Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn(341), Tyr(60) and Phe(351) in tetrahydrofolate binding

SHMT (serine hydoxymethyltransferase), a type I pyridoxal 5'-phosphate-dependent enzyme, catalyses the conversion of L-serine and THF (tetrahydrofolate) into glycine and 5,10-methylene THE SHMT also catalyses several THF-independent side reactions such as cleavage of P-hydroxy amino acids, trans-amination, racemization and decarboxylation. In the present study, the residues Asn(341), Tyr(60) and Phe(351), which are likely to influence THF binding, were mutated to alanine, alanine and glycine respectively, to elucidate the role of these residues in THF-dependent and -independent reactions catalysed by SHMT. The N341A and Y60A bsSHMT (Bacillus stearothermophilus SHMT) mutants were inactive for the THF-dependent activity, while the mutations had no effect on THF-independent activity. However, mutation of Phe(351) to glycine did not have any effect oil either of the activities. The crystal structures of the glycine binary complexes of the mutants showed that N341A bsSHMT forms an external aldimine as in bsSHMT, whereas Y60A and F351G bsSHMTs exist as a Mixture of internal/external aldimine and gem-diamine forms. Crystal structures of all of the three Mutants obtained in the presence of L-allo-threonine were similar to the respective glycine binary complexes. The structure of the ternary complex of F351G bsSHMT with glycine and FTHF (5-formyl THF) showed that the monoglutamate side chain of FTHF is ordered in both the subunits of the asymmetric unit, unlike in the wild-type bsSHMT. The present studies demonstrate that the residues Asn(341) and Tyr(60) are pivotal for the binding of THF/FTHF, whereas Phe(351) is responsible for the asymmetric binding of FTHF in the two subunits of the dimer.

Some limit theorems for regenerative queues

We consider a single server queue with the interarrival times and the service times forming a regenerative sequence. This traffic class includes the standard models: lid, periodic, Markov modulated (e.g., BMAP model of Lucantoni [18]) and their superpositions. This class also includes the recently proposed traffic models in high speed networks, exhibiting long range dependence. Under minimal conditions we obtain the rates of convergence to stationary distributions, finiteness of stationary moments, various functional limit theorems and the continuity of stationary distributions and moments. We use the continuity results to obtain approximations for stationary distributions and moments of an MMPP/GI/1 queue where the modulating chain has a countable state space. We extend all our results to feedforward networks where the external arrivals to each queue can be regenerative. In the end we show that the output process of a leaky bucket is regenerative if the input process is and hence our results extend to a queue with arrivals controlled by a leaky bucket.

Structural correlations in GexSe1-x glasses - a neutron diffraction study

Neutron diffraction measurement is carried out on GexSe1-x glasses, where 0.1 less than or equal to x less than or equal to 0.4, in a Q interval of 0.55-13.8 Angstrom(-1). The first sharp diffraction peak (FSDP) in the structure factor, S(Q), shows a systematic increase in the intensity and shifts to a lower Q with increasing Ge concentration. The coherence length of FSDP increases with x and becomes maximum for 0.33 less than or equal to x less than or equal to 0.4. The Monte-Carlo method, due to Soper, is used to generate S(Q) and also the pair correlation function, g(r). The generated S(Q) is in agreement with the experimental data for all x. Analysis of the first four peaks in the total correlation function, T(r), shows that the short range order in GeSe2 glass is due to Ge(Se-1/2)(4) tetrahedra, in agreement with earlier reports. Se-rich glasses contain Se-chains which are cross-linked with Ge(Se-1/2)(4) tetrahedra. Ge-2(Se-1/2)(6) molecular units are the basic structural units in Ge-rich, x = 0.4, glass. For x = 0.2, 0.33 and 0.4 there is evidence for some of the tetrahedra being in an edge-shared configuration. The number of edge-shared tetrahedra in these glasses increase with increasing Ge content.

Study of the processes occurring when sputtering YBa2Cu3O7-x in pure oxygen

The sputter deposition of YBa2Cu3O7-x in a de-diode was performed in pure oxygen medium and an optical spectroscopic study of the resultant discharge revealed strong emissions from both metal atoms and oxygen ions. Emission intensities were studied in pressure range from 0.5 to 3 mbar, with substrate temperatures from 150 to 850 degrees C. Raising the substrate temperature to 850 degrees C increased the number of positive ions and excited neutral atoms. Raising the pressure decreased the emission intensities of excited neutral and ionic species. The results have been compared with those obtained from Langmuir probe measurements. The rise in emission intensities of excited neutrals and ions with temperature suggested the possibility of chemically enhanced physical sputtering of YBa2Cu3O7-x. The effect of process conditions on film composition and quality is also discussed.

Damage assessment of basaltic rock mass due to repeated blasting in a railway tunnelling project - A case study

The demand for tunnelling and underground space creation is rapidly growing due to the requirement of civil infrastructure projects and urbanisation. Blasting remains the most inexpensive method of underground excavations in hard rock. Unfortunately, there are no specific safety guidelines available for the blasted tunnels with regards to the threshold limits of vibrations caused by repeated blasting activity in the close proximity. This paper presents the results of a comprehensive study conducted to find out the effect of repeated blast loading on the damage experienced by jointed basaltic rock mass during tunnelling works. Conducting of multiple rounds of blasts for various civil excavations in a railway tunnel imparted repeated loading on rock mass of sidewall and roof of the tunnel. The blast induced damage was assessed by using vibration attenuation equations of charge weight scaling law and measured by borehole extensometers and borehole camera. Ground vibrations of each blasting round were also monitored by triaxial geophones installed near the borehole extensometers. The peak particle velocity (V-max) observations and plastic deformations from borehole extensometers were used to develop a site specific damage model. The study reveals that repeated dynamic loading imparted on the exposed tunnel from subsequent blasts, in the vicinity, resulted in rock mass damage at lesser vibration levels than the critical peak particle velocity (V-cr). It was found that, the repeated blast loading resulted in the near-field damage due to high frequency waves and far-field damage due to low frequency waves. The far field damage, after 45-50 occurrences of blast loading, was up to 55% of the near-field damage in basaltic rock mass. The findings of the study clearly indicate that the phenomena of repeated blasting with respect to number of cycles of loading should be taken into consideration for proper assessment of blast induced damage in underground excavations.

Response And Stability Of A Stochastic Beam-Column Using Stochastic Fem

A beam-column resting on continuous Winkler foundation and discrete elastic supports is considered. The beam-column is of variable cross-section and the variation of sectional properties along the axis of the beam-column is deterministic. Young's modulus, mass per unit length and distributed axial loadings of the beam-column have a stochastic distribution. The foundation stiffness coefficient of the Winkler model, the stiffnesses of discrete elastic supports, stiffnesses of end springs and the end thrust, are all considered as random parameters. The material property fluctuations and distributed axial loadings are considered to constitute independent, one-dimension uni-variate homogeneous real stochastic fields in space. The foundation stiffness coefficient, stiffnesses of the discrete elastic supports, stiffnesses of end springs and the end thrust are considered to constitute independent random variables. Static response, free vibration and stability behaviour of the beam-column are studied. Hamilton's principle is used to formulate the problem using stochastic FEM. Sensitivity vectors of the response and stability parameters are evaluated. Using these statistics of free vibration frequencies, mode shapes, buckling parameters, etc., are evaluated. A numerical example is given.

Cloning and development of pathotype-specific SCAR marker associated with Sclerospora graminicola isolates from pearl millet

Downy mildew pathogen of pearl millet in India is associated with the spread of the highly virulent Sclerospora graminicola pathotype-1. Twenty-seven S. graminicola isolates were screened using 20 intersimple sequence repeats (ISSR). Dinucleotide repeat primer [17898A-(CA)(6) AC] amplified a similar to 600 bp fragment specific to five isolates of pathotype-1 (Sg 048, Sg 153, Sg 212, DM-11 and DM-90). The ISSR fragment linked with pathotype-1 was cloned successfully and sequenced. To convert ISSR fragments into pathotype-specific sequence characterised amplified region (SCAR) markers, PCR primers were designed using a sequence of the cloned DNA fragment. PCR amplification using SCAR primer pair (UOM3-Sg-Path1-F/R) amplified a single 284 bp band only in isolates of S. graminicola pathotype-1. This SCAR primer pair did not amplify the 284 bp product from the other five S. graminicola pathotypes or a negative control, which demonstrates primer specificity for pathotype-1. The SCAR primer pair (UOM3-Sg-Path1-F/R) obtained in this study will provide a valuable tool for rapid identification and specific detection of S. graminicola pathotype-1.

Mechanism of coupling periodate-oxidized nucleosides to proteins

This paper describes a mechanism of coupling periodate-oxidized nucleosides to proteins. Each of the dialdehyde groups of a periodate-oxidized nucleoside is shown to couple to lysine residues on different protein molecules through Schiff bases, thereby cross-linking different protein molecules, forming a polymer. This is in contrast to the previous model in which nucleosides were suggested to couple to proteins through a morpholine structure. The cross-linked structure of the nucleoside-antigen, significantly different when compared to the native protein, may affect the specificity and the efficiency of antibody production.

Distribution of black nodes at various levels in a linear quadtree

The distribution of black leaf nodes at each level of a linear quadtree is of significant interest in the context of estimation of time and space complexities of linear quadtree based algorithms. The maximum number of black nodes of a given level that can be fitted in a square grid of size 2n × 2n can readily be estimated from the ratio of areas. We show that the actual value of the maximum number of nodes of a level is much less than the maximum obtained from the ratio of the areas. This is due to the fact that the number of nodes possible at a level k, 0≤k≤n − 1, should consider the sum of areas occupied by the actual number of nodes present at levels k + 1, k + 2, …, n − 1.

Kinetics of thermal decomposition of strontium zirconyl carbonate, Sr2Zr2O5CO3

The kinetics of decomposition of the carbonate Sr2Zr2O5CO3, are greatly influenced by the thermal effects during its formation. (α−t) curves are found to be sigmoidal and they could be analysed based on power law equations followed by first-order decay. The presence of carbon in the vacuum-prepared sample of carbonate has a strong deactivating effect. The carbonate is fairly crystalline and its decomposition leads to the formation of crystalline strontium zirconate.

Electrical transport and crystallization studies of glassy semiconducting Si20Te80 alloy at high pressure

The effect of pressure on the electrical resistivity of bulk Si20Te80 glass is reported. Results of calorimetric, X-ray and transmission electron microscopy investigations at different stages of crystallization of bulk Si20Te80 glass are also presented. A pressure induced glass-to-crystal transition occurs at a pressure of 7 GPa. Pressure and temperature dependence of the electrical resistivity of Si20Te80 glass show the observed transition is a pressure induced glassy semiconductor to crystalline metal transition. The glass also exhibits a double Tg effect and double stage crystallization, under heating. The differences between the temperature induced crystallization (primary crystallization) and pressure induced congruent crystallization are discussed.

Phagocytosis Of Mast Cell Granules By Cultured Fibroblasts

Cultured rat embryonic skin fibroblasts phagocytosed rat mast cell granules added to the medium or released from co-cultured mast cells by rabbit anti-rat IgE or Compound 48/80. Electron microscopy of fibroblasts incubated with mast cell granules revealed that granules adjacent to the plasmalemma were engulfed by long, thin cytoplasmic processes.

Influence of electroslag refining on the hot ductility of AISI 4340 steel in torsion

Electroslag refining is a useful remelting process by which clean steels can be produced for sophisticated applications. In this investigation, AISI 4340 steel has been electroslag refined and the improvement in its hot ductility has been assessed using hot torsion tests; electroslag refining has improved the hot ductility considerably. The temperature at which peak ductility is obtained has also increased — from 1473 K in the unrefined steel to 1573 K in ESR steel. Results indicate that it should be possible to subject the ESR ingot to much higher strains per unit operation during industrial hot working processes such as forging, which would result in a considerable saving of power. The improvement in hot ductility in ESR steel has been attributed primarily to the removal of non-metallic inclusions and the reduction in sulphur content. From the apparent activation energy estimated from the hot torsion data, the dynamic recrystallization process is identified as the mechanism controlling the rate of hot deformation.

A one-step process for the preparation ofγ-Fe2O3

Abstract is not available.

Monte Carlo simulation of mictomagnets

Monte Carlo simulations of a binary alloy with impurity concentrations between 20 and 45 at.% have been carried out. The proportion of large clusters relative to that of small clusters increases with the number of MC diffusion steps as well as impurity concentration. Magnetic susceptibility peaks become more prominent and occur at higher temperatures with increasing impurity concentration. The different peaks in the susceptibility and specific heat curves seem to correspond to different sized clusters. A freezing model would explain the observed behaviour with the large clusters freezing first and the small clusters contributing to susceptibility (specific heat) peaks at lower temperatures.