Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism

Kinases are ubiquitous enzymes that are pivotal to many biochemical processes. There are contrasting views on the phosphoryl-transfer mechanism in propionate kinase, an enzyme that reversibly transfers a phosphoryl group from propionyl phosphate to ADP in the final step of non-oxidative catabolism of L-threonine to propionate. Here, X-ray crystal structures of propionate- and nucleotide-bound Salmonella typhimurium propionate kinase are reported at 1.8-2.0 angstrom resolution. Although the mode of nucleotide binding is comparable to those of other members of the ASKHA superfamily, propionate is bound at a distinct site deeper in the hydrophobic pocket defining the active site. The propionate carboxyl is at a distance of approximate to 5 angstrom from the -phosphate of the nucleotide, supporting a direct in-line transfer mechanism. The phosphoryl-transfer reaction is likely to occur via an associative S(N)2-like transition state that involves a pentagonal bipyramidal structure with the axial positions occupied by the nucleophile of the substrate and the O atom between the - and the -phosphates, respectively. The proximity of the strictly conserved His175 and Arg236 to the carboxyl group of the propionate and the -phosphate of ATP suggests their involvement in catalysis. Moreover, ligand binding does not induce global domain movement as reported in some other members of the ASKHA superfamily. Instead, residues Arg86, Asp143 and Pro116-Leu117-His118 that define the active-site pocket move towards the substrate and expel water molecules from the active site. The role of Ala88, previously proposed to be the residue determining substrate specificity, was examined by determining the crystal structures of the propionate-bound Ala88 mutants A88V and A88G. Kinetic analysis and structural data are consistent with a significant role of Ala88 in substrate-specificity determination. The active-site pocket-defining residues Arg86, Asp143 and the Pro116-Leu117-His118 segment are also likely to contribute to substrate specificity.

Active learning in keyword search-based data integration

The problem of scaling up data integration, such that new sources can be quickly utilized as they are discovered, remains elusive: Global schemas for integrated data are difficult to develop and expand, and schema and record matching techniques are limited by the fact that data and metadata are often under-specified and must be disambiguated by data experts. One promising approach is to avoid using a global schema, and instead to develop keyword search-based data integration-where the system lazily discovers associations enabling it to join together matches to keywords, and return ranked results. The user is expected to understand the data domain and provide feedback about answers' quality. The system generalizes such feedback to learn how to correctly integrate data. A major open challenge is that under this model, the user only sees and offers feedback on a few ``top-'' results: This result set must be carefully selected to include answers of high relevance and answers that are highly informative when feedback is given on them. Existing systems merely focus on predicting relevance, by composing the scores of various schema and record matching algorithms. In this paper, we show how to predict the uncertainty associated with a query result's score, as well as how informative feedback is on a given result. We build upon these foundations to develop an active learning approach to keyword search-based data integration, and we validate the effectiveness of our solution over real data from several very different domains.

Fusing the Navigation Information of Dual Foot-Mounted Zero-Velocity-Update-Aided Inertial Navigation Systems

A range constraint method viz. centroid method is proposed to fuse the navigation information of dual (right and left) foot-mounted Zero-velocity-UPdaTe (ZUPT)-aided Inertial Navigation Systems (INSs). Here, the range constraint means that the distance of separation between the position estimates of right and left foot ZUPT-aided INSs cannot be greater than a quantity known as foot-to-foot maximum separation. We present the experimental results which illustrate the applicability of the proposed method. The results show that the proposed method significantly enhances the accuracy of the navigation solution when compared to using two uncoupled foot-mounted ZUPT-aided INSs. Also, we compare the performance of the proposed method with the existing data fusion methods.

Air microjet system for non-contact force application and the actuation of micro-structures

We demonstrate a non-contact technique to apply calibrated and localized forces in the micro-Newton to milli-Newton range using an air microjet. An electromagnetically actuated diaphragm controlled by a signal generator is used to generate the air microjet. With a nozzle diameter of 150 mu m, the microjet diameter was maintained to a maximum of 1 mm at a distance of 5 mm from the nozzle. The force generated by the microjet was measured using a commercial force sensor to determine the velocity profile of the jet. Axial flow velocities of up to 25 m s(-1) were obtained at distances as long as 6 mm. The microjet exerted a force up to 1 mu N on a poly dimethyl siloxane (PDMS) micropillar (50 mu m in diameter, 157 mu m in height) and 415 mu N on a PDMS membrane (3 mm in diameter, 28 mu m thick). We also demonstrate that from a distance of 6 mm our microjet can exert a peak pressure of 187 Pa with a total force of about 84 mu N on a flat surface with 8 V operating voltage. Out of the cleanroom fabrication and robust design make this system cost effective and durable.

Electronic and Magnetic Properties of Yttrium-doped Silicon Carbide Nanotubes: Density Functional Theory Investigations

The electronic structure of yttrium-doped Silicon Carbide Nanotubes has been theoretically investigated using first principles density functional theory (DFT). Yttrium atom is bonded strongly on the surface of the nanotube with a binding energy of 2.37 eV and prefers to stay on the hollow site at a distance of around 2.25 angstrom from the tube. The semi-conducting nanotube with chirality (4, 4) becomes half mettalic with a magnetic moment of 1.0 mu(B) due to influence of Y atom on the surface. There is strong hybridization between d orbital of Y with p orbital of Si and C causing a charge transfer from d orbital of the Y atom to the tube. The Fermi level is shifted towards higher energy with finite Density of States for only upspin channel making the system half metallic and magnetic which may have application in spintronic devices.

Characterization of a liquid crystal microlens array using multiwalled carbon nanotube electrodes.

Reconfigurable liquid crystal microlenses employing arrays of multiwalled carbon nanotubes (MWNTs) have been designed and fabricated. The cells consist of arrays of 2 microm high MWNTs grown by plasma-enhanced chemical vapor deposition on silicon with a top electrode of indium tin oxide coated glass positioned 20 microm above the silicon and the gap filled with the nematic liquid crystal BLO48. Simulations have found that, while its nematic liquid crystal aligns with MWNTs within a distance of 10nm, this distance is greatly enhanced by the application of an external electric field. Polarized light experiments show that light is focused with focal lengths ranging from approximately 7 microm to 12 microm.

Diffusion dominated process for the crystal growth of a binary alloy

The pure diffusion process has been often used to study the crystal growth of a binary alloy in the microgravity environment. In the present paper, a geometric parameter, the ratio of the maximum deviation distance of curved solidification and melting interfaces from the plane to the radius of the crystal rod, was adopted as a small parameter, and the analytical solution was obtained based on the perturbation theory. The radial segregation of a diffusion dominated process was obtained for cases of arbitrary Peclet number in a region of finite extension with both a curved solidification interface and a curved melting interface. Two types of boundary conditions at the melting interface were analyzed. Some special cases such as infinite extension in the longitudinal direction and special range of Peclet number were reduced from the general solution and discussed in detail.

Combustion tube studies of dust flame acceleration

A new pneumatic dispersion system for obtaining a good quality uniform dust suspension in a horizontal dust combustion tube was developed. The effect of three different dispersion techniques on self-sustained dust flame acceleration in such a combustion tube was examined. The importance of the dispersion quality in the test tube for maintaining a self-sustained dust flame acceleration was demonstrated. A combustion tube for studies of flame acceleration in fine aluminum dust-air mixture and its transition to detonation under industrial ignition conditions was constructed in the course of the present study. It consists mainly of an initiation section and a test section. The initiation section must be equipped in a well-developed dispersion system for creating a good dispersion condition in the test tube. The length of this section is 3 meters. The test tube requires only to distribute uniformly the dust over the bottom of the tube prior to the experiment. The aluminum dust spherical in shape with 6 mu m in diameter was used for tests. Experimental results demonstrated that the increase in flame velocity is roughly linear through the entire length of the test tube. The highest flame propagation velocity in fine aluminum dust-air mixture approaches some 1200m/s at a distance of 4.8m from the ignition plate.

Some theoretical aspects of the simplified Navier-Stokes(SNS) equations

This study deals with the formulation, mathematical property and physical meaning of the simplified Navier-Stokes (SNS) equations. The tensorial SNS equations proposed is the simplest in form and is applicable to flow fields with arbitrary body boundaries. The zones of influence and dependence of the SNS equations, which are of primary importance to numerical solutions, are expounded for the first time from the viewpoint of subcharacteristics. Besides, a detailed analysis of the diffusion process in flow fields shows that the diffusion effect has an influence zone globally windward and an upwind propagation greatly depressed by convection. The maximum upwind influential distance of the viscous effect and the relative importance of the viscous effect in the flow direction to that in the direction normal to the flow are represented by the Reynolds number, which illustrates the conversion of the complete Navier-Stokes (NS) equations to the SNS equations for flows with large Reynolds number.

Modeling Study of Shrouding Gas Effects on a Laminar Argon Plasma Jet Impinging Upon a Flat Substrate in Air Surroundings

With the laminar plasma materials processing as the research background, modeling study is conducted concerning the effects of argon shroud on the characteristics of the laminar argon plasma jet impinging normally upon a flat substrate located in air surroundings. It is shown that adding shrouding gas is an effective method to reduce and control the entrainment of ambient air into the laminar plasma jet. The shrouding gas flow rate or velocity, the injection slot width and the stand-off distance of the substrate appreciably affect the air contents in the plasma near the substrate surface.

Crossing the Threshold: Moving e-portfolios into the mainstream

Crossing the Threshold, one of a series of advice and guidance publications, is designed to support use of the online e-Portfolio Implementation Toolkit and video case studies by those involved in wide-scale implementation of e-portfolios in their institutions. As the resources address the needs of both managers and practitioners, the publication has relevance for a wide range of readers in further and higher education and work-based learning. To assist the planning and effective management of a large-scale e-portfolio implementation, Crossing the Threshold follows the stages of an implementation journey with insights and guidance drawn from the toolkit and its supporting case studies. Links are provided throughout the publication to more detailed information in the two online resources.

Preliminary study on the construction and management of integrated rice-cum-fish culture system at Karabande, New Bussa

Details are given of a study carried out in Nigeria, to introduce the practice of fish-cum-rice culture, using Sarotherodon galilaeus. Two plots each measuring 360m super(2) were used for this study and were compared with the farmer's two plots measuring 300m super(2) and 350m super(2). The plots were modified and had two central canals. Rice seedlings were transplanted into the plots after 19 days using a planting distance of 20 x 20cm. Three rice seedlings were planted per hole, using rice variety FARO 40, and grown for 90 days. About 240 and 180 S. galilaeus fingerlings of mean weight of 30g and 26g were stocked in the two experimental plots, respectively. They were fed with pelleted feed of 25% C.P. and monitored for 100 days. A yield of 22.8kg was obtained in plot A while 15.66kg was obtained in plot B. A rice yield of 250kg (i.e 5 bags) was obtained in each of the plots. The results obtained were compared with plots with no fish

Preparation and characterization of an intramolecular electron transfer in a pentaammineruthenium derivative of Candida krisei cytochrome c

A semisynthetic binuclear metalloprotein has been prepared by appending the pentaammineruthenium moiety to histidine 39 of the cytochrome c from the yeast Candida krusei. The site of ruthenium binding was identified by peptide mapping. Spectroscopic and electrochemical properties of the derivative indicate the protein conformation is unperturbed by the modification. A preliminary (minimum) rate constant of 170s^(-1) has been determined for the intramolecular electron transfer from ruthenium(II) to iron(III), which occurs over a distance of at least 13Å (barring major conformational changes). Electrochemical studies indicate that this reaction should proceed with a driving force of ~170mV. The rate constant is an order of magnitude faster than that observed in horse heart cytochrome c for intramolecular electron transfer from pentaammineruthenium(II)(histidine 33) to iron(III) (over a similar distance, and with a similar driving force), suggesting a medium or orientation effect makes the Candida intramolecular electron transfer more favorable.

Self-compression of femtosecond pulses in argon with a power close to the self-focusing threshold

Self-compression of femtosecond pulses in noble gases with an input power close to the self-focusing threshold has been investigated experimentally and theoretically. It is demonstrated that either multiphoton ionization (MPI) or space time focusing and self-steepening effects can induce pulse shortening, but they predominate at different beam intensities during the propagation. The latter effects play a key role in the final pulse self-compression. By choosing an appropriate focusing parameter, action distance of the space time focusing and self-steepening effects can be lengthened, which can promote a shock pulse structure with a duration as short as two optical cycles. It is also found that, for our calculation cases in which an input pulse power is close to the self-focusing threshold, either group velocity dispersion (GVD) or multiphoton absorption (MPA) has a negligible influence on pulse characteristics in the propagation process.

Structure and properties of an amorphous ferromagnetic alloy

The structure and the electrical and magnetic properties of an amorphous alloy containing approximately 80 at .% iron, 13 at.% phos phorus and 7 at.% carbon (Fe_(80)Fe_(13)C_7) obtained by rapid quenching from the liquid state have been studied. Transmission electron diffraction data confirm the amorphous nature of this alloy. An analysis of the radial distribution function obtained from X-ray diffraction data indicates that the number of nearest neighbors is approximately seven, at a distance of 2.6A. The structure of the alloy can be related to that of silicate glasses and is based on a random arrangement of trigonal prisms of Fe_2P and Fe_3C types in which the iron atoms have an average ligancy of seven. Electrical resistance measurements show that the alloys are metallic. A minimum in the electrical resistivity vs. temperature curve is observed between 10° K to 50° K depending on the specimen, and the temperature at which the minimum occurs is related to the degree of local ordering. The Fe-P-C amorphous alloys are ferromagnetic. The Curie temperature measured by the induction method and by Mossbauer spectroscopy is 315° C. The field dependence of the magneto-resistance at temperatures from liquid helium to room temperature is similar to that found in crystalline iron. The ordinary Hall coefficient is approximately 10^(-11) volt-cm/amp-G. The spontaneous Hall coefficient is about 0.6 x 10^(-9) volt-cm/amp-G and is practically independent of temperature from liquid helium temperature up to 300° c.