Sub-Cellular Localization and Complex Formation by Aminoacyl-tRNA Synthetases in Cyanobacteria: Evidence for Interaction of Membrane-Anchored ValRS with ATP Synthase

tRNAs are charged with cognate amino acids by aminoacyl-tRNA synthetases (aaRSs) and subsequently delivered to the ribosome to be used as substrates for gene translation. Whether aminoacyl-tRNAs are channeled to the ribosome by transit within translational complexes that avoid their diffusion in the cytoplasm is a matter of intense investigation in organisms of the three domains of life. In the cyanobacterium Anabaena sp. PCC 7120, the valyl-tRNA synthetase (ValRS) is anchored to thylakoid membranes by means of the CAAD domain. We have investigated whether in this organism ValRS could act as a hub for the nucleation of a translational complex by attracting other aaRSs to the membranes. Out of the 20 aaRSs, only ValRS was found to localize in thylakoid membranes whereas the other enzymes occupied the soluble portion of the cytoplasm. To investigate the basis for this asymmetric distribution of aaRSs, a global search for proteins interacting with the 20 aaRSs was conducted. The interaction between ValRS and the FoF1 ATP synthase complex here reported is of utmost interest and suggests a functional link between elements of the gene translation and energy production machineries.

Exploring several nonconventional interactions of ice-binding proteins

Traditionally, ice-binding proteins (IBPs), also known as antifreeze proteins (AFPs), have been defined by two universal activities: ice recrystallization inhibition and thermal hysteresis. However, there remains the possibility IBPs have other complementary functions given the diversity found within this protein group. This thesis explores some of these in both natural and applied settings, in the hopes of furthering our understanding of this remarkable group of proteins. Plant IBPs could function as part of a defensive strategy against ice nucleators produced by certain pathogens. To assess this hypothesis, recombinant IBPs from perennial ryegrass and purple false brome were combined with the ice nucleation protein (INP) from the plant pathogen, Pseudomonas syringae. Strikingly, the plant proteins depressed the freezing point of the bacterial INP, while a fish AFP could not, nor did the INPs have any effect on IBP activity. Thus, the interaction between these two different proteins suggests a role in plant defensive strategies against pathogenic bacteria as another IBP function. In addition, the potential use of hyperactive insect IBPs in organ preservation was investigated. Current kidney preservation techniques involve storing the organ at 4 °C for a maximum of 24 h prior to transplantation. Extending this “safe” time would have profound effects on renal transplants, however, ischemic injury is prevalent when storage periods are prolonged. Experiments described here allowed subzero preservation for 72 h with the addition of a beetle IBP to CryoStasis® solution. Kidneys stored using the traditional technique for 24 h and the method developed here for 72 h showed similar levels of biomarker enzymes, underscoring the potential utility of insect IBPs for future transplant purposes. Finally, IBP function in the freeze-tolerant gall fly, Eurosta solidaginis, was examined. Larvae representing the mid-autumn stage displayed ice-binding activity, suggesting an IBP is being expressed, possibly as a protective measure against freezing damage when fall temperatures can unpredictably drop. IBP activity was also observed in the larvae’s host plant, Solidago spp. Mass spectrometry analysis of ice-affinity purified plant extracts provided three candidate pathogenesis-related proteins that could be responsible for the detected activity, further demonstrating additional functions of IBPs.

A two-step mechanism for epigenetic specification of centromere identity and function

The basic determinant of chromosome inheritance, the centromere, is specified in many eukaryotes by an epigenetic mark. Using gene targeting in human cells and fission yeast, chromatin containing the centromere-specific histone H3 variant CENP-A is demonstrated to be the epigenetic mark that acts through a two-step mechanism to identify, maintain and propagate centromere function indefinitely. Initially, centromere position is replicated and maintained by chromatin assembled with the centromere-targeting domain (CATD) of CENP-A substituted into H3. Subsequently, nucleation of kinetochore assembly onto CATD-containing chromatin is shown to require either the amino- or carboxy-terminal tail of CENP-A for recruitment of inner kinetochore proteins, including stabilizing CENP-B binding to human centromeres or direct recruitment of CENP-C, respectively.

Lithology and approximate sub-bottom depths and ages of the transition of soft to firm ooze and of firm ooze to chalk at DSDP Leg 89 and 90 Sites

Leg 90 recovered approximately 3705 m of core at eight sites lying at middle bathyal depths (1000-2200 m) (Sites 587 to 594) in a traverse from subtropical to subantarctic latitudes in the southwest Pacific region, chiefly on Lord Howe Rise in the Tasman Sea. This chapter summarizes some preliminary lithostratigraphic results of the leg and includes data from Site 586, drilled during DSDP Leg 89 on the Ontong-Java Plateau that forms the northern equatorial point of the latitudinal traverse. The lithofacies consist almost exclusively of continuous sections of very pure (>95% CaCO3) pelagic calcareous sediment, typically foraminifer-bearing nannofossil ooze (or chalk) and nannofossil ooze (or chalk), which is mainly of Neogene age but extends back into the Eocene at Sites 588, 592, and 593. Only at Site 594 off southeastern New Zealand is there local development of hemipelagic sediments and several late Neogene unconformities. Increased contents of foraminifers in Leg 90 sediments, notably in the Quaternary interval, correspond to periods of enhanced winnowing by bottom currents. Significant changes in the rates of sediment accumulation and in the character and intensity of sediment bioturbation within and between sites probably reflect changes in calcareous biogenic productivity as a result of fundamental paleoceanographic events in the region during the Neogene. Burial lithification is expressed by a decrease in sediment porosity from about 70 to 45% with depth. Concomitantly, microfossil preservation slowly deteriorates as a result of selective dissolution or recrystallization of some skeletons and the progressive appearance of secondary calcite overgrowths, first about discoasters and sphenoliths, and ultimately on portions of coccoliths. The ooze/chalk transition occurs at about 270 m sub-bottom depth at each of the northern sites (Sites 586 to 592) but is delayed until about twice this depth at the two southern sites (Sites 593 and 594). A possible explanation for this difference between geographic areas is the paucity of discoasters and sphenoliths at the southern sites; these nannofossil elements provide ideal nucleation sites for calcite overgrowths. Toward the bottom of some holes, dissolution seams and flasers appear in recrystallized chalks. The very minor terrigenous fraction of the sediment consists of silt- through clay-sized quartz, feldspar, mica, and clay minerals (smectite, illite, kaolinite, and chlorite), supplied as eolian dust from the Australian continent and by wind and ocean currents from erosion on South Island, New Zealand. Changes in the mass accumulation rates of terrigenous sediment and in clay mineral assemblages through time are related to various external controls, such as the continued northward drift of the Indo-Australian Plate, the development of Antarctic ice sheets, the increased desertification of the Australian continent after 14 m.y. ago, and the progressive increase in tectonic relief of New Zealand through the late Cenozoic. Disseminated glass shards and (altered) tephra layers occur in Leg 90 cores. They were derived from major silicic eruptions in North Island, New Zealand, and from basic to intermediate explosive volcanism along the Melanesian island chains. The tephrostratigraphic record suggests episodes of increased volcanicity in the southwest Pacific centered near 17, 13, 10, 5 and 1 m.y. ago, especially in the middle and early late Miocene. In addition, submarine basaltic volcanism was widespread in the southeast Tasman Sea around the Eocene/Oligocene boundary, possibly related to the propagation of the Southeast Indian Ridge through western New Zealand as a continental rift system.

Condensation of vapor as induced by nuclei and ions.

"The contemporaneous variations of the nucleation and the ionization of the atmosphere of Providence, by Lulu B. Joslin": p. 123-154.

A population balance model for high shear granulation

In a previous paper, Hoornaert et al. (Powder Technol. 96 (1998); 116-128) presented data from granulation experiments performed in a 50 L Lodige high shear mixer. In this study that same data was simulated with a population balance model. Based on an analysis of the experimental data, the granulation process was divided into three separate stages: nucleation, induction, and coalescence growth. These three stages were then simulated separately, with promising results. it is possible to derive a kernel that fit both the induction and the coalescence growth stage. Modeling the nucleation stage proved to be more challenging due to the complex mechanism of nucleus formation. From this work some recommendations are made for the improvement of this type of model.

Effects of boron on eutectic modification of hypoeutectic Al-Si alloys

The effects of boron on the eutectic modification and solidification mode of hypoeutectic Al-Si alloys have been studied adding different boride phases. The results show that boron does not cause modification of the eutectic silicon. Boron-containing samples display eutectic nucleation and growth characteristics similar to that of unmodified alloys. (C) 2002 Acta Materialia Inc. Published by Elsevier Science Ltd. All rights reserved.

Microanalysis of epitaxially grown diamond tip array

Electron backscattering diffraction has been applied on polycrystalline diamond films grown using microwave plasma assisted chemical vapour deposition on silicon substrate, in order to provide a map of the individual diamond grains, grain boundary, and the crystal orientation of discrete crystallites. The nucleation rate and orientation are strongly affected by using a voltage bias on the substrate to influence and enhance the nucleation process, the bias enhanced nucleation process. In this work, the diamond surface is mapped using electron backscattering diffraction, then a layer of a few microns is ion milled away exposing a lower layer for analysis and so on. This then permits a three dimensions reconstruction of the film texture.

The 3-D Structure of Polycrystalline Diamond Film by Electron Backscattering Diffraction (EBSD)

A lithographic method was used to produce polycrystalline diamond films having highly defined surface geometry, showing an array of diamond tips for possible application as a field emitter device. The films grown in this study used microwave plasma assisted chemical vapour deposition (MACVD) on a silicon substrate; the substrate was then dissolved away to reveal the surface features on the diamond film. It is possible to align the crystallite direction and affect the electron emission properties using a voltage bias to enhance the nucleation process and influence the nuclei to a preferred orientation. This study focuses on the identification of the distribution of crystal directions in the film, using electron backscattering diffraction (EBSD) to identify the crystallographic character of the film surface. EBSD allows direct examination of the individual diamond grains, grains boundaries and the crystal orientation of each individual crystallite. The EBSD maps of the bottom (nucleation side) of the films, following which a layer of film is ion-milled away and the mapping process repeated. The method demonstrates experimentally that oriented nucleation occurs and the thin sections allow the crystal texture to be reconstructed in 3-D. (C) 2003 Elsevier B.V. All rights reserved.

Nanostructures, Semicrytalline Morphology, and Nanoscale Confinement Effect on the Crystallization Kinetics in Self-Organized Block Copolymer/Thermoset Blends

This work reports the first instance of self-organized thermoset blends containing diblock copolymers with a crystallizable thermoset-immiscible block. Nanostructured thermoset blends of bisphenol A-type epoxy resin (ER) and a low-molecular-weight (M-n = 1400) amphiphilic polyethylene-block-poly(ethylene oxide) (EEO) symmetric diblock copolymer were prepared using 4,4'-methylenedianiline (MDA) as curing agent and were characterized by transmission electron microscopy (TEM), atomic force microscopy (AFM), small-angle X-ray scattering (SAXS), and differential scanning calorimetry (DSC). All the MDA-cured ER/EEO blends do not show macroscopic phase separation but exhibit microstructures. The ER selectively mixes with the epoxy-miscible PEO block in the EEO diblock copolymer whereas the crystallizable PE blocks that are immiscible with ER form separate microdomains at nanoscales in the blends. The PE crystals with size on nanoscales are formed and restricted within the individual spherical micelles in the nanostructured ER/EEO blends with EEO content up to 30 wt %. The spherical micelles are highly aggregated in the blends containing 40 and 50 wt % EEO. The PE dentritic crystallites exist in the blend containing 50 wt % EEO whereas the blends with even higher EEO content are completely volume-filled with PE spherulites. The semicrystalline microphase-separated lamellae in the symmetric EEO diblock copolymer are swollen in the blend with decreasing EEO content, followed by a structural transition to aggregated spherical micellar phase morphology and, eventually, spherical micellar phase morphology at the lowest EEO contents. Three morphological regimes are identified, corresponding precisely to the three regimes of crystallization kinetics of the PE blocks. The nanoscale confinement effect on the crystallization kinetics in nanostructured thermoset blends is revealed for the first time. This new phenomenon is explained on the basis of homogeneous nucleation controlled crystallization within nanoscale confined environments in the block copolymer/thermoset blends.

Eutectic modification of Al-Si alloys with rare earth metals

The effects of different concentrations of individual additions of rare earth metals (La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb and Lu) on eutectic modification in Al-10mass%Si has been studied by thermal analysis and optical microscopy. According to the twin-plane re-entrant edge (TPRE) and impurity induced twinning mechanism, rare earth metals with atomic radii of about 1.65 times larger than that of silicon, are possible candidates for eutectic modification. All of the rare earth elements caused a depression of the eutectic growth temperature, but only Eu modified the eutectic silicon to a fibrous morphology. At best, the remaining elements resulted in only a small degree of refinement of the plate-like silicon. The samples were also quenched during the eutectic arrest to examine the eutectic solidification modes. Many of the rare-earth additions significantly altered the eutectic solidification mode from that of the unmodified alloy. It is concluded that the impurity induced twinning model of modification, based on atomic radius alone, is inadequate and other mechanisms are essential for the modification process. Furthermore, modification and the eutectic nucleation and growth modes are controlled independently of each other.

Solidification mechanisms of unmodified and strontium-modified hypereutectic aluminium-silicon alloys

The effects of strontium on the solidi. cation mode of hypereutectic aluminium-silicon alloys have been studied. Samples were prepared from an aluminium-17wt% silicon-based alloy and strontium was added at several different concentrations. The development of the microstructure was investigated by cooling curve analysis, interrupted solidi. cation experiments and optical and scanning electron microscopy. It was found that nucleation of primary silicon is suppressed by additions of strontium. The suppressed nucleation results in supersaturation of the liquid prior to nucleation, and an increased growth rate after nucleation. As a result, the silicon crystals become less faceted and more dendritic with increasing strontium additions. Increasing the strontium concentration slightly refined the eutectic spacing and introduced a small amount of fibrous silicon. Electron back-scatter diffraction measurements were performed to determine the crystallographic relation between the primary and eutectic silicon phases. The eutectic silicon in the unmodified alloy does not have any crystallographic relationship with the primary silicon crystals. In contrast, the eutectic silicon crystals in the strontium-modified alloys often share an identical or twin relationship with nearby primary silicon crystals. The incidence of twinning within primary silicon crystals was relatively low and did not appear to increase with strontium additions.

Aluminium phosphide as a eutectic grain nucleus in hypoeutectic Al-Si alloys

Aluminium phosphide (AlP) particles arc often suggested to be the nucleation site for eutectic silicon in Al-Si alloys, since both the crystal structure and lattice parameter of AlP (crystal structure: cubic K(4) over bar m; lattice parameter: 5.421 Angstrom) are close to that of silicon (cubic Fd3m, 5.431 Angstrom), and the melting point is higher than the Al-Si eutectic temperature. However, the crystallographic relationships between AlP particles and the surrounding eutectic silicon are seldom reported due to the difficulty in analysing the AlP particles, which react with water during sample preparation for polishing. in this study, the orientation relationships between AlP and Si are analysed by transmission electron microscopy using focused ion-beam milling for sample preparation to investigate the nucleation mechanism of eutectic silicon on AlP. The results show a clear and direct lattice relationship between centrally located AlP particles and the surrounding silicon in the hypoeutectic Al-Si alloy.

Eutectic grains in unmodified and strontium-modified hypoeutectic aluminum-silicon alloys

Additions of strontium to hypoeutectic aluminum-silicon alloys modify the morphology of the eutectic silicon phase from a coarse platelike structure to a fine fibrous structure. Thermal analysis, interrupted solidification, and microstructural examination of sand castings in this work revealed that, in addition to a change in silicon morphology, modification with strontium also causes an increase in the size of eutectic grains. The eutectic grain size increases because fewer grains nucleate, possibly due to poisoning of the phosphorus-based nucleants, that are active in the unmodified alloy. A simple growth model is developed to estimate the interface velocity during solidification of a eutectic grain. The model confirms, independent of microstructural observations, that the addition of 100 ppm strontium increases the eutectic grain size by at least an order of magnitude compared with the equivalent unmodified alloy. The model predicts that the growth velocity varies significantly during eutectic growth. At low strontium levels, these variations may be sufficient to cause transitions between flake and fibrous silicon morphologies depending on the casting conditions. The model can be used to rationally interpret the eutectic grain structure and silicon morphology of fully solidified aluminum-silicon castings and, when coupled with reliable thermal data, can be used to estimate the eutectic grain size.