Role of RNA polymerase IV in plant small RNA metabolism.

In addition to the three RNA polymerases (RNAP I-III) shared by all eukaryotic organisms, plant genomes encode a fourth RNAP (RNAP IV) that appears to be specialized in the production of siRNAs. Available data support a model in which dsRNAs are generated by RNAP IV and RNA-dependent RNAP 2 (RDR2) and processed by DICER (DCL) enzymes into 21- to 24-nt siRNAs, which are associated with different ARGONAUTE (AGO) proteins for transcriptional or posttranscriptional gene silencing. However, it is not yet clear what fraction of genomic siRNA production is RNAP IV-dependent, and to what extent these siRNAs are preferentially processed by certain DCL(s) or associated with specific AGOs for distinct downstream functions. To address these questions on a genome-wide scale, we sequenced approximately 335,000 siRNAs from wild-type and RNAP IV mutant Arabidopsis plants by using 454 technology. The results show that RNAP IV is required for the production of >90% of all siRNAs, which are faithfully produced from a discrete set of genomic loci. Comparisons of these siRNAs with those accumulated in rdr2 and dcl2 dcl3 dcl4 and those associated with AGO1 and AGO4 provide important information regarding the processing, channeling, and functions of plant siRNAs. We also describe a class of RNAP IV-independent siRNAs produced from endogenous single-stranded hairpin RNA precursors.

Genetic status of selected fish taxa in relation to conservation of genetic and species diversity in the Victoria and Kyoga Lake basins

Cichlids are known for their explosive radiation especially in the African Great Lakes marked with a high level of lake endemism. These fishes have been characterized mainly along trophic and habitat differences, by variation in morphological structures such as teeth and jaws and by differences in body shape and coloration. Cichlids are important as a microcosm of macroevolution. The explosive radiation, young evolutionary scale, and the isolation of groups characterized with high levels of endemism and presence of living fossils makes the group important for evolutionary and genetic studies. Lake Victoria region cichlids which are isolated and relatively more recent in evolution were the last to be appreciated in their diversity. Recently Ole Seehausen has found scores of rock fishes in Lake Victoria which were up to then thought to be absent from the Lake and only known to occur in Lakes Malawi and Tanganyika. Greenwood put together the species groups of Lake Victoria, and later in the early 1980's revised the classification of haplochromine species to reflect the phyletic origin and interrelationship of the various groups in Lake Victoria region. Melan Stiassny has been interested in early evolution of cichlids while the likes of Paul Fuerst and Lees Kaufman and Axel Meyer have been interested and are working to explain the speciation mechanisms responsible for the explosive radiation and evolution of cichlids. Locally S.B Wandera and his student Getrude Narnulemo are spearheading the biodiversity and taxonomic studies of cichlids in Lake Victoria region

The increased fishing pressure and the future of the fish stocks of Lake Victoria, Uganda

The Uganda sector of Lake Victoria occupies 29,580 km2 (43%). The lake used to boast of a multi-species fishery but presently relies on three major species Lates niloticus, Oreochromis niloticus and Rastrineobola argentea. During the past decade the total fish production on the Ugandan sector increased drastically from 17,000 tonnes in 1981 to about 13,000 tonnes 1991, indicating a healthy state of the fishery. This was contributed by a combination of factors including the explosive establishment of the introduced L. niloticus which contributed 60.8% in 1991 and the increase in the number of fishing canoes from 3470 in 1988 to 8000 in 1990. Isolated fishery resources studies carried out in different areas of the lake since 1971 seem, however, to indicate contrary trends in the available stocks and, therefore, the status of the fishery. In the experimental fishery, continued decline in catch rates have been recorded. Similarly, in the commercial fishery catch per unit of effort has been considerably poor (33 kg per canoe during January - March 1992) and the average size of individual fish laRded continued to decline, obviously pointing at possible over-fishing. This, therefore, calls for further urgent research on the available stocks for proper management strategies to be formulated.

Marine Vertebrates and Low Frequency Sound: Technical Report for LFA EIS

Over the past 50 years, economic and technological developments have dramatically increased the human contribution to ambient noise in the ocean. The dominant frequencies of most human-made noise in the ocean is in the low-frequency range (defined as sound energy below 1000Hz), and low-frequency sound (LFS) may travel great distances in the ocean due to the unique propagation characteristics of the deep ocean (Munk et al. 1989). For example, in the Northern Hemisphere oceans low-frequency ambient noise levels have increased by as much as 10 dB during the period from 1950 to 1975 (Urick 1986; review by NRC 1994). Shipping is the overwhelmingly dominant source of low-frequency manmade noise in the ocean, but other sources of manmade LFS including sounds from oil and gas industrial development and production activities (seismic exploration, construction work, drilling, production platforms), and scientific research (e.g., acoustic tomography and thermography, underwater communication). The SURTASS LFA system is an additional source of human-produced LFS in the ocean, contributing sound energy in the 100-500 Hz band. When considering a document that addresses the potential effects of a low-frequency sound source on the marine environment, it is important to focus upon those species that are the most likely to be affected. Important criteria are: 1) the physics of sound as it relates to biological organisms; 2) the nature of the exposure (i.e. duration, frequency, and intensity); and 3) the geographic region in which the sound source will be operated (which, when considered with the distribution of the organisms will determine which species will be exposed). The goal in this section of the LFA/EIS is to examine the status, distribution, abundance, reproduction, foraging behavior, vocal behavior, and known impacts of human activity of those species may be impacted by LFA operations. To focus our efforts, we have examined species that may be physically affected and are found in the region where the LFA source will be operated. The large-scale geographic location of species in relation to the sound source can be determined from the distribution of each species. However, the physical ability for the organism to be impacted depends upon the nature of the sound source (i.e. explosive, impulsive, or non-impulsive); and the acoustic properties of the medium (i.e. seawater) and the organism. Non-impulsive sound is comprised of the movement of particles in a medium. Motion is imparted by a vibrating object (diaphragm of a speaker, vocal chords, etc.). Due to the proximity of the particles in the medium, this motion is transmitted from particle to particle in waves away from the sound source. Because the particle motion is along the same axis as the propagating wave, the waves are longitudinal. Particles move away from then back towards the vibrating source, creating areas of compression (high pressure) and areas of rarefaction (low pressure). As the motion is transferred from one particle to the next, the sound propagates away from the sound source. Wavelength is the distance from one pressure peak to the next. Frequency is the number of waves passing per unit time (Hz). Sound velocity (not to be confused with particle velocity) is the impedance is loosely equivalent to the resistance of a medium to the passage of sound waves (technically it is the ratio of acoustic pressure to particle velocity). A high impedance means that acoustic particle velocity is small for a given pressure (low impedance the opposite). When a sound strikes a boundary between media of different impedances, both reflection and refraction, and a transfer of energy can occur. The intensity of the reflection is a function of the intensity of the sound wave and the impedances of the two media. Two key factors in determining the potential for damage due to a sound source are the intensity of the sound wave and the impedance difference between the two media (impedance mis-match). The bodies of the vast majority of organisms in the ocean (particularly phytoplankton and zooplankton) have similar sound impedence values to that of seawater. As a result, the potential for sound damage is low; organisms are effectively transparent to the sound – it passes through them without transferring damage-causing energy. Due to the considerations above, we have undertaken a detailed analysis of species which met the following criteria: 1) Is the species capable of being physically affected by LFS? Are acoustic impedence mis-matches large enough to enable LFS to have a physical affect or allow the species to sense LFS? 2) Does the proposed SURTASS LFA geographical sphere of acoustic influence overlap the distribution of the species? Species that did not meet the above criteria were excluded from consideration. For example, phytoplankton and zooplankton species lack acoustic impedance mis-matches at low frequencies to expect them to be physically affected SURTASS LFA. Vertebrates are the organisms that fit these criteria and we have accordingly focused our analysis of the affected environment on these vertebrate groups in the world’s oceans: fishes, reptiles, seabirds, pinnipeds, cetaceans, pinnipeds, mustelids, sirenians (Table 1).

The parameter space of graphene chemical vapor deposition on polycrystalline Cu

A systematic study of the parameter space of graphene chemical vapor deposition (CVD) on polycrystalline Cu foils is presented, aiming at a more fundamental process rationale in particular regarding the choice of carbon precursor and mitigation of Cu sublimation. CH 4 as precursor requires H 2 dilution and temperatures ≥1000 °C to keep the Cu surface reduced and yield a high-quality, complete monolayer graphene coverage. The H 2 atmosphere etches as-grown graphene; hence, maintaining a balanced CH 4/H 2 ratio is critical. Such balance is more easily achieved at low-pressure conditions, at which however Cu sublimation reaches deleterious levels. In contrast, C 6H 6 as precursor requires no reactive diluent and consistently gives similar graphene quality at 100-150 °C lower temperatures. The lower process temperature and more robust processing conditions allow the problem of Cu sublimation to be effectively addressed. Graphene formation is not inherently self-limited to a monolayer for any of the precursors. Rather, the higher the supplied carbon chemical potential, the higher the likelihood of film inhomogeneity and primary and secondary multilayer graphene nucleation. For the latter, domain boundaries of the inherently polycrystalline CVD graphene offer pathways for a continued carbon supply to the catalyst. Graphene formation is significantly affected by the Cu crystallography; i.e., the evolution of microstructure and texture of the catalyst template form an integral part of the CVD process. © 2012 American Chemical Society.

A high performance oxygen storage material for chemical looping processes with CO2 capture

Chemical looping combustion (CLC) is a novel combustion technology that involves cyclic reduction and oxidation of oxygen storage materials to provide oxygen for the combustion of fuels to CO2 and H2O, whilst giving a pure stream of CO2 suitable for sequestration or utilisation. Here, we report a method for preparing of oxygen storage materials from layered double hydroxides (LDHs) precursors and demonstrate their applications in the CLC process. The LDHs precursor enables homogeneous mixing of elements at the molecular level, giving a high degree of dispersion and high-loading of active metal oxide in the support after calcination. Using a Cu-Al LDH precursor as a prototype, we demonstrate that rational design of oxygen storage materials by material chemistry significantly improved the reactivity and stability in the high temperature redox cycles. We discovered that the presence of sodium-containing species were effective in inhibiting the formation of copper aluminates (CuAl2O4 or CuAlO 2) and stabilising the copper phase in an amorphous support over multiple redox cycles. A representative nanostructured Cu-based oxygen storage material derived from the LDH precursor showed stable gaseous O2 release capacity (∼5 wt%), stable oxygen storage capacity (∼12 wt%), and stable reaction rates during reversible phase changes between CuO-Cu 2O-Cu at high temperatures (800-1000 °C). We anticipate that the strategy can be extended to manufacture a variety of metal oxide composites for applications in novel high temperature looping cycles for clean energy production and CO2 capture. © The Royal Society of Chemistry 2013.

Deformation and fracture of impulsively loaded sandwich panels

Light metal sandwich panel structures with cellular cores have attracted interest for multifunctional applications which exploit their high bend strength and impact energy absorption. This concept has been explored here using a model 6061-T6 aluminum alloy system fabricated by friction stir weld joining extruded sandwich panels with a triangular corrugated core. Micro-hardness and miniature tensile coupon testing revealed that friction stir welding reduced the strength and ductility in the welds and a narrow heat affected zone on either side of the weld by approximately 30%. Square, edge clamped sandwich panels and solid plates of equal mass per unit area were subjected to localized impulsive loading by the impact of explosively accelerated, water saturated, sand shells. The hydrodynamic load and impulse applied by the sand were gradually increased by reducing the stand-off distance between the test charge and panel surfaces. The sandwich panels suffered global bending and stretching, and localized core crushing. As the pressure applied by the sand increased, face sheet fracture by a combination of tensile stretching and shear-off occurred first at the two clamped edges of the panels that were parallel with the corrugation and weld direction. The plane of these fractures always lay within the heat affected zone of the longitudinal welds. For the most intensively loaded panels additional cracks occurred at the other clamped boundaries and in the center of the panel. To investigate the dynamic deformation and fracture processes, a particle-based method has been used to simulate the impulsive loading of the panels. This has been combined with a finite element analysis utilizing a modified Johnson-Cook constitutive relation and a Cockcroft-Latham fracture criterion that accounted for local variation in material properties. The fully coupled simulation approach enabled the relationships between the soil-explosive test charge design, panel geometry, spatially varying material properties and the panel's deformation and dynamic failure responses to be explored. This comprehensive study reveals the existence of a strong instability in the loading that results from changes in sand particle reflection during dynamic evolution of the panel's surface topology. Significant fluid-structure interaction effects are also discovered at the sample sides and corners due to changes of the sand reflection angle by the edge clamping system. © 2012 Elsevier Ltd. All rights reserved.

Investigation of DyBa2Cu3O7-d superconducting domains grown by the infiltration technique starting with small size Dy-211 particles

An infiltration and growth process is here used as an alternative to the classical top-seeded melt-textured growth process for the production of Dy-123 single-domains with finely dispersed small size Dy-211 particles. The starting materials are the 211-particles and a barium and copper rich liquid phase precursor. The infiltration and growth process allows for controlling both the spatial and size distribution of the 211-particles in the final superconducting 123-single-domain. The main parameters (set-ups, maximum processing temperature with respect to the peritectic temperature, nature of reactant, porosity of the 211-preform) of the infiltration and growth process are discussed. Moreover, different processes of chimie douce are shown in order to produce Dy-211 particles with controlled shape and size, particles that can be used as precursors for the infiltration and growth process. © 2005 IOP Publishing Ltd.

High purity GaAs nanowires free of planar defects: Growth and characterization

We investigate how to tailor the structural, crystallographic and optical properties of GaAs nanowires. Nanowires were grown by Au nanoparticle-catalyzed metalorganic chemical vapor deposition. A high arsine flow rate, that is, a high ratio of group V to group III precursors, imparts significant advantages. It dramatically reduces planar crystallographic defects and reduces intrinsic carbon dopant incorporation. Increasing V/III ratio further, however, instigates nanowire kinking and increases nanowire tapering. By choosing an intermediate V/III ratio we achieve uniform, vertically aligned GaAs nanowires, free of planar crystallographic defects, with excellent optical properties and high purity. These findings will greatly assist the development of future GaAs nanowire-based electronic and optoelectronic devices, and are expected to be more broadly relevant to the rational synthesis of other III-V nanowires. © 2008 WILEY-VCH Verlag GmbH & Co. KGaA.

The dynamic response of edge clamped plates loaded by spherically expanding sand shells

The dynamic deformation of both edge clamped stainless steel sandwich panels with a pyramidal truss core and equal mass monolithic plates loaded by spherically expanding shells of dry and water saturated sand has been investigated, both experimentally and via a particle based simulation methodology. The spherically expanding sand shell is generated by detonating a sphere of explosive surrounded by a shell of either dry or water saturated synthetic sand. The measurements show that the sandwich panel and plate deflections decrease with increasing stand-off between the center of the charge and the front of the test structures. Moreover, for the same charge and sand mass, the deflections of the plates are significantly higher in the water saturated sand case compared to that of dry sand. For a given stand-off, the mid-span deflection of the sandwich panel rear faces was substantially less than that of the corresponding monolithic plate for both the dry and water saturated sand cases. The experiments were simulated via a coupled discrete-particle/ finite element scheme wherein the high velocity impacting sand is modeled by interacting particles while the plate is modeled within a Lagrangian finite element setting. The simulations are in good agreement with the measurements for the dry sand impact of both the monolithic and sandwich structures. However, the simulations underestimate the effect of stand-off in the case of the water saturated sand explosion, i.e. the deflections decrease more sharply with increasing stand-off in the experiments compared to the simulations. The simulations reveal that the momentum transmitted into the sandwich and monolithic plate structures by the sand shell is approximately the same, consistent with a small fluid-structure interaction effect. The smaller deflection of the sandwich panels is therefore primarily due to the higher bending strength of sandwich structures. © 2013 The Authors. Published by Elsevier Ltd. All rights reserved.

Sand column impact onto a Kolsky pressure bar

A laboratory-based methodology to launch cylindrical sand slugs at high velocities is developed. The methodology generates well-characterised soil ejecta without the need for detonation of an explosive; this laboratory-based tool thereby allows for the experimental investigation of the soil-structure events. The experimental set-up comprises a launcher with a cylindrical cavity and a piston to push out the sand slug. The apparatus is used to launch both dry and water-saturated sand slugs. High speed photography is used to characterise the evolution of the sand slugs after launch. We find that the diameter of the slugs remains unchanged, and the sand particles possess only an axial component of velocity. However, the sand particles have a uniform spatial gradient of axial velocity and this results in lengthening of the slugs as they travel towards their target. Thus, the density of the sand slugs remains spatially homogenous but decreases with increasing time. The velocity gradient is typically higher in the dry sand slugs than that of the water-saturated slugs. The pressure exerted by the slugs on a rigid-stationary target is measured by impacting the slugs against a direct impact Kolsky bar. After an initial high transient pressure, the pressure reduces to a value of approximately ρv 2 where ρ is the density of the impacting sand slug and v is the particle velocity. This indicates that loading due to the sand is primarily inertial in nature. The momentum transmitted to the Kolsky bar was approximately equal to the incident momentum of the sand slugs, regardless of whether they are dry or water-saturated. © 2013 Elsevier Ltd. All rights reserved.

A laboratory-scale buried charge simulator

An experimental technique has been developed in order to mimic the effect of landmine loading on materials and structures to be studied in a laboratory setting, without the need for explosives. Compressed gas is discharged beneath a sand layer, simulating the dynamic flow generated by a buried explosive. High speed photography reveals that the stages of soil motion observed during a landmine blast are replicated. The effect of soil saturation and the depth of the sand layer on sand motion are evaluated. Two series of experiments have been performed with the buried charge simulator to characterise subsequent impact of the sand. First, the time variation in pressure and impulse during sand impact on a stationary target is evaluated using a Kolsky bar apparatus. It is found that the pressure pulse imparted to the Kolsky bar consists of two phases: an initial transient phase of high pressure (attributed to wave propagation effects in the impacting sand), followed by a lower pressure phase of longer duration (due to lateral flow of the sand against the Kolsky bar). Both phases make a significant contribution to the total imparted impulse. It is found that wet sand exerts higher peak pressures and imparts a larger total impulse than dry sand. The level of imparted impulse is determined as a function of sand depth, and of stand-off distance between the sand and the impacted end of the Kolsky bar. The second study uses a vertical impulse pendulum to measure the momentum imparted by sand impact to a target which is free to move vertically. The effect of target mass upon imparted momentum is investigated. It is concluded that the laboratory-scale sand impact apparatus is a flexible tool for investigating the interactions between structures and dynamic sand flows. © 2013 Elsevier Ltd. All rights reserved.

Effects of adrenergic agents on the expression of zebrafish (Danio rerio) vitellogenin Ao1

Teleost vitellogenins (VTGs) are large multidomain apolipoproteins, traditionally considered to be estrogen-responsive precursors of the major egg yolk proteins, expressed and synthesized mainly in hepatic tissue. The inducibility of VTGs has made them one of the most frequently used in vivo and in vitro biomarkers of exposure to estrogen-active substances. A significant level of zebrafish vtgAo1, a major estrogen responsive form, has been unexpectedly found in heart tissue in our present studies. Our studies on zebrafish cardiomyopathy, caused by adrenergic agonist treatment, suggest a similar protective function of the cardiac expressed vtgAo1. We hypothesize that its function is to unload surplus intracellular lipids in cardiomyocytes for "reverse triglyceride transportation" similar to that found in lipid transport proteins in mammals. Our results also demonstrated that zebrafish vtgAo1 mRNA expression in heart can be suppressed by both (x-adrenergic agonist, phenylephrine (PE) and beta-adrenergic agonist, isoproterenol (ISO). Furthermore, the strong stimulation of zebrafish vtgAo1 expression in plasma induced by the beta-adrenergic antagonist, MOXIsylyl, was detected by Enzyme-Linked ImmunoSorbent Assay (ELISA). Such stimulation cannot be suppressed by taMOXIfen, an antagonist to estrogen receptors. Thus, Our present data indicate that the production of teleost VTG in vivo can be regulated not only by estrogenic agents, but by adrenergic signals as well. (c) 2009 Elsevier Inc. All rights reserved.

Zebrafish eaf1 and eaf2/u19 Mediate Effective Convergence and Extension Movements through the Maintenance of wnt11 and wnt5 Expression

Studies have attributed several functions to the Eaf family, including tumor suppression and eye development. Given the potential association between cancer and development, we set forth to explore Eaf1 and Eaf2/U19 activity in vertebrate embryogenesis, using zebrafish. In situ hybridization revealed similar eaf1 and eaf2/u19 expression patterns. Morpholino-mediated knockdown of either eaf1 or eaf2/u19 expression produced similar morphological changes that could be reversed by ectopic expression of target or reciprocal-target mRNA. However, combination of Eaf1 and Eaf2/U19 (Eafs)-morpholinos increased the severity of defects, suggesting that Eaf1 and Eaf2/U19 only share some functional redundancy. The Eafs knockdown phenotype resembled that of embryos with defects in convergence and extension movements. Indeed, knockdown caused expression pattern changes for convergence and extension movement markers, whereas cell tracing experiments using kaeda mRNA showed a correlation between Eafs knockdown and cell migration defects. Cardiac and pancreatic differentiation markers revealed that Eafs knockdown also disrupted midline convergence of heart and pancreatic organ precursors. Noncanonical Wnt signaling plays a key role in both convergence and extension movements and midline convergence of organ precursors. We found that Eaf1 and Eaf2/U19 maintained expression levels of wnt11 and wnt5. Moreover, wnt11 or wnt5 mRNA partially rescued the convergence and extension movement defects occurring in eafs morphants. Wnt11 and Wnt5 converge on rhoA, so not surprisingly, rhoA mRNA more effectively rescued defects than either wnt11 or wnt5 mRNA alone. However, the ectopic expression of wnt11 and wnt5 did not affect eaf1 and eaf2/u19 expression. These data indicate that eaf1 and eaf2/u19 act upstream of noncanonical Wnt signaling to mediate convergence and extension movements.

Effects of adrenergic agonists on the extrahepatic expression of vitellogenin Ao1 in heart and brain of the Chinese rare minnow (Gobiocypris rarus)

Teleost vitellogenins (VTGs) are large multidomain apolipoproteins and traditionally considered as the estrogen responsive precursors of the major egg yolk proteins. We identified five clones encoding VTGs, about 16% of the random EST clones from our constructed cDNA library from Chinese rare minnow liver tissue treated with 17 beta-estradiol (E2). Full-length vtgAo1 has been obtained based on the sequence information of four partial cDNA inserts by RACE. The inducibility of the vtgAo1 expression in liver by E2 was confirmed by RT-PCR. The presence of vtgAo1 transcripts have been observed primarily in liver. However. a significant level of the vtgAo1 was found in an unexpected location, heart, particularly in atrial cells by RT-PCR and whole mount in situ hybridization analyses. The vtgAo1 mRNA expression in heart and liver tissue could be suppressed by both alpha-adrenergic agonist, phenylephrine (PE) and beta-adrenergic agonist, isoproterenol (ISO). The expression of VTG in the heart observed in the present studies suggested it may provide protection from surplus intracellular lipids in fish cardiomyocytes as triglyceride transport proteins do in mammals. The results also indicated that the production of teleost vtg in vivo can be regulated by riot only estrogenic agents, but adrenergic signals as well. (c) 2008 Elsevier B.V. All rights reserved.