Dynamic regulation of ARGONAUTE4 within multiple nuclear bodies in Arabidopsis thaliana.

DNA methylation directed by 24-nucleotide small RNAs involves the small RNA-binding protein ARGONAUTE4 (AGO4), and it was previously shown that AGO4 localizes to nucleolus-adjacent Cajal bodies, sites of snRNP complex maturation. Here we demonstrate that AGO4 also localizes to a second class of nuclear bodies, called AB-bodies, which are found immediately adjacent to condensed 45S ribosomal DNA (rDNA) sequences. AB-bodies also contain other proteins involved in RNA-directed DNA methylation including NRPD1b (a subunit of the RNA Polymerase IV complex, RNA PolIV), NRPD2 (a second subunit of this complex), and the DNA methyltransferase DRM2. These two classes of AGO4 bodies are structurally independent--disruption of one class does not affect the other--suggesting a dynamic regulation of AGO4 within two distinct nuclear compartments in Arabidopsis. Abolishing Cajal body formation in a coilin mutant reduced overall AGO4 protein levels, and coilin dicer-like3 double mutants showed a small decrease in DNA methylation beyond that seen in dicer-like3 single mutants, suggesting that Cajal bodies are required for a fully functioning DNA methylation system in Arabidopsis.

The identification and quantification of highly stable 'common hairpin' in the dynamic process of co-transcriptional mRNA folding

In our studies, 88 human mRNA samples were collected from the Integrated Sequence-Structure database and then the dynamic process in co-transcriptional mRNA folding was simulated using the RNAstructure version 4.1 program. Through statistical analyses of the frequencies of occurrence of hairpins, a group of special folding structures-the 'common hairpins'-were identified. These 'common hairpins' have lower energies and occur in all the subsequent folding units that formed in the dynamic folding process. By applying the formulas (1)-(4) of the 'common hairpins' statistical model, 163 'common hairpins' were found, to make up about 7% of the total of 2286 hairpins. Classified studies further show that the 'common hairpins' that were studied may oscillate in the dynamic folding process. However, the hairpin loops of the 'common hairpins' and stems proximal to those 'common hairpins' loops maintain topologically stable structures, while other loops and stems distal to the 'common hairpins' loops are shown to be alterable structures. Strikingly, further studies indicate that the stable structures of these 'common hairpins' may have unbeknown effects on controlling the formation of protein structures in the translation process (unpublished results). (c) 2005 Elsevier B.V. All rights reserved.

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

Evolutionary Conservation of Dazl Genomic Organization and its Continuous and Dynamic Distribution Throughout Germline Development in Gynogenetic Gibel Carp

To investigate germline development and germ cell specification, we identified a Dazl homolog (CagDazl) from gynogenetic gibel carp (Carassius auratus gibelio). Its cDNA sequence and BAC clone sequence analyses revealed the genomic organization conservation and conserved synteny of the Dazl family members and their neighborhood genes among vertebrates, especially in fish. Moreover, a polyclonal antibody specific to CagDazl was produced and used to examine its expression and distribution throughout germline development at protein level. Firstly, ovary-specific expression pattern of CagDazl was confirmed in adult tissues by RT-PCR and Western blot. In addition, in situ hybridization and immunofluorescence localization demonstrated its specific expression in germ cells, and both its transcript and protein were localized to germ plasm. Then, co-localization of CagDazl and mitochondrial cloud was found, confirming that CagDazl transcript and its protein are germ plasm component and move via METRO pathway during oogenesis. Furthermore, the CagDazl is abundant and continuous throughout germline development and germ cell specification including primordial germ cell (PGC) formation, oogonium differentiation, oocyte development, and embryogenesis, and the dynamic distribution occurs at different development stages. The data suggest that maternal CagDazl might play an important role in gibel carp PGC formation. Therefore, CagDazl is a useful and specific marker for tracing germ plasm and germ cell development in the gynogenetic gibel carp. In addition, in comparison with previous studies in sexual reproduction species, the continuous and dynamic distribution of CagDazl protein in the germ plasm throughout the life cycle seems to have significant implication in sex evolution of vertebrates. J. Exp. Zool. (Mol. Deu. Euol.) 312B:855-871, 2009. (C) 2009 Wiley-Liss, Inc.

Study on dynamic fusion barrier in heavy-ion fusion reactions

By means of the improved quantum molecular dynamics model, the incident energy dependent dynamical fusion potential barriers for heavy nucleus reaction systems are investigated. It is found that with decrease of incident energy the lowest dynamic barrier is obtained which approaches to the adiabatic static barrier and with increase of the incident energy the dynamic barrier goes up to the diabatic static barrier. Based on the dynamical study a microscopic understanding of the extra-push in fusion reactions of heavy systems and a new explanation of tunneling process for the fusion at the incident energy below the static and above the lowest dynamic barrier are presented. In order to understand the energy dependence of the dynamical barrier we also pay a great attention to study the neck formation and shape deformation during the dynamic lowering of the barrier.

In Situ Scanning Tunneling Microscopy on the Dynamic Process of the Replacement of Coronene on Au (111) by 6-Mercapto-1-Hexanol

The replacement of coronene monolayer on Au (111) by 6-mercapto-1-hexanol (MHO) was studied by in situ scanning tunneling microscopy (STM) in solutions. It was found that the rate of replacement depends strongly on the concentration of MHO. The replacement finished within a second at a higher concentration of MHO. At a lower concentration, the slow replacement could be followed by in situ STM. The replacement occurred initially near the elbow position of reconstructed Au (111) with the formation of pits in a single or several missing molecules. With the proceeding of replacement, these small pits expanded, and the surrounding coronene molecules were gradually substituted by MHO, which developed into ordered domains within a spatial confined environment. Meanwhile, the reconstruction of Au (111) was lifted. The replacement expanded fast along the reconstruction lines in the domain. For the fast replacement, a (root 3 x root 3) R30 degrees adlattice was observed, while a c(4 x 2) superlattice was observed for the slow replacement.

Dynamic mechanical studies of the sulfonated butyl rubber ionomers and their blends

Dynamic mechanical properties of sulfonated butyl rubber ionomers neutralized with different amine or metallic ion (zinc or barium) and their blends with polypropylene (PP), high-density polyethylene (HDPE), or styrene-butadiene-styrene (SBS) triblock copolymer were studied using viscoelastometry. The results showed that glass transition temperatures of ion pair-containing matrix and ionic domains (T-g1 and T-g2, respectively) of amine-neutralized ionomers were lower than those of ionomers neutralized with metallic ions, and the temperature range of the rubbery plateau on the storage modulus plot for amine-neutralized ionomers was narrower. The modulus of the rubbery plateau for amine-neutralized ionomers was lower than that of ionomers neutralized with zinc or barium ion. With increasing size of the amine, the temperature range for the rubbery plateau decreased, and the height of the loss peak at higher temperature increased. Dynamic mechanical properties of blends of the zinc ionomer with PP or HDPE showed that, with decreasing ionomer content, the T-m of PP or HDPE increased and T-g1 decreased, whereas T-g2 or the upper loss peak temperature changed only slightly. The T-g1 for the blend with SBS also decreased with decreasing ionomer content. The decrease of T-g1 is attributed to the enhanced compatibilization of the matrix of the ionomer-containing ion pairs with amorphous regions of PP or HDPE or the continuous phase of SBS due to the formation of thermoplastic interpenetrating polymer networks by ionic domains and crystalline or glassy domains.

Diffusion-limited kinetics modeling of one-step polyimide formation

A diffusion-limited kinetic model was developed to describe the imidization of one-step polythioetherimide formation based on an endgroup diffusion model. The changes of conversion and viscosity during the imidization were monitored with thermogravimetric analysis and dynamic stress rheometry, respectively. It was observed that the imidization rate began to decelerate after a fast early stage, whereas the viscosity in the system increased dramatically after a period of low value. Amic acid and imide formations concurrently take place in the one-step polyimide formation, but the formation of amic acid is much slower than that of imide and is the rate-limiting step of imidization. When a second-order kinetic model was used to describe the imidization, the effect of viscosity on the diffusion resistance of reactive groups needed to be included. In order to predict the change of viscosity during the imidization, the Lipshitz-Macosko model was modified and introduced into the diffusion-limited kinetic model by the Stokes-Einstein equation. The comparison of the modeled results with experimental data indicated that the diffusion-limited kinetic model and the modified Lipshitz-Macosko model were able to efficiently predict the changes of conversion and viscosity with temperature and time during the one-step polythioetherimide formation. (C) 2001 John Wiley & Sons, Inc.

MORPHOLOGY AND DYNAMIC-MECHANICAL PROPERTIES OF NYLON 66/POLY(ETHER IMIDE) BLENDS

The morphology and dynamic mechanical properties of blends of poly(ether imide) (PEI) and nylon 66 over the full composition range have been investigated. Torque changes during mixing were also measured. Lower torque values than those calculated by the log-additivity rule were obtained, resulting from the slip at the interface due to low interaction between the components. The particle size of the dispersed phase and morphology of the blends were examined by scanning electron microscopy. The composition of each phase was calculated. The blends of PEI and nylon 66 showed phase-separated structures with small spherical domains of 0.3 similar to 0.7 mu m. The glass transition temperatures (T(g)s) of the blends were shifted inward, compared with those of the homopolymers, which implied that the blends were partially miscible over a range of compositions. T-g1, corresponding to PEI-rich phase, was less affected by composition than T-g2, corresponding to nylon 66-rich phase. This indicated that the fraction of PEI mixed into nylon 66-rich phase increased with decreasing PEI content and that nylon 66 was rarely mixed into the PEI-rich phase. The effect of composition on the secondary relaxations was examined. Both T-beta, corresponding to the motion of amide groups in nylon 66, and T-gamma, corresponding to that of ether groups in PEI, were shifted to higher temperature, probably because of the formation of intermolecular interactions between the components.

MORPHOLOGY AND DYNAMIC MECHANICAL-PROPERTIES OF AB CROSS-LINKED POLYMERS BASED ON POLYURETHANES

Polyoxypropylene glycol (PPG) (or castor oil) and toluene diisocyanate (TDI) were mixed, and the prepolymer polyurethane (PU) (I) was formed. Vinyl-terminated polyurethane (II) was prepared from (I), and hydroxyethyl acrylate, AB crosslinked polymers (ABCPs) were synthesized from (II) and vinyl monomers such as styrene, methyl methacrylate, vinyl acetate, etc. The dynamic mechanical properties and morphology of ABCPs were measured. The ABCPs based on PPG have double glass transition temperatures (T(g)) on the sigma-vs. temperature curves. They display a two-phase morphology with plastic components forming the continous phase and PU-rich domains forming the separated phase on the electron micrographs. Irregular shapes and a highly polydisperse distribution of PU-rich domain sizes were observed. The crosslink density of ABCPs has a notable effect on the morphology and properties. The average diameter of the PU-rich domains depends on the molecular weight of prepolymer PPG. The highly crosslinked structures will produce large numbers of very small domains. ABCPs based on castor oil show a single T(g) relaxation on the dynamic mechanical spectra. The compatibility between the two components is much better in ABCPs based on castor oil than in those based on PPG, because there is a high crosslink density in the former. Comparison of the dynamic mechanical spectra of ABCP and interpenetrating networks (IPN) based on castor oil with similar crosslink density and composition imply that the two components in ABCP are compatible whereas microphase separation occurs in IPN. An improvement in the compatibility is achieved by the crosslinking between the two networks.

Modern sedimentary environments and dynamic depositional systems in the southern Yellow Sea

Based on analyses of more than 600 surface sediment samples together with large amounts of previous sedimentologic and hydrologic data, the characteristics of modern sedimentary environments and dynamic depositional systems in the southern Yellow Sea (SYS) are expounded, and the controversial formation mechanism of muddy sediments is also discussed. The southern Yellow Sea shelf can be divided into low-energy sedimentary environment and high-energy sedimentary environment; the low-energy sedimentary environment can be further divided into cyclonic and anticyclonic ones, and the high-energy environment is subdivided into high-energy depositional and eroded environments. In the shelf low-energy environments, there developed muddy depositional system. In the central part of the southern Yellow Sea, there deposited the cold eddy sediments under the actions of a meso-scale cyclonic eddy (cold eddy), and in the southeast of the southern Yellow Sea, an anticyclonic eddy muddy depositional system (warm eddy sediment) was formed. These two types of sediments showed evident differences in grain size, sedimentation rate, sediment thickness and mineralogical characteristics. The high-energy environments were covered with sandy sediments on seabed; they appeared mainly in the west, south and northeast of the southern Yellow Sea. In the high-energy eroded environment, large amounts of sandstone gravels were distributed on seabed. In the high-energy depositional environment, the originally deposited fine materials (including clay and fine silt) were gradually re-suspended and then transported to a low-energy area to deposit again. In this paper, the sedimentation model of cyclonic and anticyclonic types of muddy sediments is established, and a systematic interpretation for the formation cause of muddy depositional systems in the southern Yellow Sea is given.

Formation of nano-crystalline corrosion products on Zn-Al alloy coating exposed to seawater

Hot dip Zn-Al alloy coating performs better than hot dip galvanized coating and 55% Al-Zn-Si coating as well with regard to general seawater corrosion protection. A characterization of the corrosion products on Zn-Al alloy coating immersed in dynamic aerated seawater has been performed mainly based on transmission electron microscopy (TEM) for morphological analysis and X-ray diffraction (XRD) technique for crystalline phase identification. The XRD and TEM analyses showed that the corrosion products mainly were typical nanometer Zn4CO3(OH)(6).H2O, Zn-5(OH)(8)Cl-2 and Zn6Al2CO3(OH)(16). 4H(2)O microcrystals. This probably is connected to the co-precipitation of Zn2+ and Al3+ ions caused by adsorption. Zn-Al alloy coating being suffered seawater attacks, AI(OH)(3) gel was first produced on the coating surface. Zn and Al hydroxides would co-precipitate and form double-hydroxide when the concentration of adsorbed Zn2+ ions by the newly produced gel exceeded the critical degree of supersaturation of the interphase nucleation. However, because the growth of the crystals was too low to keep in step with the nucleation, a layer of nano-crystalline corrosion products were produced on the surface of the coating finally. (C) 2001 Elsevier Science Ltd. All rights reserved.

Atomic oxygen formation in a radio-frequency driven micro-atmospheric pressure plasma jet

Atomic oxygen formation in a radio-frequency driven micro-atmospheric pressure plasma jet is investigated using both advanced optical diagnostics and numerical simulations of the dynamic plasma chemistry. Laser spectroscopic measurements of absolute densities of ground state atomic oxygen reveal steep gradients at the interface between the plasma core and the effluent region. Spatial profiles resolving the interelectrode gap within the core plasma indicate that volume processes dominate over surface reactions. Details of the production and destruction processes are investigated in numerical simulations benchmarked by phase-resolved optical emission spectroscopy. The main production mechanisms are electron induced and hence most efficient in the vicinity of the plasma boundary sheath, where electrons are energized. The destruction is driven through chemical heavy particle reactions. The resulting spatial profile of atomic oxygen is relatively flat. The power dependence of the atomic oxygen density obtained by the numerical simulation is in very good agreement with the laser spectroscopic measurements.

Influence of social status on the welfare of sows in static and dynamic groups

Forty-eight Large White x Landrace multiparous sows were mixed into twelve groups of four animals after their piglets were weaned. These groups were defined as static, with no animals being added to or removed from the groups after their formation. Aggressive and submissive behaviours were recorded continuously for 9 h after the sows were mixed, and the sows were assigned high or low social status on the basis of their relative aggressiveness and success in aggressive interactions. After five weeks, each static group was mixed into a dynamic group of 40+/-2 sows for an 11-week period. Three static groups (ie 12 animals) at a time were added to the dynamic group at three-week intervals; the same number of animals was removed at these time-points in order to maintain the group number at 40+/-2. Injury levels increased significantly with the transition from static groups to the dynamic group (P