Mapping of B-cell epitopes of hemagglutinin protein of rinderpest virus

Monoclonal antibodies (mAbs) against secreted hemagglutinin (H) protein of rinderpest virus (RPV) expressed by a recombinant baculovirus were generated to characterize the antigenic sites on H protein and regions of functional significance. Three of the mAbs displayed hemagglutination inhibition activity and these mAbs were unable to neutralize virus infectivity. Western immunoblot analysis of overlapping deletion mutants indicated that three mAbs recognize antigenic regions at the extreme carboxy terminus (between amino acids 569 and 609) and the fourth mAb between amino acids 512 and 568. Using synthetic peptides, aa 569-577 and 575-583 were identified as the epitopes for E2G4 and D2F4, respectively. The epitopic domains of A12A9 and E2B6 mAbs were mapped to regions encompassing aa 527-554 and 588-609. Two epitopes spanning the extreme carboxy terminal region of aa 573 to 587 and 588 to 609 were shown to be immunodominant employing a competitive ELISA with polyclonal sera form vaccinated cattle. The D2F4 mAb which recognizes a unique epitope on RPV-H is not present on the closely related peste des petits ruminant virus FIN protein and this mAb could serve as a tool in the seromonitoring program after rinderpest vaccination. (C) 2002 Elsevier Science (USA).

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.

Mapping of local electronic properties in nanostructured CMR thin films by Scanning Tunneling Microscopy (STM) and Local Conductance Map (LCMAP)

We have investigated the local electronic properties and the spatially resolved magnetoresistance of a nanostructured film of a colossal magnetoresistive (CMR) material by local conductance mapping (LCMAP) using a variable temperature Scanning Tunneling Microscope (STM) operating in a magnetic field. The nanostructured thin films (thickness ≈500nm) of the CMR material La0.67Sr0.33MnO3 (LSMO) on quartz substrates were prepared using chemical solution deposition (CSD) process. The CSD grown films were imaged by both STM and atomic force microscopy (AFM). Due to the presence of a large number of grain boundaries (GB's), these films show low field magnetoresistance (LFMR) which increases at lower temperatures. The measurement of spatially resolved electronic properties reveal the extent of variation of the density of states (DOS) at and close to the Fermi level (EF) across the grain boundaries and its role in the electrical resistance of the GB. Measurement of the local conductance maps (LCMAP) as a function of magnetic field as well as temperature reveals that the LFMR occurs at the GB. While it was known that LFMR in CMR films originates from the GB, this is the first investigation that maps the local electronic properties at a GB in a magnetic field and traces the origin of LFMR at the GB.

PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures

A fundamental task in bioinformatics involves a transfer of knowledge from one protein molecule onto another by way of recognizing similarities. Such similarities are obtained at different levels, that of sequence, whole fold, or important substructures. Comparison of binding sites is important to understand functional similarities among the proteins and also to understand drug cross-reactivities. Current methods in literature have their own merits and demerits, warranting exploration of newer concepts and algorithms, especially for large-scale comparisons and for obtaining accurate residue-wise mappings. Here, we report the development of a new algorithm, PocketAlign, for obtaining structural superpositions of binding sites. The software is available as a web-service at http://proline.physicslisc.emetin/pocketalign/. The algorithm encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site. Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second, followed by a greedy approach that incrementally combines residue pairings into a mapping. The mappings in different frames are then evaluated by different metrics encoding the extent of alignment of individual geometric perspectives. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three-dimensional grid, and the best 500 stored in a database. Alignments are then ranked, and the top scoring alignments reported, which are then streamed into Pymol for visualization and analyses. The method is validated for accuracy and sensitivity and benchmarked against existing methods. An advantage of PocketAlign, as compared to some of the existing tools available for binding site comparison in literature, is that it explores different schemes for identifying an alignment thus has a better potential to capture similarities in ligand recognition abilities. PocketAlign, by finding a detailed alignment of a pair of sites, provides insights as to why two sites are similar and which set of residues and atoms contribute to the similarity.

Mapping of large scale 158 mu m [CII] line emission: Orion A

We present the first results of an observational programme undertaken to map the fine structure line emission of singly ionized carbon ([ CII] 157 : 7409 mum) over extended regions using a Fabry Perot spectrometer newly installed at the focal plane of a 100 cm balloon- borne far- infrared telescope. This new combination of instruments has a velocity resolution of similar to 200 km s(-1) and an angular resolution of 1.'5. During the first flight, an area of 30' x 15' in Orion A was mapped. These observations extend over a larger area than previous observations, the map is fully sampled and the spectral scanning method used enables reliable estimation of the continuum emission at frequencies adjacent to the [ CII] line. The total [ CII] line luminosity, calculated by considering up to 20% of the maximum line intensity is 0.04% of the luminosity of the far- infrared continuum. We have compared the [ CII] intensity distribution with the velocity- integrated intensity distributions of (CO)-C-13(1- 0), CI(1- 0) and CO( 3- 2) from the literature. Comparison of the [ CII], [ CI] and the radio continuum intensity distributions indicates that the largescale [ CII] emission originates mainly from the neutral gas, except at the position of M 43, where no [ CI] emission corresponding to the [ CII] emission is seen. Substantial part of the [ CII] emission from here originates from the ionized gas. The observed line intensities and ratios have been analyzed using the PDR models by Kaufman et al. ( 1999) to derive the incident UV flux and volume density at a few selected positions. The models reproduce the observations reasonably well at most positions excepting the [ CII] peak ( which coincides with the position of theta(1) Ori C). Possible reason for the failure could be the simplifying assumption of a homogeneous plane parallel slab in place of a more complicated geometry.

Contrained linear spectral unmixing technique for regional land cover mapping using MODIS data

Over the last few decades, there has been a significant land cover (LC) change across the globe due to the increasing demand of the burgeoning population and urban sprawl. In order to take account of the change, there is a need for accurate and up- to-date LC maps. Mapping and monitoring of LC in India is being carried out at national level using multi-temporal IRS AWiFS data. Multispectral data such as IKONOS, Landsat- TM/ETM+, IRS-1C/D LISS-III/IV, AWiFS and SPOT-5, etc. have adequate spatial resolution (~ 1m to 56m) for LC mapping to generate 1:50,000 maps. However, for developing countries and those with large geographical extent, seasonal LC mapping is prohibitive with data from commercial sensors of limited spatial coverage. Superspectral data from the MODIS sensor are freely available, have better temporal (8 day composites) and spectral information. MODIS pixels typically contain a mixture of various LC types (due to coarse spatial resolution of 250, 500 and 1000 m), especially in more fragmented landscapes. In this context, linear spectral unmixing would be useful for mapping patchy land covers, such as those that characterise much of the Indian subcontinent. This work evaluates the existing unmixing technique for LC mapping using MODIS data, using end- members that are extracted through Pixel Purity Index (PPI), Scatter plot and N-dimensional visualisation. The abundance maps were generated for agriculture, built up, forest, plantations, waste land/others and water bodies. The assessment of the results using ground truth and a LISS-III classified map shows 86% overall accuracy, suggesting the potential for broad-scale applicability of the technique with superspectral data for natural resource planning and inventory applications.

Landslide susceptibility mapping in the downstream region of Sharavathi river basin, Central Western Ghats

Landslides are hazards encountered during monsoon in undulating terrains of Western Ghats causing geomorphic make over of earth surface resulting in significant damages to life and property. An attempt is made in this paper to identify landslides susceptibility regions in the Sharavathi river basin downstream using frequency ratio method based on the field investigations during July- November 2007. In this regard, base layers of spatial data such as topography, land cover, geology and soil were considered. This is supplemented with the field investigations of landslides. Factors that influence landslide were extracted from the spatial database. The probabilistic model -frequency ratio is computed based on these factors. Landslide susceptibility indices were computed and grouped into five classes. Validation of LHS, showed an accuracy of 89% as 25 of the 28 regions tallied with the field condition of highly vulnerable landslide regions. The landslide susceptible map generated for the downstream would be useful for the district officials to implement appropriate mitigation measures to reduce hazards.

Image fusion in GRDSS for Land use Mapping

Image fusion techniques are useful to integrate the geometric detail of a high-resolution panchromatic (PAN) image and the spectral information of a low-resolution multispectral (MSS) image, particularly important for understanding land use dynamics at larger scale (1:25000 or lower), which is required by the decision makers to adopt holistic approaches for regional planning. Fused images can extract features from source images and provide more information than one scene of MSS image. High spectral resolution aids in identification of objects more distinctly while high spatial resolution allows locating the objects more clearly. The geoinformatics technologies with an ability to provide high-spatial-spectral-resolution data helps in inventorying, mapping, monitoring and sustainable management of natural resources. Fusion module in GRDSS, taking into consideration the limitations in spatial resolution of MSS data and spectral resolution of PAN data, provide high-spatial-spectral-resolution remote sensing images required for land use mapping on regional scale. GRDSS is a freeware GIS Graphic User Interface (GUI) developed in Tcl/Tk is based on command line arguments of GRASS (Geographic Resources Analysis Support System) with the functionalities for raster analysis, vector analysis, site analysis, image processing, modeling and graphics visualization. It has the capabilities to capture, store, process, analyse, prioritize and display spatial and temporal data.

Two-level Mapping Based Cache Index Selection for Packet Forwarding Engines

Packet forwarding is a memory-intensive application requiring multiple accesses through a trie structure. The efficiency of a cache for this application critically depends on the placement function to reduce conflict misses. Traditional placement functions use a one-level mapping that naively partitions trie-nodes into cache sets. However, as a significant percentage of trie nodes are not useful, these schemes suffer from a non-uniform distribution of useful nodes to sets. This in turn results in increased conflict misses. Newer organizations such as variable associativity caches achieve flexibility in placement at the expense of increased hit-latency. This makes them unsuitable for L1 caches.We propose a novel two-level mapping framework that retains the hit-latency of one-level mapping yet incurs fewer conflict misses. This is achieved by introducing a secondlevel mapping which reorganizes the nodes in the naive initial partitions into refined partitions with near-uniform distribution of nodes. Further as this remapping is accomplished by simply adapting the index bits to a given routing table the hit-latency is not affected. We propose three new schemes which result in up to 16% reduction in the number of misses and 13% speedup in memory access time. In comparison, an XOR-based placement scheme known to perform extremely well for general purpose architectures, can obtain up to 2% speedup in memory access time.