Genome analysis: A new approach for visualization of sequence organization in genomes

In this article we describe and demonstrate the versatility of a computer program, GENOME MAPPING, that uses interactive graphics and runs on an IRIS workstation. The program helps to visualize as well as analyse global and local patterns of genomic DNA sequences. It was developed keeping in mind the requirements of the human genome sequencing programme, which requires rapid analysis of the data. Using GENOME MAPPING one can discern signature patterns of different kinds of sequences and analyse such patterns for repetitive as well as rare sequence strings. Further, one can visualize the extent of global homology between different genomic sequences. An application of our method to the published yeast mitochondrial genome data shows similar sequence organizations in the entire sequence and in smaller subsequences.

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.

Evidence for supramolecular organization of alkane and surfactant molecules in the process of forming mesoporous silica

Investigations of the pore expansion in mesoporous silica in the presence of n-alkanes suggest a cooperative organization of the surfactant and alkane molecules, involving additivity of chain lengths.

Role of spacer chain length in dimeric micellar organization. Small angle neutron scattering and fluorescence studies

Micelles of different dimeric amphiphiles Br-, n-C(16)H(33)NMe(2)(+) -(CH)(m)-N(+)Me(2)-n-C16H33, Br- (where m = 3, 4, 5, 6, 8, 10, and 12) adapt different morphologies and internal packing arrangements in aqueous media depending on their spacer chain length (m). Detailed measurements of small angle neutron scattering (SANS) cross sections from different bis-cationic, dimeric surfactant micelles in aqueous media (D2O) are reported. The data have been analyzed using the Hayter and Penfold model for macro ion solution to compute the interparticle structure factor S(Q) taking into account the screened Coulomb interactions between the dimeric micelles. The SANS analysis clearly indicated that the extent of aggregate growth and the variations of shapes of the dimeric micelles depend primarily on the spacer chain length. With spacer chain length, m less than or equal to 4, the propensity of micellar growth was particularly pronounced. The effects of the variation of the concentration of dimeric surfactants with m = 5 and 10 on the SANS spectra and the effects of the temperature variation for the micellar system with m = 10 were also examined. The critical micelle concentrations (cmc) and their microenvironmental feature, namely, the microviscosities that the dimeric micellar aggregates offer to a solubilized, extrinsic fluorescence probe, 1,6-diphenyl-1,3,5-hexatriene, were also determined. The changes of cmcs and microviscosities as a function of spacer chain length have been explained in terms of conformational variations and progressive looping of the spacer in micellar core upon increasing m values.

Molecular organization of the gene encoding Xenopus laevis transforming growth factor-beta 5

Transforming growth factor-beta s (TGF-beta 5) are multifunctional polypeptides, known to influence proliferation and differentiation of many cell types. TGF-beta 5 cDNA was cloned from Xenopus laevis and this isoform is unique to the amphibians. Here, we report the isolation and characterization of the TGF-beta 5 genomic clones to determine the structure of TGF-beta 5 gene. The gene consists of seven exons and all intron-exon boundaries follow the GT-AG consensus. The organization of TGF-beta 5 gene was identical to that of the mammalian TGF-beta isoforms, with the exception of position of the first splice junction. We determined the size of TGF-beta 5 gene to be approximately 20 kb.

Self-organization of multiple components in a steroidal hydrogel matrix: design, construction and studies on novel tunable luminescent gels and xerogels

The present work combines two rapidly growing research areas-functional supramolecular gels and lanthanide based hybrid materials. Facile hydrogel formation from several lanthanide(III) cholates has been demonstrated. The morphological and mechanical properties of these cholate gels were investigated by TEM and rheology. The hydrogel matrix was subsequently utilized for the sensitization of Tb(III) by doping a non-coordinating chromophore, 2,3-dihydroxynaphthalene (DHN), at micromolar concentrations. In the mixed gels of Tb(III)-Eu(III), an energy transfer pathway was found to operate from Tb(III) to Eu(III) and by utilizing this energy transfer, tunable multiple-color luminescent hydrogels were obtained. The emissive properties of the hydrogels were also retained in the xerogels and their suspensions in n-hexane were used for making luminescent coating on glass surface.

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.

SELF-ORGANIZATION AND FRICTION DURING SLIDING

In self-organized sliding processes, the surfaces align to each other during sliding. This alignment leads to a more ordered contact state and significantly influences the frictional behavior. To understand the self-organization sliding processes, experiments were conducted on a pin-on-plate reciprocating sliding tester for various numbers of cycles. In the experiments, soft magnesium pins were slid against hard steel plates of various surface textures (undirectional, 8-ground, and random). Experimental results showed that the transfer layer formation on the steel plates increased with increasing number of cycles for all surfaces textures under both dry and lubricated conditions. The friction also increased with the number of cycles under dry conditions for all of the textures studied. During lubricated conditions, the friction decreased for unidirectional and 8-ground surfaces and increased for random surfaces with the number of cycles. Furthermore, the friction and transfer layer formation depend on the surface textures under both dry and lubricated conditions during the first few sliding cycles. Later on, it is less dependent of surface textures. The variation in the coefficient of friction under both dry and lubrication conditions were attributed to the self-organization process that occurred during repeated sliding.

Effect of myonuclear number and mitochondrial fusion on Drosophila indirect flight muscle organization and size

Mechanisms involved in establishing the organization and numbers of fibres in a muscle are not completely understood. During Drosophila indirect flight muscle (IFM) formation, muscle growth is achieved by both incorporating hundreds of nuclei, and hypertrophy. As a result, IFMs provide a good model with which to understand the mechanisms that govern overall muscle organization and growth. We present a detailed analysis of the organization of dorsal longitudinal muscles (DLMs), a subset of the IFMs. We show that each DLM is similar to a vertebrate fascicle and consists of multiple muscle fibres. However, increased fascicle size does not necessarily change the number of constituent fibres, but does increase the number of myofibrils packed within the fibres. We also find that altering the number of myoblasts available for fusion changes DLM fascicle size and fibres are loosely packed with myofibrils. Additionally, we show that knock down of genes required for mitochondrial fusion causes a severe reduction in the size of DLM fascicles and fibres. Our results establish the organization levels of DLMs and highlight the importance of the appropriate number of nuclei and mitochondrial fusion in determining the overall organization, growth and size of DLMs. (C) 2013 Elsevier Inc. All rights reserved.

Organization of Mn-Clusters in pcu and bcu Networks: Synthesis, Structure, and Properties

Two new anionic inorganic-organic hybrid compounds H3O]Mn-3(mu(3)-OH)(C14H8O6S)(3)(H2O)](DMF)(5), I, and H3O](2)Mn-7(mu(3)-OH)(4)(C14H8O6S)(6)(H2O)(4)](H2O)(2)(DMF)(8), II have been prepared by employing mild solvothennal methods. Both the compounds have three-dimensionally extended structures formed by Mn-6 and Mn-7 clusters, respectively. The connectivity between Mn-6 and Mn-7 clusters and 4,4'-sulfonyldibenzoic acid anions (SDBA(2-)) results in a six connected pcu network in I and an eight connected bcu network in II. The presence of hydronium ion (H-3(O+)) along with the solvent molecules in the channels of both the compounds suggested proton conduction in the solids. Proton conductivity studies gave values of similar to 3 x 10(-4) Omega(-1) cm(-1) 98% relative humidity in both the compounds. The high activation energies indicate a vehicle mechanism in the compounds I and II. Magnetic studies indicate antiferromagnetic behavior in both the compounds.

Unraveling the Intricate Organization of Mammalian Mitochondrial Presequence Translocases: Existence of Multiple Translocases for Maintenance of Mitochondrial Function

Mitochondria are indispensable organelles implicated in multiple aspects of cellular processes, including tumorigenesis. Heat shock proteins play a critical regulatory role in accurately delivering the nucleus-encoded proteins through membrane-bound presequence translocase (Tim23 complex) machinery. Although altered expression of mammalian presequence translocase components had been previously associated with malignant phenotypes, the overall organization of Tim23 complexes is still unsolved. In this report, we show the existence of three distinct Tim23 complexes, namely, B1, B2, and A, involved in the maintenance of normal mitochondrial function. Our data highlight the importance of Magmas as a regulator of translocase function and in dynamically recruiting the J-proteins DnaJC19 and DnaJC15 to individual translocases. The basic housekeeping function involves translocases B1 and B2 composed of Tim17b isoforms along with DnaJC19, whereas translocase A is nonessential and has a central role in oncogenesis. Translocase B, having a normal import rate, is essential for constitutive mitochondrial functions such as maintenance of electron transport chain complex activity, organellar morphology, iron-sulfur cluster protein biogenesis, and mitochondrial DNA. In contrast, translocase A, though dispensable for housekeeping functions with a comparatively lower import rate, plays a specific role in translocating oncoproteins lacking presequence, leading to reprogrammed mitochondrial functions and hence establishing a possible link between the TIM23 complex and tumorigenicity.

Biomimetic molecular organization of naphthalene diimide in the solid state: tunable (chiro-) optical, viscoelastic and nanoscale properties

The interfacing of aromatic molecules with biomolecules to design functional molecular materials is a promising area of research. Intermolecular interactions determine the performance of these materials and therefore, precise control over the molecular organization is necessary to improve functional properties. Herein we describe the tunable biomimetic molecular engineering of a promising n-type organic semiconductor, naphthalene diimide (NDI), in the solid state by introducing minute structural mutations in the form of amino acids with variable Ca-functionality. For the first time we could achieve all four possible crystal packing modes, namely cofacial, brickwork, herringbone and slipped stacks of the NDI system. Furthermore, amino acid conjugated NDIs exhibit ultrasonication induced organogels with tunable visco-elastic and temperature responsive emission properties. The amino acid-NDI conjugates self-assemble into 0D nanospheres and 1D nanofibers in their gel state while the ethylamine-NDI conjugate forms 2D sheets from its solution. Photophysical studies indicated the remarkable influence of molecular ordering on the absorption and fluorescence properties of NDIs. Interestingly, the circular dichroism (CD) and X-ray diffraction (XRD) studies revealed the existence of helical ordering of NDIs in both solution and solid state. The chiral amino acids and their conformations with respect to the central NDI core are found to influence the nature of the helical organization of NDIs. Consequently, the origin of the preferential handedness in the helical organization is attributed to transcription of chiral information from the amino acid to the NDI core. On account of these unique properties, the materials derived from NDI-conjugates might find a wide range of future interdisciplinary applications from materials to biomedicine.