measured coordinates of the control points were on the order of 0.1 mm or less, which were less than one tenth of the voxel's dimensions of the phantom image. The calculated three-dimensional distortion map, i.e., the differences between the image positions and true positions of the control points, can then be used to compensate for geometric distortion for a full image restoration. It is anticipated that this novel method will have an impact on the applicability of MRI in both clinical and research settings. especially in areas where geometric accuracy is highly required, such as in MR neuro-imaging. (C) 2004 Elsevier Inc. All rights reserved.

Microfluidic interferometer

We present a class of compact, fluid-based, interferometric, tunable optical components: the single-beam microfluidic Mach-Zender interferometer. Phase delay is achieved through light propagation across a fluid-air interface (meniscus). The effect of meniscus curvature on the device transmission is considered using the three-dimensional beam propagation method and shown to be an important device parameter. We engineer the meniscus curvature using monomer surface chemistry, rendering it flat, and find that the experimental response corresponds well with simulation. The device has a resonance at 1.3 mum with a 25 dB extinction ratio; the latter can be adjusted by shifting the meniscus position.

Identification of three gene candidates for multicellular resistance in colon carcinoma

Solid tumours display elevated resistance to chemo- and radiotherapies compared to individual tumour derived cells. This so-called multicellular resistance (MCR) phenomenon can only be partly explained by reduced diffusion and altered cell cycle status; even fast growing cells on the surface of solid tumours display MCR. Multicellular spheroids (MCS) recapture this phenomenon ex vivo and here we compare gene expression in exponentially growing MCS with gene expression in monolayer culture. Using an 18,664 gene microarray, we identified 42 differentially expressed genes and three of these genes can be linked to potential mechanisms of MCR. A group of interferon response genes were also up-regulated in MCS, as were a number of genes that that are indicative of greater differentiation in three-dimensional cultures.

Flow focusing in microchannels

A volume-of-fluid numerical method is used to predict the dynamics of drop formation in an axi-symmetric microfluidic flow-focusing geometry for a liquid-liquid system. The Reynolds numbers and Weber numbers approximate those of a three-dimensional flow in recently published experiments. We compare the predicted drop formation with the experimental results at various flow rates, and discuss the mechanisms of drop formation in this context. Despite the differences in geometry, we find qualitative correspondence between the numerical and experimental results. Both end-pinching and capillary-wave instability are important for droplet break-up at the higher flow rates.

Modelling predicts positive and negative interactions between three Australian tropical tree species in monoculture and binary mixture

Computer modelling promises to. be an important tool for analysing and predicting interactions between trees within mixed species forest plantations. This study explored the use of an individual-based mechanistic model as a predictive tool for designing mixed species plantations of Australian tropical trees. The 'spatially explicit individually based-forest simulator' (SeXI-FS) modelling system was used to describe the spatial interaction of individual tree crowns within a binary mixed-species experiment. The three-dimensional model was developed and verified with field data from three forest tree species grown in tropical Australia. The model predicted the interactions within monocultures and binary mixtures of Flindersia brayleyana, Eucalyptus pellita and Elaeocarpus grandis, accounting for an average of 42% of the growth variation exhibited by species in different treatments. The model requires only structural dimensions and shade tolerance as species parameters. By modelling interactions in existing tree mixtures, the model predicted both increases and reductions in the growth of mixtures (up to +/- 50% of stem volume at 7 years) compared to monocultures. This modelling approach may be useful for designing mixed tree plantations. (c) 2006 Published by Elsevier B.V.

Numerical method for determination of the NMR frequency of the single-qubit operation in a silicon-based solid-state quantum computer

A numerical method is introduced to determine the nuclear magnetic resonance frequency of a donor (P-31) doped inside a silicon substrate under the influence of an applied electric field. This phosphorus donor has been suggested for operation as a qubit for the realization of a solid-state scalable quantum computer. The operation of the qubit is achieved by a combination of the rotation of the phosphorus nuclear spin through a globally applied magnetic field and the selection of the phosphorus nucleus through a locally applied electric field. To realize the selection function, it is required to know the relationship between the applied electric field and the change of the nuclear magnetic resonance frequency of phosphorus. In this study, based on the wave functions obtained by the effective-mass theory, we introduce an empirical correction factor to the wave functions at the donor nucleus. Using the corrected wave functions, we formulate a first-order perturbation theory for the perturbed system under the influence of an electric field. In order to calculate the potential distributions inside the silicon and the silicon dioxide layers due to the applied electric field, we use the multilayered Green's functions and solve an integral equation by the moment method. This enables us to consider more realistic, arbitrary shape, and three-dimensional qubit structures. With the calculation of the potential distributions, we have investigated the effects of the thicknesses of silicon and silicon dioxide layers, the relative position of the donor, and the applied electric field on the nuclear magnetic resonance frequency of the donor.

FDTD study of an UWB radar technique for breast tumor detection

A finite difference time domain (FDTD) method is applied to investigate capabilities of an ultra-wide band (UWB) radar system to detect a breast tumor. The first part of the investigations concerns FDTD simulations of a phantom formed by a plastic container with liquid and a small reflecting target. The second part focuses on a three-dimensional numerical breast model with a small tumor. FDTD simulations are carried out assuming a planar incident wave. Various time snap shots of the electromagnetic field are recorded to learn about the physical phenomenon of reflection and scattering in different layers of the phantom.

Transition in homogeneously heated inclined plane parallel shear flows

The transition of internally heated inclined plane parallel shear flows is examined numerically for the case of finite values of the Prandtl number Pr. We show that as the strength of the homogeneously distributed heat source is increased the basic flow loses stability to two-dimensional perturbations of the transverse roll type in a Hopf bifurcation for the vertical orientation of the fluid layer, whereas perturbations of the longitudinal roll type are most dangerous for a wide range of the value of the angle of inclination. In the case of the horizontal inclination transverse roll and longitudinal roll perturbations share the responsibility for the prime instability. Following the linear stability analysis for the general inclination of the fluid layer our attention is focused on a numerical study of the finite amplitude secondary travelling-wave solutions (TW) that develop from the perturbations of the transverse roll type for the vertical inclination of the fluid layer. The stability of the secondary TW against three-dimensional perturbations is also examined and our study shows that for Pr=0.71 the secondary instability sets in as a quasi-periodic mode, while for Pr=7 it is phase-locked to the secondary TW. The present study complements and extends the recent study by Nagata and Generalis (2002) in the case of vertical inclination for Pr=0.