Glycosphingolipids in microdomain formation and their spatial organization

Plasma membranes regulate the influx and efflux of molecules across themselves and are also responsible for primary signal transduction between cells or within the same cell. Presence of lateral heterogeneity and the ability of reorganization are essential requirements for effective functioning of biomembranes. Lipid rafts are small, heterogeneous, dynamic domains enriched in glycosphingolipids, sphingomyelin and cholesterol, and profoundly influence membrane organization. Glycosphingolipids are inclined towards formation of liquid-ordered phases in membranes, both with and without cholesterol; they are therefore prime players in domain formation. Here, we discuss the role of glycosphingolipids in microdomain formation and their spatial organization within these rafts.

Unveiling the Role of Dps in the Organization of Mycobacterial Nucleoid

In order to preserve genetic information in stress conditions, bacterial DNA is organized into higher order nucleoid structure. In this paper, with the help of Atomic Force Microscopy, we show the different structural changes in mycobacterial nucleoid at different points of growth in the presence of different concentrations of glucose in the medium. We also observe that in Mycobacterium smegmatis, two different Dps proteins (Dps1 and Dps2) promote two types of nucleoid organizations. At the late stationary phase, under low glucose availability, Dps1 binds to DNA to form a very stable toroid structure. On the other hand, under the same condition, Dps2-DNA complex forms an incompletely condensed toroid and finally forms a further stable coral reef structure in the presence of RNA. This coral reef structure is stable in high concentration of bivalent ion like Mg2+.

Diversity in Functional Organization of Class I and Class II Biotin Protein Ligase

The cell envelope of Mycobacterium tuberculosis (M. tuberculosis) is composed of a variety of lipids including mycolic acids, sulpholipids, lipoarabinomannans, etc., which impart rigidity crucial for its survival and pathogenesis. Acyl CoA carboxylase (ACC) provides malonyl-CoA and methylmalonyl-CoA, committed precursors for fatty acid and essential for mycolic acid synthesis respectively. Biotin Protein Ligase (BPL/BirA) activates apo-biotin carboxyl carrier protein (BCCP) by biotinylating it to an active holo-BCCP. A minimal peptide (Schatz), an efficient substrate for Escherichia coli BirA, failed to serve as substrate for M. tuberculosis Biotin Protein Ligase (MtBPL). MtBPL specifically biotinylates homologous BCCP domain, MtBCCP87, but not EcBCCP87. This is a unique feature of MtBPL as EcBirA lacks such a stringent substrate specificity. This feature is also reflected in the lack of self/promiscuous biotinylation by MtBPL. The N-terminus/HTH domain of EcBirA has the selfbiotinable lysine residue that is inhibited in the presence of Schatz peptide, a peptide designed to act as a universal acceptor for EcBirA. This suggests that when biotin is limiting, EcBirA preferentially catalyzes, biotinylation of BCCP over selfbiotinylation. R118G mutant of EcBirA showed enhanced self and promiscuous biotinylation but its homologue, R69A MtBPL did not exhibit these properties. The catalytic domain of MtBPL was characterized further by limited proteolysis. Holo-MtBPL is protected from proteolysis by biotinyl-59 AMP, an intermediate of MtBPL catalyzed reaction. In contrast, apo-MtBPL is completely digested by trypsin within 20 min of co-incubation. Substrate selectivity and inability to promote self biotinylation are exquisite features of MtBPL and are a consequence of the unique molecular mechanism of an enzyme adapted for the high turnover of fatty acid biosynthesis.

Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or ``sequence conservation'' as the basis for their understanding. Recently ``interaction energy'' based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the ``interaction conservation'' viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

NUcache: an efficient multicore cache organization based on next-use distance

The effectiveness of the last-level shared cache is crucial to the performance of a multi-core system. In this paper, we observe and make use of the DelinquentPC - Next-Use characteristic to improve shared cache performance. We propose a new PC-centric cache organization, NUcache, for the shared last level cache of multi-cores. NUcache logically partitions the associative ways of a cache set into MainWays and DeliWays. While all lines have access to the MainWays, only lines brought in by a subset of delinquent PCs, selected by a PC selection mechanism, are allowed to enter the DeliWays. The PC selection mechanism is an intelligent cost-benefit analysis based algorithm that utilizes Next-Use information to select the set of PCs that can maximize the hits experienced in DeliWays. Performance evaluation reveals that NUcache improves the performance over a baseline design by 9.6%, 30% and 33% respectively for dual, quad and eight core workloads comprised of SPEC benchmarks. We also show that NUcache is more effective than other well-known cache-partitioning algorithms.

The evolution of complexity in social organization-A model using dominance-subordinate behavior in two social wasp species

Dominance and subordinate behaviors are important ingredients in the social organizations of group living animals. Behavioral observations on the two eusocial species Ropalidia marginata and Ropalidia cyathiformis suggest varying complexities in their social systems. The queen of R. cyathiformis is an aggressive individual who usually holds the top position in the dominance hierarchy although she does not necessarily show the maximum number of acts of dominance, while the R. marginata queen rarely shows aggression and usually does not hold the top position in the dominance hierarchy of her colony. In R. marginata, more workers are involved in dominance-subordinate interactions as compared to R. cyathiformis. These differences are reflected in the distribution of dominance-subordinate interactions among the hierarchically ranked individuals in both the species. The percentage of dominance interactions decreases gradually with hierarchical ranks in R. marginata while in R. cyathiformis it first increases and then decreases. We use an agent-based model to investigate the underlying mechanism that could give rise to the observed patterns for both the species. The model assumes, besides some non-interacting individuals, the interaction probabilities of the agents depend on their pre-differentiated winning abilities. Our simulations show that if the queen takes up a strategy of being involved in a moderate number of dominance interactions, one could get the pattern similar to R. cyathiformis, while taking up the strategy of very low interactions by the queen could lead to the pattern of R. marginata. We infer that both the species follow a common interaction pattern, while the differences in their social organization are due to the slight changes in queen as well as worker strategies. These changes in strategies are expected to accompany the evolution of more complex societies from simpler ones.

Organization dependent collective magnetic properties of secondary nanostructures with differential spatial ordering and magnetic easy axis orientation

Achieving control on the formation of different organization states of magnetic nanoparticles is crucial to harness their organization dependent physical properties in desired ways. In this study, three organization states of iron oxide nanoparticles (gamma-Fe2O3), defining as (i) assembly (ii) network aggregate and (iii) cluster, have been developed by simply changing the solvent evaporation conditions. All three systems have retained the same phase and polydispersity of primary particles. Magnetic measurements show that the partial alignment of the easy axes of the particles in the network system due to the stacking aggregation morphology can result in significant enhancement of the coercivity and remanence values, while the opposite is obtained for the cluster system due to the random orientation of easy axes. Partial alignment in the aggregate system also results in noticeable non -monotonic field dependence of ZFC peak temperature (TpeaB). The lowest value of the blocking temperature (TB) for the cluster system is related to the lowering of the effective anisotropy due to the strongest demagnetizing effect. FC (Field cooled) memory effect was observed to be decreasing with the increasing strength of dipolar interaction of organization states. Therefore, the stacking aggregation and the cluster formation are two interesting ways of magnetic nanoparticles organization for modulating collective magnetic properties significantly, which can have renewed application potentials from recording devices to biomedicine. (C) 2016 Elsevier B.V. All rights reserved.

A comparative study of multiple attribute tree and inverted file structures for large bibliographic files

A variety of data structures such as inverted file, multi-lists, quad tree, k-d tree, range tree, polygon tree, quintary tree, multidimensional tries, segment tree, doubly chained tree, the grid file, d-fold tree. super B-tree, Multiple Attribute Tree (MAT), etc. have been studied for multidimensional searching and related problems. Physical data base organization, which is an important application of multidimensional searching, is traditionally and mostly handled by employing inverted file. This study proposes MAT data structure for bibliographic file systems, by illustrating the superiority of MAT data structure over inverted file. Both the methods are compared in terms of preprocessing, storage and query costs. Worst-case complexity analysis of both the methods, for a partial match query, is carried out in two cases: (a) when directory resides in main memory, (b) when directory resides in secondary memory. In both cases, MAT data structure is shown to be more efficient than the inverted file method. Arguments are given to illustrate the superiority of MAT data structure in an average case also. An efficient adaptation of MAT data structure, that exploits the special features of MAT structure and bibliographic files, is proposed for bibliographic file systems. In this adaptation, suitable techniques for fixing and ranking of the attributes for MAT data structure are proposed. Conclusions and proposals for future research are presented.

Organization and bidirectional transcription of H2A, H2B and H4 histone genes in rice embryos

Our current understanding of the evolution of the histone gene family suffers from a lack of information on plant histone genes1. With a view to gathering some much needed information on these genes, we studied a rice genomic clone in pBR322 carrying H2A, H2B and H4 histone genes on a DNA fragment2 of 6.64 kilobases (kb). A restriction map of the insert was constructed and the organization of the three genes on this insert was determined. H2A and H2B histone genes were located at one end of the insert and H4 gene at the other with a 3.1 kb spacer in between. This cluster of three histone genes was found to be transcribed in a bidirectional fashion with H2A and H2B genes being encoded by one strand and the H4 gene by the other. These results indicate that plant histone gene organization differs from that of the sea urchin, but shows many similarities to the systems in other animals.

Access path query language for relational database systems

Database management systems offer a very reliable and attractive data organization for fast and economical information storage and processing for diverse applications. It is much more important that the information should be easily accessible to users with varied backgrounds, professional as well as casual, through a suitable data sublanguage. The language adopted here (APPLE) is one such language for relational database systems and is completely nonprocedural and well suited to users with minimum or no programming background. This is supported by an access path model which permits the user to formulate completely nonprocedural queries expressed solely in terms of attribute names. The data description language (DDL) and data manipulation language (DML) features of APPLE are also discussed. The underlying relational database has been implemented with the help of the DATATRIEVE-11 utility for record and domain definition which is available on the PDP-11/35. The package is coded in Pascal and MACRO-11. Further, most of the limitations of the DATATRIEVE-11 utility have been eliminated in the interface package.

Cloning Of Rice Dna And Identification Of Transfer-Rna Gene Clones

THE rapid development of recombinant DNA technology has brought forth a revolution in biology'>", it aids us to have a closer look at the 'way genes are organized, eS11 ecially in the complex eucaryotic genornes'<", Although many animal and yeast genes have been studied in detail using recombinant DNA technology, plant genes have seldom been targets for such studie., Germination is an ideal process to study gene expression .because it effects a . shift in the metabolic status of seeds from a state of 'dormancy to an active one. AJ;l understanding of gene organization and regulation darin.g germination can be accomplblted by molecular cloning of DNA from seeds lik.e rice. To study the status of histone, rRNA tRNA and other genes in the rice genome, a general method was developed to clone eucarvotic DNA in a' plasmid vector pBR 322. This essentially ~ involves the following steps. The rice embryo and plasmid pBR 322 DNAs were cut witll restriction endonuclease Bam Hi to generate stick.Y ends, The plasmid DNA was puosphatased, the DNA~ ware a~·tnealed and joined 'by T4 phage DNA ligase. The recombinant DNA molecules thus produced were transjerred into E. coli and colonies containing them Were selected by their sensitivity to tetracycline and resistance to ampicillin, Two clones were identified . 2S haVing tRNA genes by hybridization of the DNA in the clones \vitl1 32P-la.belled rice tRNAs.

Data definition and manipulation languages for a CAD database

In this paper the main features of ARDBID (A Relational Database for Interactive Design) have been described. An overview of the organization of the database has been presented and a detailed description of the data definition and manipulation languages has been given. These have been implemented on a DEC 1090 system.