Turbulent near-wake development behind a flat plate

An asymptotic analysis of the two-dimensional turbulent near-wake flow behind a Rat plate with sharp trailing edge has been formulated, The feature that the near-wake, which is dominated by the mixing of the oncoming turbulent boundary layers retains, to a large extent, the memory of the turbulent structure of the upstream boundary layer has been exploited to develop the analysis. This analysis leads to two regions of the near-wake flow (the inner near-wake and the outer near-wake) for which the governing equations are derived. The matching conditions among these regions lead to a logarithmic variation in the normal direction in the overlapping region surrounding the inner near-wake. These features are validated by the available experimental data. Similarity solutions for the velocity distribution (which satisfy the required matching conditions) in the inner near-wake and outer near-wake regions have been obtained by making the appropriate eddy-viscosity assumptions, Uniformly valid solutions for velocity distribution have been constructed for the near-wake. The solutions show good agreement with available experimental data. (C) Elsevier, Paris.

Vitellins and vitellogenins of Dysdercus koenigii (Heteroptera : Pyrrhocoridae) - identification, purification and temporal pattern

Two vitellins, VtA and VtB, were purified from the eggs of Dysdercus koenigii by gel filtration and ion exchange chromatography. VtA and VtB have molecular weights of 290 and 260 kDa, respectively. Both Vts are glycolipoproteinaceous in nature. VtA is composed of three polypeptides of M-r 116, 92 and 62 kDa while VtB contained an additional subunit of M-r 40 kDa. All subunits except the 116-kDa subunit are glycolipopolypeptides. Polyclonal antibody raised against VtA (anti-VtA antibody) cross-reacted with VtB and also with vitellogenic haemolymph and ovaries and pre-vitellogenic fat bodies, but not with haemolymph from either adult male, fifth instar female, or pre-vitellogenic females demonstrating sex and stage specificity of the Vts. Immunoblots in the presence of anti-VtA revealed two proteins (of 290 and 260 kDa) in both vitellogenic haemolymph and pre-vitellogenic fat bodies that are recognised as D. koenigii Vgs. In newly emerged females, Vgs appeared on day 1 in fat bodies and on day 3 in haemolymph and ovaries. Vg concentration was maximum on day 2 in fat body, day 4 in haemolymph and day 7 in ovary. Although the biochemical and temporal characteristics of these proteins show similarity to some hemipterans, they are strikingly dissimilar with those of a very closely related species. (C) 1999 Elsevier Science Inc. All rights reserved.

A comparative analysis of regeneration in natural forests and joint forest management plantations in Uttara Kannada district, Western Ghats

Five villages undertaking joint forest management (JFM) were chosen in Uttara Kannada district, Karnataka for assessing regeneration in plantations and nearby natural forests of the village. Species number, stem density, diversity index, similarity in species composition in less disturbed and disturbed forests and plantations in the village were compared. Stem density was low in all the disturbed forests; however, the species number was low in disturbed forests of three villages and high in two villages. Plantations showed lower diversity values compared to the adjacent natural forests. Regeneration in all less disturbed forests was better compared to the disturbed counterparts. Villages were ranked based on number of landless families, per, capita forest available and number of cut stems. Assessment of village forests using ranks indicates that parameters such as per capita availability, cut stems in the forests may determine the success of JFM.

iPBA: a tool for protein structure comparison using sequence alignment strategies

With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman-Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of similar to 88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA(+) in > 80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient `sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.

Isolation and characterization of proteolytic enzymes from the latex of Synadenium grantii Hook, 'f'

Two fractions showing proteolytic enzymes have been obtained from the latex of Synadenium grantii Hook, 'f', using gel-filtration and anion-exchange chromatographic techniques. Both these proteases have the same molecular mass of 76+/-2 kDa each. They exhibit maximal activity at pH 7.0 and at a temperature of 60 degreesC. They display stability over a pH range from 5-10 and are also highly thermostable. Irreversible inhibition by PMSF indicates that they are serine proteases. In addition, histidine residues also appear to play an important role in catalysis as evidenced by inhibition with DEPC. They also exhibit similarity with respect to pH and temperature optima, kinetic properties and thermal stability. (C) 2002 Elsevier Science Ireland Ltd. All rights reserved.

Machine recognition of printed Kannada text

This paper presents the design of a full fledged OCR system for printed Kannada text. The machine recognition of Kannada characters is difficult due to similarity in the shapes of different characters, script complexity and non-uniqueness in the representation of diacritics. The document image is subject to line segmentation, word segmentation and zone detection. From the zonal information, base characters, vowel modifiers and consonant conjucts are separated. Knowledge based approach is employed for recognizing the base characters. Various features are employed for recognising the characters. These include the coefficients of the Discrete Cosine Transform, Discrete Wavelet Transform and Karhunen-Louve Transform. These features are fed to different classifiers. Structural features are used in the subsequent levels to discriminate confused characters. Use of structural features, increases recognition rate from 93% to 98%. Apart from the classical pattern classification technique of nearest neighbour, Artificial Neural Network (ANN) based classifiers like Back Propogation and Radial Basis Function (RBF) Networks have also been studied. The ANN classifiers are trained in supervised mode using the transform features. Highest recognition rate of 99% is obtained with RBF using second level approximation coefficients of Haar wavelets as the features on presegmented base characters.

Mean and fluctuating pressure in boat-tail separated flows at transonic speeds

Experiments were carried out investigating the features of mean and unsteady surface pressure fluctuations in boat-tail separated flows relevant to launch vehicle configurations at transonic speeds. The tests were performed on a generic axisymmetric body in the Mach-number range of 0.7-1.2, and the important geometrical parameters, namely, the boat-tail angle and diameter ratio, were varied systematically. The measurements made included primarily the mean and unsteady surface-pressure fluctuations on nine different model configurations. Flow-visualization studies employing a surface oil flow, and schlieren techniques were carried out to infer features like boundary-layer separation, reattachment, and shock waves in the flow. The features of mean and fluctuating surface pressures are discussed in detail including aspects of similarity. It has been observed that, on a generic configuration employed in the present study, the maximum levels of surface-pressure fluctuations in the reattachment zone are appreciably lower than those found on launch vehicle configurations having a bulbous or hammerhead nose shape. A simple correlation is suggested for the maximum value of rms pressure fluctuations in the reattachment zone at different freestream Mach numbers.

Structure, function, and mechanism of HhaI DNA methyltransferases

A vast amount of literature has accumulated on the characterization of DNA methyltransferases. The HhaI DNA methyltransferase, a C5-cytosine methyltransferase, has been the subject of investigation for the last 2 decades. Biochemical and kinetic characterization have led to an understanding of the catalytic and kinetic mechanism of the methyltransfer reaction. The HhaI methyltransferase has also been subjected to extensive structural analysis, with the availability of 12 structures with or without a cofactor and a variety of DNA substrates. The mechanism of base flipping, first described for the HhaI methyltransferase, is conserved among all DNA methyltransferases and is also found to occur in numerous DNA repair enzymes. Studies with other methyltransferase reveal a significant structural and functional similarity among different types of methyltransferases. This review aims to summarize the available information on the HhaI DNA methyltransferase.

The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations

Background: Phosphorylation by protein kinases is central to cellular signal transduction. Abnormal functioning of kinases has been implicated in developmental disorders and malignancies. Their activity is regulated by second messengers and by the binding of associated domains, which are also influential in translocating the catalytic component to their substrate sites, in mediating interaction with other proteins and carrying out their biological roles. Results: Using sensitive profile-search methods and manual analysis, the human genome has been surveyed for protein kinases. A set of 448 sequences, which show significant similarity to protein kinases and contain the critical residues essential for kinase function, have been selected for an analysis of domain combinations after classifying the kinase domains into subfamilies. The unusual domain combinations in particular kinases suggest their involvement in ubiquitination pathways and alternative modes of regulation for mitogen-activated protein kinase kinases (MAPKKs) and cyclin-dependent kinase (CDK)-like kinases. Previously unexplored kinases have been implicated in osteoblast differentiation and embryonic development on the basis of homology with kinases of known functions from other organisms. Kinases potentially unique to vertebrates are involved in highly evolved processes such as apoptosis, protein translation and tyrosine kinase signaling. In addition to coevolution with the kinase domain, duplication and recruitment of non-catalytic domains is apparent in signaling domains such as the PH, DAG-PE, SH2 and SH3 domains. Conclusions: Expansion of the functional repertoire and possible existence of alternative modes of regulation of certain kinases is suggested by their uncommon domain combinations. Experimental verification of the predicted implications of these kinases could enhance our understanding of their biological roles.

The restriction mapping problem revisited

In computational molecular biology, the aim of restriction mapping is to locate the restriction sites of a given enzyme on a DNA molecule. Double digest and partial digest are two well-studied techniques for restriction mapping. While double digest is NP-complete, there is no known polynomial-time algorithm for partial digest. Another disadvantage of the above techniques is that there can be multiple solutions for reconstruction. In this paper, we study a simple technique called labeled partial digest for restriction mapping. We give a fast polynomial time (O(n(2) log n) worst-case) algorithm for finding all the n sites of a DNA molecule using this technique. An important advantage of the algorithm is the unique reconstruction of the DNA molecule from the digest. The technique is also robust in handling errors in fragment lengths which arises in the laboratory. We give a robust O(n(4)) worst-case algorithm that can provably tolerate an absolute error of O(Delta/n) (where Delta is the minimum inter-site distance), while giving a unique reconstruction. We test our theoretical results by simulating the performance of the algorithm on a real DNA molecule. Motivated by the similarity to the labeled partial digest problem, we address a related problem of interest-the de novo peptide sequencing problem (ACM-SIAM Symposium on Discrete Algorithms (SODA), 2000, pp. 389-398), which arises in the reconstruction of the peptide sequence of a protein molecule. We give a simple and efficient algorithm for the problem without using dynamic programming. The algorithm runs in time O(k log k), where k is the number of ions and is an improvement over the algorithm in Chen et al. (C) 2002 Elsevier Science (USA). All rights reserved.

Crystal structure of Rv2118c: an AdoMet-dependent methyltransferase from Mycobacterium tuberculosis H37Rv

Rv2118c belongs to the class of conserved hypothetical proteins from Mycobacterium tuberculosis H37Rv. The crystal structure of Rv2118c in complex with S-adenosyl-Image -methionine (AdoMet) has been determined at 1.98 Å resolution. The crystallographic asymmetric unit consists of a monomer, but symmetry-related subunits interact extensively, leading to a tetrameric structure. The structure of the monomer can be divided functionally into two domains: the larger catalytic C-terminal domain that binds the cofactor AdoMet and is involved in the transfer of methyl group from AdoMet to the substrate and a smaller N-terminal domain. The structure of the catalytic domain is very similar to that of other AdoMet-dependent methyltransferases. The N-terminal domain is primarily a β-structure with a fold not found in other methyltransferases of known structure. Database searches reveal a conserved family of Rv2118c-like proteins from various organisms. Multiple sequence alignments show several regions of high sequence similarity (motifs) in this family of proteins. Structure analysis and homology to yeast Gcd14p suggest that Rv2118c could be an RNA methyltransferase, but further studies are required to establish its functional role conclusively.

Direct numerical simulation of turbulent spots

A group of high-order finite-difference schemes for incompressible flow was implemented to simulate the evolution of turbulent spots in channel flows. The long-time accuracy of these schemes was tested by comparing the evolution of small disturbances to a plane channel flow against the growth rate predicted by linear theory. When the perturbation is the unstable eigenfunction at a Reynolds number of 7500, the solution grows only if there are a comparatively large number of (equispaced) grid points across the channel. Fifth-order upwind biasing of convection terms is found to be worse than second-order central differencing. But, for a decaying mode at a Reynolds number of 1000, about a fourth of the points suffice to obtain the correct decay rate. We show that this is due to the comparatively high gradients in the unstable eigenfunction near the walls. So, high-wave-number dissipation of the high-order upwind biasing degrades the solution especially. But for a well-resolved calculation, the weak dissipation does not degrade solutions even over the very long times (O(100)) computed in these tests. Some new solutions of spot evolution in Couette flows with pressure gradients are presented. The approach to self-similarity at long times can be seen readily in contour plots.

Weekly periodicities of aerosol properties observed at an urban location in India

Multi-year (similar to 7 years) observations of aerosol optical and microphysical properties were conducted at a tropical urban location in Bangalore, India. As a consequence of rapid urbanization, Bangalore presents high local atmospheric emissions, which makes it an interesting site to study the effect of anthropogenic activities on aerosol properties. It has been found that both column (aerosol optical depth, AOD) and ground-level measurements (black carbon (BC) and composite aerosol mass) exhibit a weekly cycle with low aerosol concentrations on weekends. In comparison to the weekdays, the weekend reductions of aerosol optical depth, black carbon and composite aerosol mass concentrations were similar to 15%, 25% and 24%, respectively. The magnitude of weekend reduction of black carbon is as much as similar to 1 mu g m(-3). The similarity in the weekly cycle between the column and surface measurements suggests that the aerosol column loading at this location is governed by local anthropogenic emissions. The strongest weekly cycle in composite aerosol mass concentration was observed in the super micron mass range (>1 mu m). The weekly cycle of composite aerosol mass in the sub micron mass range (<1 mu m) was weak in comparison to the super micron aerosol mass. (C) 2011 Elsevier B.V. All rights reserved.

AlignHUSH: Alignment of HMMs using structure and hydrophobicity information

Background: Sensitive remote homology detection and accurate alignments especially in the midnight zone of sequence similarity are needed for better function annotation and structural modeling of proteins. An algorithm, AlignHUSH for HMM-HMM alignment has been developed which is capable of recognizing distantly related domain families The method uses structural information, in the form of predicted secondary structure probabilities, and hydrophobicity of amino acids to align HMMs of two sets of aligned sequences. The effect of using adjoining column(s) information has also been investigated and is found to increase the sensitivity of HMM-HMM alignments and remote homology detection. Results: We have assessed the performance of AlignHUSH using known evolutionary relationships available in SCOP. AlignHUSH performs better than the best HMM-HMM alignment methods and is observed to be even more sensitive at higher error rates. Accuracy of the alignments obtained using AlignHUSH has been assessed using the structure-based alignments available in BaliBASE. The alignment length and the alignment quality are found to be appropriate for homology modeling and function annotation. The alignment accuracy is found to be comparable to existing methods for profile-profile alignments. Conclusions: A new method to align HMMs has been developed and is shown to have better sensitivity at error rates of 10% and above when compared to other available programs. The proposed method could effectively aid obtaining clues to functions of proteins of yet unknown function. A web-server incorporating the AlignHUSH method is available at http://crick.mbu.iisc.ernet.in/similar to alignhush/

Turbulence measurements in an ‘equilibrium’ axisymmetric wall jet Journal

This paper reports measurements of turbulent quantities in an axisymmetric wall jet subjected to an adverse pressure gradient in a conical diffuser, in such a way that a suitably defined pressure-gradient parameter is everywhere small. Self-similarity is observed in the mean velocity profile, as well as the profiles of many turbulent quantities at sufficiently large distances from the injection slot. Autocorrelation measurements indicate that, in the region of turbulent production, the time scale of ν fluctuations is very much smaller than the time scale of u fluctuations. Based on the data on these time scales, a possible model is proposed for the Reynolds stress. One-dimensional energy spectra are obtained for the u, v and w components at several points in the wall jet. It is found that self-similarity is exhibited by the one-dimensional wavenumber spectrum of $\overline{q^2}(=\overline{u^2}+\overline{v^2}+\overline{w^2})$, if the half-width of the wall jet and the local mean velocity are used for forming the non-dimensional wavenumber. Both the autocorrelation curves and the spectra indicate the existence of periodicity in the flow. The rate of dissipation of turbulent energy is estimated from the $\overline{q^2}$ spectra, using a slightly modified version of a previously suggested method.