The structure of Rph, an exoribonuclease from Bacillus anthracis, at 1.7 angstrom resolution

Maturation of tRNA precursors into functional tRNA molecules requires trimming of the primary transcript at both the 5' and 3' ends. Cleavage of nucleotides from the 3' stem of tRNA precursors, releasing nucleotide diphosphates, is accomplished in Bacillus by a phosphate-dependent exoribonuclease, Rph. The crystal structure of this enzyme from B. anthracis has been solved by molecular replacement to a resolution of 1.7 angstrom and refined to an R factor of 19.3%. There is one molecule in the asymmetric unit; the crystal packing reveals the assembly of the protein into a hexamer arranged as a trimer of dimers. The structure shows two sulfate ions bound in the active-site pocket, probably mimicking the phosphate substrate and the phosphate of the 3'-terminal nucleotide of the tRNA precursor. Three other bound sulfate ions point to likely RNA-binding sites

New Genera and Species of Fossil Marine Amioid Fishes (Actinopterygii, Holostei) from the Late Cretaceous Agoult locality in Southeastern Morocco

The document is Terry C. Grande\u27s (et al.) abstract in the Society of Vertebrate Paleontology 77th Annual Meeting Program and Abstracts

A Review of Neogene and Quaternary Pikes of Southeastern Europe and a New Species from the Early Pleistocene of Nogaisk, Ukraine

The fish genus Esox (Teleostei, Esocidae) has been recorded from thirty late Miocene, Pliocene, and Pleistocene localities where forty-one bone-bearing strata are exposed in the territory of Ukraine, Russian Federation, and Republic of Moldova. From eight localities the genus is reported or described for the first time. A detailed description and morphological analysis of the currently available osteological material demonstrates the presence of four species in the studied area: (i) Esox sibiricus (late Miocene–early Pliocene); (ii) Esox moldavicus (early Pliocene–early Pleistocene); (iii) Esox nogaicus sp. nov. (early Pleistocene, Calabrian); (iv) Esox lucius (early–middle Pleistocene). The Northern Pike (Esox lucius) is recorded for the first time in the early Pleistocene fossil record of southeastern Europe. The new species E. nogaicus is characterized by a massive dentary with deep symphysis and the possible presence of a pair of fixed canine-like teeth near the anterior end of the vomer. Such canine teeth are seen also in certain species known only from North America, the extant Esox masquinongy, the fossil species E. columbianus, and an unnamed Miocene form. However, unlike in E. nogaicus, in the three North American species fixed canines also occur anteriorly on the palatines. The Miocene, Pliocene, and Pleistocene pikes from southeastern Europe document a greater diversity of morphologies in the past than exists today in the pike species of Europe. Changes in the predominant species of Esox in southeastern Europe are hypothesized to be driven by changing global and regional climates

Higher-Order Compact Schemes for Numerical Simulation of Incompressible Flows

A higher order accurate numerical procedure has been developed for solving incompressible Navier-Stokes equations for 2D or 3D fluid flow problems. It is based on low-storage Runge-Kutta schemes for temporal discretization and fourth and sixth order compact finite-difference schemes for spatial discretization. The particular difficulty of satisfying the divergence-free velocity field required in incompressible fluid flow is resolved by solving a Poisson equation for pressure. It is demonstrated that for consistent global accuracy, it is necessary to employ the same order of accuracy in the discretization of the Poisson equation. Special care is also required to achieve the formal temporal accuracy of the Runge-Kutta schemes. The accuracy of the present procedure is demonstrated by application to several pertinent benchmark problems

The Aggregation Kinetics of a Simulated Telechelic Polymer

We investigate the aggregation kinetics of a simulated telechelic polymer gel. In the hybrid Molecular Dynamics (MD) / Monte Carlo (MC) algorithm, aggregates of associating end groups form and break according to MC rules, while the position of the polymers in space is dictated by MD. As a result, the aggregate sizes change every time step. In order to describe this aggregation process, we employ master equations. They define changes in the number of aggregates of a certain size in terms of reaction rates. These reaction rates indicate the likelihood that two aggregates combine to form a large one, or that a large aggregate splits into two smaller parts. The reaction rates are obtained from the simulations for a range of temperatures. Our results indicate that the rates are not only temperature dependent, but also a function of the sizes of the aggregates involved in the reaction. Using the measured rates, solutions to the master equations are shown to be stable and in agreement with the aggregate size distribution, as obtained directly from simulation data. Furthermore, we show how temperature induced variations in these rates give rise to the observed changes in the aggregate distribution that characterizes the sol-gel transition.Comment: 9 pages, 10 figure

The morphology and sculpture of ossicles in the Cyclopteridae and Liparidae (Teleostei) of the Baltic Sea

Small to very small bones (ossicles) in one species each of the families Cyclopteridae and Liparidae (Cottiformes) of the Baltic Sea are described and for the first time illustrated with SEM images. These ossicles, mostly of dermal origin, include dermal platelets, scutes, tubercles, prickles and sensory line segments. This work was undertaken to reveal characteristics of the morphology, sculpture and ultrasculpture of these small ossicles that could be useful as additional features in taxonomy and systematics, in a manner similar to their use in fossil material. The scutes and tubercles of the cyclopterid Cyclopterus lumpus Linnaeus are built of small denticles, each having its own cavity viscerally. The thumbtack prickles of the liparid Liparis liparis (Linnaeus) have a tiny spinule on a porous basal plate; the small size of the prickles seems to be related to their occurrence in the exceptionally thin skin, to an adaptation for minimizing weight and/or metabolic cost and possibly to their evolution from isolated ctenii no longer attached to the scale plates of ctenoid scales. Nodular ultrasculpture was found on the tubercle denticles of C.lumpus, resembling some kinds of ultrasculpture seen in Palaeozoic vertebrates. Samples from the posterior part of the head of C. lumpus and the anterior part of the trunk of L. liparis each contained an ossified sensory line segment with distinct characteristics, as also reported in other cottoids

The morphology and sculpture of ossicles in the Cottidae (Teleostei) of the Baltic Sea

Small to very small ossified structures (ossicles) such as cephalic horns, dermal tubercles, fin-ray rods, lateral-line canal segments, branchial tooth plates and gill-raker tubercles of three species of the teleostean fish family Cottidae inhabiting the Baltic Sea are described and for the first time illustrated with SEM images, with emphasis on their microscopic external features. The morphology and sculpture of these small ossicles notably differ in the three genera, but differences can also occur between males and females, as documented here in Myoxocephalus scorpius (Linnaeus). The detailed features of such ossicles are potentially useful for taxonomic identification in sea-floor sediments or gut contents, in a manner similar to their use in many modern and fossil fishes, and may also prove useful as phylogenetically important characters at generic and familial levels

Anatomy of the Silurian thelodont Phlebolepis elegans Pander

The Silurian thelodont Phlebolepis elegans Pander from Saaremaa, Estonia, is one of the most-often illustrated early vertebrates, yet its external morphology has remained poorly known and experts seldom agree about its probable body form. We examined hundreds of articulated specimens from the type locality (Himmiste Quarry) to reconstruct its morphological features. We found that a reconstruction published more than four decades ago by A. Ritchie was the best available till now. We disagreed mostly in that the mouth is not terminal, but subterminal, and there is a slight development of a rostrum dorsal to the mouth. The pectoral fin originates close behind the orbits, but is otherwise similar to Ritchie’s reconstruction. We also found the caudal fin to be much larger, more flexible and more symmetrical (though not perfectly symmetrical) than earlier reconstructions, with a large dorsal lobe and an even larger ventral lobe, and a fin web supported by slender ‘ray-like’ scale-covered lobes. The shape, number and location of the branchial openings are notably still not certainly known. Our preferred morphological features are represented by an artist’s restoration. With this revised understanding, future representations of Phlebolepis elegans can be based on more reliable information and its morphology can be compared more accurately with that of other early vertebrates

Hydroxyl radical production in DC streamer discharge

Plasma-induced advanced oxidation processes do not suffer from the drawbacks, such as carcinogenic by-products, associated with conventional water treatment, and enable the removal of micro-pollutants. The high oxidation strength of hydroxyl radicals enables degradation of resistant contaminants. Many reactions are known to occur at the plasma-water interface; however, the mechanisms of hydroxyl radical production are still not clear. To understand the physical and chemical processes occurring at the plasma-water interface, this research involved investigation of the hydroxyl radicals produced during d.c. streamer discharges. A needle-plate electrode configuration in atmospheric air was used, with the treated solution used as the ground electrode. To understand the effects of polarity and gas type on hydroxyl radical production, both positive- and negative-polarity energization in air, nitrogen and helium were investigated. Plasma filaments were developed from the needle electrode, which was in contact with the solution. Terephthalic acid (TA) was used as a scavenger of hydroxyl (OH) radicals, with OH density subsequently being quantified by fluorescence emission from 2-hydroxyterephthalic acid (HTA), which is formed through specific reaction between TA and OH. The power inputs in positive pulsed streamer discharges were 0.125 W, 0.18 W and 0.26 W in air, nitrogen and helium, respectively; the corresponding hydroxyl radical production efficiencies were 0.56 mmol/kWh, 1.1 mmol/kWh and 5.94 mmol/kWh, respectively. For negative pulsed streamer discharges in air, the power input was 0.063 W and the efficiency was 1 mmol/kWh. The hydroxyl radical production rates were 2.6× 10-7 Ms-1 in negative air discharges, and 2.7× 10-7 Ms-1, 1.8× 10-6 Ms-1, and 2.2× 10-6 Ms-1 in positive air, nitrogen and helium discharges, respectively

The Willamette Valley (Oregon) Prairie Plant Trait Dataset

The Willamette Valley (Oregon) Prairie Plant Trait Dataset is a compilation of plant traits of species important in upland prairies, wetland prairies, vernal pools, and emergent wetlands, and in the restoration of prairies and wetlands of the Willamette Valley of Oregon. These species are also found widely throughout the Pacific Northwest. The dataset contains more than 6600 data points on 187 species. Three types of plant trait data are included in the dataset: quantitative, categorical, and text. Sources of plant trait data include direct measurements in the field or in the laboratory, or gathered from the published literature, including local floras, references books, and databases. Laboratory measurements include measurements of plant growth under standardized growth chamber conditions. The use of standardized conditions allows integration of results with those in the scientific literature. Standardized growth chamber conditions include specifications for germination media, transfer of germinates, pot size, growing media, nutrient solutions, growing illumination and temperatures, and dates of harvest. Growth chamber procedures followed the general recommendations of the Integrated Screening Programme (Hendry, G.A.F. and Grime, J.P. (eds) 1993. Methods in Comparative Plant Ecology: A Laboratory Manual. Chapman and Hall, London)