Medium access control schemes for local area networks with multiple priority function

This paper deals with the development and performance evaluation of three modified versions of a scheme proposed for medium access control in local area networks. The original scheme implements a collision-free and fair medium arbitration by using a control wire in conjunction with a data bus. The modifications suggested in this paper are intended to realize the multiple priority function in local area networks.

Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

DNA polymorphism and local variation in base-pair orientation: a theoretical rationale

Basepair stacking calculations have been carried out to understand the conformational polymorphism of DNA and its sequence dependence. The recently developed self-consistent parameter set, which is specially suitable for describing irregular DNA structures, has been used to describe the geometry of a basepair doublet. While for basepairs without any propeller, the favourable stacking patterns do not appear to have very strong features, much more noticeable sequence dependent stacking patterns emerge once a propeller is applied to the basepairs. The absolute minima for most sequences occurs for a doublet geometry close to the B-DNA fibre models. Hence in the B-DNA region, no strong sequence dependent features are found, but the range of doublet geometries observed in the crystal structures generally lie within the low energy contours, obtained from stacking energy calculations. The doublet geometry corresponding to the A-DNA fibre model is not energetically favourable for the purine-pyrimidine sequences, which prefer small roll angle values when the slide has a large negative value as in A-DNA. However positive roll with large negative slide is allowed for GG, GA, AG and the pyrimidine-purine steps. This is consistent with the observed geometries of various steps in A-DNA crystals. Thus the general features of the basepair doublets predicted from these theoretical studies agree very well with the results from crystal structure analysis. However, since most sequences show an overall preference for B-type doublet geometry, the B --> A transition for random sequence DNA cannot be explained on the basis of basepair stacking interactions.

Rigid and flexible region in lysozyme and the invariant features in its hydration shell

Water-mediated transformations provide a useful handle for exploring the flexibility in protein molecules and the invariant features in their hydration shells. Low-humidity monoclinic hen egg white lysozyme, resulting from such a transformation, has perhaps the lowest solvent content observed in any protein crystal so far and has a well-ordered structure. A detailed comparison involving this structure, low-humidity tetragonal lysozyme, and the other available refined crystal structures of the enzyme permits the delineation of the relatively rigid, moderately flexible and highly flexible regions of the molecule. The relatively rigid region forms a contiguous structural unit close to the molecular centroid and encompasses parts of of the main beta-structure and three alpha-helices. The hydration shell of the protein contains 30 invariant water molecules. Many of them are involved in holding different parts of the molecule together or in stabilizing local structure. Five of the six invariant water molecules attached to the substrate-binding region form part of a water cluster contiguous with the side-chains of the catalytic residues Glu-35 and Asp-52.

High-quality annotation of promoter regions for 913 bacterial genomes

Motivation: The number of bacterial genomes being sequenced is increasing very rapidly and hence, it is crucial to have procedures for rapid and reliable annotation of their functional elements such as promoter regions, which control the expression of each gene or each transcription unit of the genome. The present work addresses this requirement and presents a generic method applicable across organisms. Results: Relative stability of the DNA double helical sequences has been used to discriminate promoter regions from non-promoter regions. Based on the difference in stability between neighboring regions, an algorithm has been implemented to predict promoter regions on a large scale over 913 microbial genome sequences. The average free energy values for the promoter regions as well as their downstream regions are found to differ, depending on their GC content. Threshold values to identify promoter regions have been derived using sequences flanking a subset of translation start sites from all microbial genomes and then used to predict promoters over the complete genome sequences. An average recall value of 72% (which indicates the percentage of protein and RNA coding genes with predicted promoter regions assigned to them) and precision of 56% is achieved over the 913 microbial genome dataset.

Local texture and microstructure in cube-oriented nickel single crystal deformed by equal channel angular extrusion

Local texture and microstructure was investigated to study the deformation mechanisms during equal channel angular extrusion of a high purity nickel single crystal of initial cube orientation. A detailed texture and microstructure analysis by various diffraction techniques revealed the complexity of the deformation patterns in different locations of the billet. A modeling approach, taking into account slip system activity, was used to interpret the development of this heterogeneous deformation.

Local variability and base sequence effects in DNA crystal structures.

The importance and usefulness of local doublet parameters in understanding sequence dependent effects has been described for A- and B-DNA oligonucleotide crystal structures. Each of the two sets of local parameters described by us in the NUPARM algorithm, namely the local doublet parameters, calculated with reference to the mean z-axis, and the local helical parameters, calculated with reference to the local helix axis, is sufficient to describe the oligonucleotide structures, with the local helical parameters giving a slightly magnified picture of the variations in the structures. The values of local doublet parameters calculated by NUPARM algorithm are similar to those calculated by NEWHELIX90 program, only if the oligonucleotide fragment is not too distorted. The mean values obtained using all the available data for B-DNA crystals are not significantly different from those obtained when a limited data set is used, consisting only of structures with a data resolution of better than 2.4 A and without any bound drug molecule. Thus the variation observed in the oligonucleotide crystals appears to be independent of the quality of their crystallinity. No strong correlation is seen between any pair of local doublet parameters but the local helical parameters are interrelated by geometric relationships. An interesting feature that emerges from this analysis is that the local rise along the z-axis is highly correlated with the difference in the buckle values of the two basepairs in the doublet, as suggested earlier for the dodecamer structures (Bansal and Bhattacharyya, in Structure & Methods: DNA & RNA, Vol. 3 (Eds., R.H. Sarma and M.H. Sarma), pp. 139-153 (1990)). In fact the local rise values become almost constant for both A- and B-forms, if a correction is applied for the buckling of the basepairs. In B-DNA the AA, AT, TA and GA basepair sequences generally have a smaller local rise (3.25 A) compared to the other sequences (3.4 A) and this seems to be an intrinsic feature of basepair stacking interaction and not related to any other local doublet parameter. The roll angles in B-DNA oligonucleotides have small values (less than +/- 8 degrees), while mean local twist varies from 24 degrees to 45 degrees. The CA/TG doublet sequences show two types of preferred geometries, one with positive roll, small positive slide and reduced twist and another with negative roll, large positive slide and increased twist.(ABSTRACT TRUNCATED AT 400 WORDS)

Conformation of substituted polyacetylenes in solution : relationship between electronic properties and local order

A study of the chain conformation in solutions of polyphenylacetylene and poly(2-octyne) has been performed. The two polymers differ in many ways : polyphenylacetylene gives a red solution while poly(2-octyne) is transparent and, a marked difference on the chain rigidity is observed : the statistical length are 45 Å and 135 Å respectively. From the study of these two systems, one deduces that curvature fluctuations play a minor role on the π electrons localization, and that the torsion between monomer units is the pertinent parameter to understand the chain conformation and the π electrons localization.

Analysis of sequence dependent variations in secondary and tertiary structure of tRNA molecules

The double helical regions of the five tRNA(Phe) and two tRNA(Asp) crystal structures have been analyzed using the local basepair step parameters. The sequence dependent effects in the mini double helices of tRNA are very similar to those observed in the crystal structures of oligonucleotides in the A-form, the purine-pyrimidine and purine-purine steps have small roll angles when compared to the fiber models of A-DNA as well as A-RNA, while the pyrimidine-purine doublet steps have large roll angles. The orientation of the basepairs in the D-stem is unusual and invariant i.e. they are different from the other three stems but are very similar in all the five tRNA(Phe) crystal structures, presumably due to tertiary interaction of the Watson-Crick basepairs with other bases, with all bases being highly conserved. The origin of the differences between the tertiary structures of tRNA(Phe) and tRNA(Asp) from yeast has also been investigated. It is found that even though the angle between the acceptor arm and the D-stem is very similar in the two structures, the angle subtended by the acceptor arm and the anticodon arm is smaller in the tRNA(Phe) structure (by more than 10 degrees). This is due to differences in the orientation of the two mini helices constituting the anticodon arm, which are inclined to each other by approximately 25 degrees in tRNA(Phe) and 16 degrees in tRNA(Asp). In addition, the acceptor arm, the D-stem and the anticodon stem are nearly coplanar in tRNA(Phe), while in tRNA(Asp) the anticodon stem projects out of the plane defined by the acceptor arm and the anticodon stem. These two features together lead to a larger separation between the acceptor and anticodon ends in tRNA(Asp) and indicate that the junction between the D-stem and the anticodon stem is quite variable, with features characteristic of a ball-and-socket type joint and determined for each tRNA molecule by the base sequence at the junction.

Can equipartition fields produce the tilts of bipolar magnetic regions?

The effect of turbulence on the nonaxisymmetric flux rings of equipartition field strength in bipolar magnetic regions is studied on the basis of the small-scale momentum exchange mechanism and the giant cell drag combined with the Kelvin-Helmholtz drag mechanism. It is shown that the giant cell drag and small-scale momentum exchange mechanism can make equipartition flux loops emerge at low latitudes, in addition to making them exhibit the observed tilts. However, the sizes of the flux tubes have to be restricted to a couple of hundred kilometers. An ad hoc constraint on the footpoints of the flux loops is introduced by not letting them move in the phi direction, and it is found that equipartition fields of any size can be made to emerge at sunspot latitudes with the observed tilts by suitably adjusting the footpoint separations.

Impact of physical processes on the chlorophyll distribution in the Bay of Bengal

Satellite-derived chlorophyll a concentration (chl a) maps show three regions with high chl a in the Bay of Bengal. First among these is close to the coast, particularly off river mouths, with high values coinciding with the season of peak discharge; second is in the southwestern bay during the northeast monsoon, which is forced by local Ekman pumping; and the third is to the east of Sri Lanka in response to the summer monsoon winds. Chlorophyll-rich water from the mouths of rivers flows either along the coast or in an offshore direction, up to several hundred kilometers, depending on the prevailing ocean current pattern. The Irrawady River plume flows toward offshore and then turns northwestward during October–December, but it flows along the coast into the Andaman Sea for the rest of the year. From the Ganga-Brahmaputra river mouth, chl a–rich water flows directly southward into the open bay during spring but along the Indian coast during summer and winter. Along the Indian coast, the flow of chl a–rich water is determined by the East India Coastal Current (EICC). Whenever the EICC meanders off the Indian coast, it leads to an offshore outbreak of chl a–rich water from the coastal region into open ocean. The EICC as well as open ocean circulation in the bay is made up of several eddies, and these eddies show relatively higher chl a. Eddies near the coast, however, can often have higher chl a because of advection from the coastal region rather than generation within the eddy itself. The bay experiences several cyclones in a year, most of them occurring during October–November. These cyclones cause a drop in the sea surface temperature, a dip in the sea level, and a local increase in chl a. The impact of a cyclone is weaker in the northern part of the bay because of stronger stratification compared to the southern parts.

Nucleotide sequence of the first cosmid from the Mycobacterium leprae genome project: structure and function of the Rif-Str regions

The nucleotide sequence of cosmid B1790, carrying the Rif-Str regions of the Mycobacterium leprae chromosome, has been determined. Twelve open reading frames were identified in the 36716bp sequence, representing 40% of the coding capacity. Five ribosomal proteins, two elongation factors and the β and β'subunits of RNA polymerase have been characterized and two novel genes were found. One of these encodes a member of the so-called ABC family of ATP-binding proteins while the other appears to encode an enzyme involved in repairing genomic lesions caused by free radicals. This finding may well be significant as M. leprae, an intracellular pathogen, lives within macrophages.

Inefficient excision of uracil from loop regions of DNA oligomers by E.coli uracil DNA glycosylase

Kinetic parameters for uracil DNA glycosylase (E.coli)-catalysed excision of uracil from DNA oligomers containing dUMP in different structural contexts were determined. Our results show that single-stranded oligonucleotides (unstructured) are used as somewhat better substrates than the double-stranded oligonucleotides. This is mainly because of the favourable V-max value of the enzyme for single-stranded substrates. More interestingly, however, we found that uracil release from loop regions of DNA hairpins is extremely inefficient. The poor efficiency with which uracil is excised from loop regions is a result of both increased K-m and lowered V-max values. This observation may have significant implications in uracil DNA glycosylase-directed repair of DNA segments that can be extruded as hairpins. In addition, these studies are useful in designing oligonucleotides for various applications in DNA research where the use of uracil DNA glycosylase is sought.

Star formation in giant extragalactic H II regions

Star formation properties in Giant Extragalactic H II Regions (GEHRs) are investigated using optical photometry and evolutionary population synthesis models. Photometric data in $BVR$ bands and in the emission line of H-alpha are obtained by CCD imaging at Vainu Bappu Observatory, Kavalur. Aperture photometry is performed for 180 GEHRs in galaxies NGC 1365, 1566, 2366, 2903, 2997, 3351, 4303, 4449, 4656 and 5253. Thirty six of these GEHRs having published spectroscopic data are studied for star formation properties. The population synthesis model is constructed based on Maeder's stellar evolutionary and Kurucz stellar atmosphere models, to synthesize observational quantities of embedded clusters in GEHRs. The observed H-alpha luminosity is a measure of the number of massive stars while the contribution to BVR bands is from intermediate mass (5-15 solar mass) stars when the cluster is young and from evolving supergiants when the cluster is old (age >/= 6~Myr). Differential reddening between gas and embedded stars is essential to constrain the dereddened cluster colors within the range of youngest clusters. Obscuring dust closely associated with gas, which is distributed in filaments and clumps, as in the case of 30 Doradus, is the most likely configuration giving rise to net reduction of extinction towards stars. The fraction of the stellar photons escaping the nebula unattenuated is estimated to be 50%. GEHRs are rarely found to be simple systems containing stars from single generation. In the present sample such regions in addition to being older than 3~Myr, have their Lyman continuum luminosity reduced by as much as 60%, compared to the observed $B$ band luminosity for a normal IMF. The missing ionizing photons may be escaping the nebula, leading to the ionization of extra-H II region ionized medium. Co-existence of young (age

Anomalous X-ray scattering study of local structures in the superionic conducting class (CuI)(0.3)(Cu2O)(0.35)(MoO3)(0.35)

The anomalous X-ray scattering (AXS) method using Cu and Mo K absorption edges has been employed for obtaining the local structural information of superionic conducting glass having the composition (CuI)(0.3)(Cu2O)(0.35)(MoO3)(0.35). The possible atomic arrangements in near-neighbor region of this glass were estimated by coupling the results with the least-squares analysis so as to reproduce two differential intensity profiles for Cu and Mo as well as the ordinary scattering profile. The coordination number of oxygen around Mo is found to be 6.1 at the distance of 0.187 nm. This implies that the MoO6 octahedral unit is a more probable structural entity in the glass rather than MoO4 tetrahedra which has been proposed based on infrared spectroscopy. The pre-peak shoulder observed at about 10 nm(-1) may be attributed to density fluctuation originating from the MoO6 octahedral units connected with the corner sharing linkage, in which the correlation length is about 0.8 nm. The value of the coordination number of I- around Cu+ is estimated as 4.3 at 0.261 nm, suggesting an arrangement similar to that in molten CuI.