Homology between jacalin and artocarpin from jackfruit (Artocarpus integrifolia) seeds. Partial sequence and preliminary crystallographic studies of artocarpin

Jacalin and artocarpin, the two lectins from jackfruit (Artocarpus integrifolia) seeds, have different physicochemical properties and carbohydrate-binding specificities. However, comparison of the partial amino-acid sequence of artocarpin with the known sequence of jacalin indicates close to 50% sequence identity. Artocarpin crystallizes in two forms, both monoclinic P2(1), with one and two tetramic molecules, respectively, in the asymmetric units of form I (a = 69.9, b = 73.7, c = 60.6 Angstrom and beta = 95.1 degrees) and form II (a = 87.6, b = 72.2, c = 92.6 Angstrom and beta = 101.1 degrees). Both the crystal structures have been solved by the molecular replacement method using the known structure of jacalin as the search model and ope of them partially refined, confirming that the two lectins are indeed homologous.

Zero-bias conductance and energy gap measurements in LaNiO3-YBa2Cu3O7-x junctions

Conductance measurements of junctions between a high- superconductor and a metallic oxide have been carried out along the a-b plane to examine the tunnel-junction spectra. For these measurements, in situ films have been grown on c-axis oriented thin films using the pulsed laser deposition technique. Two distinctive energy gaps have been observed along with conductance peaks around zero bias. The analysis of zero-bias conductance and energy gap data suggests the presence of midgap states located at the centre of a finite energy gap. The results obtained are also in accordance with the d-wave nature of high- superconductors.

Structural and Sequence Characteristics of Long alpha Helices in Globular Proteins

Elucidation of the detailed structural features and sequence requirements for iv helices of various lengths could be very important in understanding secondary structure formation in proteins and, hence. in the protein folding mechanism. An algorithm to characterize the geometry of an alpha helix from its C-alpha coordinates has been developed and used to analyze the structures of long cu helices (number of residues greater than or equal to 25) found in globular proteins, the crystal structure coordinates of which are available from the Brookhaven Protein Data Bank, Ail long a helices can be unambiguously characterized as belonging to one of three classes: linear, curved, or kinked, with a majority being curved. Analysis of the sequences of these helices reveals that the long alpha helices have unique sequence characteristics that distinguish them from the short alpha helices in globular proteins, The distribution and statistical propensities of individual amino acids to occur in long alpha heices are different from those found in short alpha helices, with amino acids having longer side chains and/or having a greater number of functional groups occurring more frequently in these helices, The sequences of the long alpha helices can be correlated with their gross structural features, i.e., whether they are curved, linear, or kinked, and in case of the curved helices, with their curvature.

Axially homogeneous, zero mean flow buoyancy-driven turbulence in a vertical pipe

We report an experimental study of a new type of turbulent flow that is driven purely by buoyancy. The flow is due to an unstable density difference, created using brine and water, across the ends of a long (length/diameter = 9) vertical pipe. The Schmidt number Sc is 670, and the Rayleigh number (Ra) based on the density gradient and diameter is about 10(8). Under these conditions the convection is turbulent, and the time-averaged velocity at any point is `zero'. The Reynolds number based on the Taylor microscale, Re-lambda, is about 65. The pipe is long enough for there to be an axially homogeneous region, with a linear density gradient, about 6-7 diameters long in the midlength of the pipe. In the absence of a mean flow and, therefore, mean shear, turbulence is sustained just by buoyancy. The flow can be thus considered to be an axially homogeneous turbulent natural convection driven by a constant (unstable) density gradient. We characterize the flow using flow visualization and particle image velocimetry (PIV). Measurements show that the mean velocities and the Reynolds shear stresses are zero across the cross-section; the root mean squared (r.m.s.) of the vertical velocity is larger than those of the lateral velocities (by about one and half times at the pipe axis). We identify some features of the turbulent flow using velocity correlation maps and the probability density functions of velocities and velocity differences. The flow away from the wall, affected mainly by buoyancy, consists of vertically moving fluid masses continually colliding and interacting, while the flow near the wall appears similar to that in wall-bound shear-free turbulence. The turbulence is anisotropic, with the anisotropy increasing to large values as the wall is approached. A mixing length model with the diameter of the pipe as the length scale predicts well the scalings for velocity fluctuations and the flux. This model implies that the Nusselt number would scale as (RaSc1/2)-Sc-1/2, and the Reynolds number would scale as (RaSc-1/2)-Sc-1/2. The velocity and the flux measurements appear to be consistent with the Ra-1/2 scaling, although it must be pointed out that the Rayleigh number range was less than 10. The Schmidt number was not varied to check the Sc scaling. The fluxes and the Reynolds numbers obtained in the present configuration are Much higher compared to what would be obtained in Rayleigh-Benard (R-B) convection for similar density differences.

Micro-scale anaerobic digestion of point source components of organic fraction of municipal solid waste

The fermentation characteristics of six specific types of the organic fraction of municipal solid waste (OFMSW) were examined, with an emphasis on properties that are needed when designing plug-flow type anaerobic bioreactors. More specifically, the decomposition patterns of a vegetable (cabbage), fruits (banana and citrus peels), fresh leaf litter of bamboo and teak leaves, and paper (newsprint) waste streams as feedstocks were studied. Individual OFMSW components were placed into nylon mesh bags and subjected to various fermentation periods (solids retention time, SRT) within the inlet of a functioning plug-flow biogas fermentor. These were removed at periodic intervals, and their composition was analyzed to monitor decomposition rates and changes in chemical composition. Components like cabbage waste, banana peels, and orange peels fermented rapidly both in a plug-flow biogas reactor (PFBR) as well as under a biological methane potential (BMP) assay, while other OFMSW components (leaf litter from bamboo and teak leaves and newsprint) fermented slowly with poor process stability and moderate biodegradation. For fruit and vegetable wastes (FVW), a rapid and efficient removal of pectins is the main cause of rapid disintegration of these feedstocks, which left behind very little compost forming residues (2–5%). Teak and bamboo leaves and newsprint decomposed only to 25–50% in 30 d. These results confirm the potential for volatile fatty acids accumulation in a PFBR’s inlet and suggest a modification of the inlet zone or operation of a PFBR with the above feedstocks.

Turbulent mixed convection in a shallow enclosure with a series of heat generating components

Turbulent mixed convection flow and heat transfer in a shallow enclosure with and without partitions and with a series of block-like heat generating components is studied numerically for a range of Reynolds and Grashof numbers with a time-dependent formulation. The flow and temperature distributions are taken to be two-dimensional. Regions with the same velocity and temperature distributions can be identified assuming repeated placement of the blocks and fluid entry and exit openings at regular distances, neglecting the end wall effects. One half of such module is chosen as the computational domain taking into account the symmetry about the vertical centreline. The mixed convection inlet velocity is treated as the sum of forced and natural convection components, with the individual components delineated based on pressure drop across the enclosure. The Reynolds number is based on forced convection velocity. Turbulence computations are performed using the standard k– model and the Launder–Sharma low-Reynolds number k– model. The results show that higher Reynolds numbers tend to create a recirculation region of increasing strength in the core region and that the effect of buoyancy becomes insignificant beyond a Reynolds number of typically 5×105. The Euler number in turbulent flows is higher by about 30 per cent than that in the laminar regime. The dimensionless inlet velocity in pure natural convection varies as Gr1/3. Results are also presented for a number of quantities of interest such as the flow and temperature distributions, Nusselt number, pressure drop and the maximum dimensionless temperature in the block, along with correlations.

Similarities in the Genomic Sequence and Coat Protein-Structure of Plant Viruses

The genomic sequences of several RNA plant viruses including cucumber mosaic virus, brome mosaic virus, alfalfa mosaic virus and tobacco mosaic virus have become available recently. The former two viruses are icosahedral while the latter two are bullet and rod shaped, respectively in particle morphology. The non-structural 3a proteins of cucumber mosaic virus and brome mosaic virus have an amino acid sequence homology of 35% and hence are evolutionarily related. In contrast, the coat proteins exhibit little homology, although the circular dichroism spectrum of these viruses are similar. The non-coding regions of the genome also exhibit variable but extensive homology. Comparison of the brome mosaic virus and alfalfa mosaic virus sequences reveals that they are probably related although with a much larger evolutionary distance. The polypeptide folds of the coat protein of three biologically distinct isometric plant viruses, tomato bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been shown to display a striking resemblance. All of them consist of a topologically similar 8-standard β-barrel. The implications of these studies to the understanding of the evolution of plant viruses will be discussed.

Elastic analysis of pin joints in plates under some combined pin and plate loads

Joints are primary sources of weakness in structures. Pin joints are very common and are used where periodic disassembly of components is needed. A circular pin in a circular hole in an infinitely large plate is an abstraction of such a pin joint. A two-dimensional plane-stress analysis of such a configuration is carried out, here, subjected to pin-bearing and/or biaxial-plate loading. The pin is assumed to be rigid compared to the plate material. For pin load the reactive stresses at the edges of the infinite plate tend to zero though their integral over the external boundary equals to the pin load. The pin-hole interface is unbonded and so beyond some load levels the plate separates from the pin and the extent of separation is a non-linear function of load level. The problem is solved by inverse technique where the extent of contact is specified and the causative loads are evaluated directly. In the situations where combined load is acting the separation-contact zone specification generally needs two parameters (angles) to be specified. The present report deals with analysing such a situation in metallic (or isotropic) plates. Numerical results are provided for parametric representation and the methodology is demonstrated.

Large cryptic internal sequence repeats in protein structures from Homo sapiens

Amino acid sequences are known to constantly mutate and diverge unless there is a limiting condition that makes such a change deleterious. However, closer examination of the sequence and structure reveals that a few large, cryptic repeats are nevertheless sequentially conserved. This leads to the question of why only certain repeats are conserved at the sequence level. It would be interesting to find out if these sequences maintain their conservation at the three-dimensional structure level. They can play an active role in protein and nucleotide stability, thus not only ensring proper functioning but also potentiating malfunction and disease. Therefore, insights into any aspect of the repeats - be it structure, function or evolution - would prove to be of some importance. This study aims to address the relationship between protein sequence and its three-dimensional structure, by examining if large cryptic sequence repeats have the same structure.

Sequence-dependent conformation of an A-DNA double helix: The crystal structure of the octamer d(G-G-T-A-T-A-C-C)

The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1·8 and 2·25 Å, respectively. The molecules adopt an A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.

Quantum behaved Particle Swarm Optimization (QPSO) for multi-objective design optimization of composite structures

We present a new, generic method/model for multi-objective design optimization of laminated composite components using a novel multi-objective optimization algorithm developed on the basis of the Quantum behaved Particle Swarm Optimization (QPSO) paradigm. QPSO is a co-variant of the popular Particle Swarm Optimization (PSO) and has been developed and implemented successfully for the multi-objective design optimization of composites. The problem is formulated with multiple objectives of minimizing weight and the total cost of the composite component to achieve a specified strength. The primary optimization variables are - the number of layers, its stacking sequence (the orientation of the layers) and thickness of each layer. The classical lamination theory is utilized to determine the stresses in the component and the design is evaluated based on three failure criteria; Failure Mechanism based Failure criteria, Maximum stress failure criteria and the Tsai-Wu Failure criteria. The optimization method is validated for a number of different loading configurations - uniaxial, biaxial and bending loads. The design optimization has been carried for both variable stacking sequences as well as fixed standard stacking schemes and a comparative study of the different design configurations evolved has been presented. Also, the performance of QPSO is compared with the conventional PSO.

Sequences that adopt non-B-DNA conformation in form V DNA as probed by enzymic methylation

pBR322 form V DNA is a highly torsionally strained molecule with a linking number of zero. We have used sequence- specific DNA methylases as probes for B-DNA in this molecule, exploiting the inability of methylases to methylate single-stranded DNA and Z-DNA, both of which are known to occur in form V DNA. Some sequences in form V DNA were shown to be totally in the B-form, others were totally in an altered, unmethylatable conformation, while still other sites appeared to exist partly in altered and partly in normal B-conformation. Some potential Z-forming sequences (alternating pyrimidine/purine) of less than seven base-pairs were not in the Z conformation in form V DNA, whereas others did adopt an altered structure, indicating a modulating influence of flanking sequences. Furthermore, regions of imperfect alternating pyrimidine/purine structure were sometimes capable of adopting an altered structure. In addition, some regions of altered structure had no apparent Z-forming sequences, nor were they in polypurine stretches, which have also been proposed to form left-handed DNA. These non-B-DNA conformations may represent novel left-handed helical structures or sequences that become single stranded under torsional strain. Long regions of either altered (unmethylatable) DNA or B-DNA were not always observed. In fact, one region showed three transitions between B-like DNA and altered structure within 26 base-pairs.

Vapour composition and activities in Mg-Zn liquid alloy at 923 K

Vapour species effusing from a magnesia Knudsen cell containing Mg-Zn alloy at 923 K were condensed on a water cooled copper plate. The equilibrium composition of the vapour phase over the alloy was determined from chemical analysis of the condensate. The activity coefficients of both components in the alloy have been derived from the data using a modified Gibbs-Duhem relation. The ratio of saturation vapour pressures of pure Zn and Mg obtained from the analysis of alloy data agree well with values from the literature, providing an internal check on the accuracy of data obtained in this study. Both components of the alloy exhibit negative deviations from Raoult's law. The concentration-concentration structure factor of Bhatia and Thomton at zero wave vector, evaluated from the measurements, indicate the presence of MgZn2 type complex in the liquid state. The associated regular solution model has been used for the thermodynamic description of liquid Mg-Zn alloys.

Steady state design of a sequence of sparger reactors

Abstract is not available.

Solid state and solution conformation of Boc-L-Met-Aib-L-Phe-OMe. Beta-turn conformation of a sequence related to an active chemotactic peptide analog

The conformation of the peptide Boc-L-Met-Aib-L-Phe-OMe has been studied in the solid state and solution by X-ray diffraction and 1H n.m.r., respectively. The peptide differs only in the N-terminal protecting group from the biologically active chemotactic peptide analog formyl-L-Met-Aib-L-Phe-OMe. The molecules adopt a type-II beta-turn in the solid state with Met and Aib as the corner residues (phi Met = -51.8 degrees, psi Met = 139.5 degrees, phi Aib = 58.1 degrees, psi Aib = 37.0 degrees). A single, weak 4----1 intramolecular hydrogen bond is observed between the Boc CO and Phe NH groups (N---O 3.25 A, N-H---O 128.4 degrees). 1H n.m.r. studies, using solvent and temperature dependencies of NH chemical shifts and paramagnetic radical induced line broadening of NH resonances, suggest that the Phe NH is solvent shielded in CDCl3 and (CD3)2SO. Nuclear Overhauser effects observed between Met C alpha H and Aib NH protons provide evidence of the occurrence of Met-Aib type-II beta-turns in these solvents.