Differential Reaction Kinetics, Cleavage Complex Formation, and Nonamer Binding Domain Dependence Dictate the Structure-Specific and Sequence-Specific Nuclease Activity of RAGs

During V(D)J recombination, RAG (recombination-activating gene) complex cleaves DNA based on sequence specificity. Besides its physiological function, RAG has been shown to act as a structure-specific nuclease. Recently, we showed that the presence of cytosine within the single-stranded region of heteroduplex DNA is important when RAGs cleave on DNA structures. In the present study, we report that heteroduplex DNA containing a bubble region can be cleaved efficiently when present along with a recombination signal sequence (RSS) in cis or trans configuration. The sequence of the bubble region influences RAG cleavage at RSS when present in cis. We also find that the kinetics of RAG cleavage differs between RSS and bubble, wherein RSS cleavage reaches maximum efficiency faster than bubble cleavage. In addition, unlike RSS, RAG cleavage at bubbles does not lead to cleavage complex formation. Finally, we show that the ``nonamer binding region,'' which regulates RAG cleavage on RSS, is not important during RAG activity in non-B DNA structures. Therefore, in the current study, we identify the possible mechanism by which RAG cleavage is regulated when it acts as a structure-specific nuclease. (C) 2011 Elsevier Ltd. All rights reserved.

Saccharomyces cerevisiae NineTeen Complex (NTC)-associated Factor Bud31/Ycr063w Assembles on Precatalytic Spliceosomes and Improves First and Second Step Pre-mRNA Splicing Efficiency

Pre-mRNA splicing occurs in spliceosomes whose assembly and activation are critical for splice site selection and catalysis. The highly conserved NineTeen complex protein complex stabilizes various snRNA and protein interactions early in the spliceosome assembly pathway. Among several NineTeen complex-associated proteins is the nonessential protein Bud31/Ycr063w, which is also a component of the Cef1p subcomplex. A role for Bud31 in pre-mRNA splicing is implicated by virtue of its association with splicing factors, but its specific functions and spliceosome interactions are uncharacterized. Here, using in vitro splicing assays with extracts from a strain lacking Bud31, we illustrate its role in efficient progression to the first catalytic step and its requirement for the second catalytic step in reactions at higher temperatures. Immunoprecipitation of functional epitope-tagged Bud31 from in vitro reactions showed that its earliest association is with precatalytic B complex and that the interaction continues in catalytically active complexes with stably bound U2, U5, and U6 small nuclear ribonucleoproteins. In complementary experiments, wherein precatalytic spliceosomes are selected from splicing reactions, we detect the occurrence of Bud31. Cross-linking of proteins to pre-mRNAs with a site-specific 4-thio uridine residue at the -3 position of exon 1 was tested in reactions with WT and bud31 null extracts. The data suggest an altered interaction between a similar to 25-kDa protein and this exonic residue of pre-mRNAs in the arrested bud31 null spliceosomes. These results demonstrate the early spliceosomal association of Bud31 and provide plausible functions for this factor in stabilizing protein interactions with the pre-mRNA.

Synthesis, spectroscopic properties and biological evaluation of transition metal complexes of salicylhydrazone of anthranilhydrazide: X-ray crystal structure of copper complex

The transition metal complexes of salicylhydrazone of anthranilhydrazide (H2L) were synthesised. The structures of metal complexes were characterized by various spectroscopic [IR, NMR, UV-Vis, EPR], thermal and other physicochemical methods. The single-crystal X-ray diffraction study of [Cu(HL)Cl]center dot H2O reveal its orthorhombic system with space group P2(1)2(1)2 and Z=4. The copper center has a distorted square planar geometry with ONO and Cl as the donor atoms. The ligand and its metal chelates have been screened for their antimicrobial and anti-tubercular activities using serial dilution method. Metal complexes in general have exhibited better antibacterial and antifungal activity than the free ligand and in few cases better than the standard used. Among the bacterial strains used, the complexes are highly potent against Gram-positive strains compared to Gram-negative. Anti-tubercular activity exhibited by the Co(II) complex is comparable with the standard used. (C) 2011 Elsevier B. V. All rights reserved.

Combined Electron Transfer Dissociation-Collision-Induced Dissociation Fragmentation in the Mass Spectrometric Distinction of Leucine, Isoleucine, and Hydroxyproline Residues in Peptide Natural Products

Distinctions between isobaric residues have been a major challenge in mass spectrometric peptide sequencing. Here, we propose a methodology for distinction among isobaric leucine, isoleucine, and hydroxyproline, a commonly found post-translationally modified amino acid with a nominal mass of 113 Da, through a combined electron transfer dissociation-collision-induced dissociation approach. While the absence of c and z(center dot) ions, corresponding to the Yyy-Xxx (Xxx = Leu, Ile, or Hyp) segment, is indicative of the presence of hydroxyproline, loss of isopropyl (Delta m = 43 Da) or ethyl radicals (Delta m = 29 Da), through collisional activation of z(center dot) radical ions, are characteristic of leucine or isoleucine, respectively. Radical migration processes permit distinctions even in cases where the specific e ions, corresponding to the Yyy-Leu or -Ile segments, are absent or of low intensity. This tandem mass spectrometric (MSn) method has been successfully implemented in a liquid chromatography MSn platform to determine the identity of 23 different isobaric residues from a mixture of five different peptides. The approach is convenient for distinction of isobaric residues from any crude peptide mixture, typically encountered in natural peptide libraries or proteomic analysis.

Low-Delay, High-Rate Nonsquare Complex Orthogonal Designs

The maximal rate of a nonsquare complex orthogonal design for transmit antennas is 1/2 + 1/n if is even and 1/2 + 1/n+1 if is odd and the codes have been constructed for all by Liang (2003) and Lu et al. (2005) to achieve this rate. A lower bound on the decoding delay of maximal-rate complex orthogonal designs has been obtained by Adams et al. (2007) and it is observed that Liang's construction achieves the bound on delay for equal to 1 and 3 modulo 4 while Lu et al.'s construction achieves the bound for n = 0, 1, 3 mod 4. For n = 2 mod 4, Adams et al. (2010) have shown that the minimal decoding delay is twice the lower bound, in which case, both Liang's and Lu et al.'s construction achieve the minimum decoding delay. For large value of, it is observed that the rate is close to half and the decoding delay is very large. A class of rate-1/2 codes with low decoding delay for all has been constructed by Tarokh et al. (1999). In this paper, another class of rate-1/2 codes is constructed for all in which case the decoding delay is half the decoding delay of the rate-1/2 codes given by Tarokh et al. This is achieved by giving first a general construction of square real orthogonal designs which includes as special cases the well-known constructions of Adams, Lax, and Phillips and the construction of Geramita and Pullman, and then making use of it to obtain the desired rate-1/2 codes. For the case of nine transmit antennas, the proposed rate-1/2 code is shown to be of minimal delay. The proposed construction results in designs with zero entries which may have high peak-to-average power ratio and it is shown that by appropriate postmultiplication, a design with no zero entry can be obtained with no change in the code parameters.

Amplitude death in complex networks induced by environment

We present a mechanism for amplitude death in coupled nonlinear dynamical systems on a complex network having interactions with a common environment like external system. We develop a general stability analysis that is valid for any network topology and obtain the threshold values of coupling constants for the onset of amplitude death. An important outcome of our study is a universal relation between the critical coupling strength and the largest nonzero eigenvalue of the coupling matrix. Our results are fully supported by the detailed numerical analysis for different network topologies.

Pleiotropic Roles of a Ribosomal Protein in Dictyostelium discoideum

The cell cycle phase at starvation influences post-starvation differentiation and morphogenesis in Dictyostelium discoideum. We found that when expressed in Saccharomyces cerevisiae, a D. discoideum cDNA that encodes the ribosomal protein S4 (DdS4) rescues mutations in the cell cycle genes cdc24, cdc42 and bem1. The products of these genes affect morphogenesis in yeast via a coordinated moulding of the cytoskeleton during bud site selection. D. discoideum cells that over-or under-expressed DdS4 did not show detectable changes in protein synthesis but displayed similar developmental aberrations whose intensity was graded with the extent of over-or under-expression. This suggested that DdS4 might influence morphogenesis via a stoichiometric effect - specifically, by taking part in a multimeric complex similar to the one involving Cdc24p, Cdc42p and Bem1p in yeast. In support of the hypothesis, the S. cerevisiae proteins Cdc24p, Cdc42p and Bem1p as well as their D. discoideum cognates could be co-precipitated with antibodies to DdS4. Computational analysis and mutational studies explained these findings: a C-terminal domain of DdS4 is the functional equivalent of an SH3 domain in the yeast scaffold protein Bem1p that is central to constructing the bud site selection complex. Thus in addition to being part of the ribosome, DdS4 has a second function, also as part of a multi-protein complex. We speculate that the existence of the second role can act as a safeguard against perturbations to ribosome function caused by spontaneous variations in DdS4 levels.

Synthesis and characterization of cobalt(II), nickel(II), copper(II) and zinc(II) complexes of 2-nitrobenzoic acid with methyl carbazate as ancillary ligand. Crystal structure of the copper(II) complex

Divalent metal complexes of general formula M(2-nb)(2)(mc)(2)].2(2-nbH), where M = Co(II), Ni(II), Cu(II) or Zn(II), 2-nbH = 2-nitrobenzoic acid and mc = methyl carbazate (NH2NHCOOCH3), have been prepared and characterized by physicochemical and spectroscopic methods. Single-crystal X-ray study of the Cu(II) complex revealed that the molecule is centrosymmetric, with two N,O-chelating mc ligands in equatorial positions and a pair of monodentate 2-nb anions in the axial positions. The lattice 2-nbH molecules help to establish the packing of monomers through hydrogen-bonding interactions. Thermal stability and reactivity of the complexes were studied by TG-DTA. Emission studies show that these complexes are fluorescent.

Human action recognition using a fast learning fully complex-valued classifier

In this paper, we use optical flow based complex-valued features extracted from video sequences to recognize human actions. The optical flow features between two image planes can be appropriately represented in the Complex plane. Therefore, we argue that motion information that is used to model the human actions should be represented as complex-valued features and propose a fast learning fully complex-valued neural classifier to solve the action recognition task. The classifier, termed as, ``fast learning fully complex-valued neural (FLFCN) classifier'' is a single hidden layer fully complex-valued neural network. The neurons in the hidden layer employ the fully complex-valued activation function of the type of a hyperbolic secant function. The parameters of the hidden layer are chosen randomly and the output weights are estimated as the minimum norm least square solution to a set of linear equations. The results indicate the superior performance of FLFCN classifier in recognizing the actions compared to real-valued support vector machines and other existing results in the literature. Complex valued representation of 2D motion and orthogonal decision boundaries boost the classification performance of FLFCN classifier. (c) 2012 Elsevier B.V. All rights reserved.

Remarkable photocytotoxicity of curcumin in HeLa cells in visible light and arresting its degradation on oxovanadium(IV) complex formation

Curcumin (Hcur) as a cellular imaging and PDT agent shows remarkable photocytotoxicity in HeLa cells in visible light of 400-700 nm giving IC50 = 8.2 +/- 0.2 mu M and its degradation is arrested on formation of photocytotoxic dipyridophenazine (dppz) complex VO(cur)(dppz)Cl] (IC50 = 3.3 +/- 0.4 mu M), while both are less toxic in the dark.

Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative `Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed `3interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.

Synthetic studies toward geranylated PPAP natural products oblongifolin A, oblongifolin D, and enervosanone

A concise approach of general utility toward mono- and di-geranylated PPAP frameworks employing `reconstructive aldol cyclization' as the key step is delineated. (C) 2012 Elsevier Ltd. All rights reserved.

Enantioselective syntheses of bioactive epoxyquinone natural products (+)-harveynone and (-)-asperpentyn

Stereo- and enantioselective syntheses of (+)-harveynone and (-)-asperpentyn are reported. (C) 2012 Elsevier Ltd. All rights reserved.

Ultrahigh-temperature metamorphism from an unusual corundum plus orthopyroxene intergrowth bearing Al-Mg granulite from the Southern Marginal Zone, Limpopo Complex, South Africa

The Southern Marginal Zone of the Limpopo Complex is composed of granite-greenstone cratonic rocks reworked by a Neoarchean high-grade tectono-metamorphic event. Petrographic and mineral chemical characterization of an Al-Mg granulite from this zone is presented here. The granulite has a gneissic fabric with distinct Al-rich and Si-rich layers, with the former preserving the unusual lamellar (random and regular subparallel) intergrowths of corundum and symplectic intergrowth of spinel with orthopyroxene. The Al-rich layer preserves mineral assemblages such as rutile with orthopyroxene + sillimanite +/- A quartz, Al-rich orthopyroxene (similar to 11 wt%), spinel + quartz, and corundum in possible equilibrium with quartz, while the Si-rich layer preserves antiperthites and orthopyroxene + sillimanite +/- A quartz, all considered diagnostic of ultrahigh-temperature metamorphism. Application of Al-in-opx thermometry, ternary feldspar thermometry and construction of suitable pressure-temperature phase diagrams, compositional and model proportion isopleth results indicate P-T conditions as high as similar to 1,050-1,100 A degrees C, and similar to 10-12 kbars for the Al-Mg granulite. Our report of ultrahigh-temperature conditions is significant considering that the very high temperature was reached during decompression of an otherwise high-pressure granulite complex (clockwise P-T path), whereas most other ultrahigh-temperature granulites are linked to magma underplating at the base of the crust (counterclockwise P-T path).

Model synthetic studies toward jiadifenin and majucin type seco-prezizaane natural products via a stereo- and enantioselective approach

A concise stereo- and enantioselective approach to seco-prezizaane sesquiterpenoids, leading to the acquisition of two bicyclic fragments, is delineated. (c) 2012 Elsevier Ltd. All rights reserved.