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.

Association rule mining activity : A general formalism

Mining association rules from a large collection of databases is based on two main tasks. One is generation of large itemsets; and the other is finding associations between the discovered large itemsets. Existing formalism for association rules are based on a single transaction database which is not sufficient to describe the association rules based on multiple database environment. In this paper, we give a general characterization of association rules and also give a framework for knowledge-based mining of multiple databases for association rules.

Exceptional activity of mesoporous beta-MnO2 in the catalytic thermal sensitization of ammonium perchlorate

Mesoporous beta-MnO2 has been prepared, characterized and demonstrated to possess excellent catalytic activity in the thermal decomposition of ammonium perchlorate. The observed unprecedentedly low decomposition temperatures, fast reaction rates and enhanced heat releases in the catalysed formulations make mesoporous beta-MnO2 promising as a high-performing ballistic modifier in AP-based composite solid rocket propellants.

Ferrocene-Conjugated Copper(II) Complexes of L-Methionine and Phenanthroline Bases: Synthesis, Structure, and Photocytotoxic Activity

Ferrocene-conjugated reduced Schiff base (Fc-metH) copper(II) complexes of L-methionine and phenanthroline bases, namely, Cu(Fc-met)(B)](NO3), where B is 1,10-phenanthroline (phen in 1), dipyrido3,2-d:2',3'-f]quinoxaline (dpq in 2), dipyrido3,2-a:2',3'-c]phenazine (dppz in 3), and 2-(naphthalen-1-yl)-1H-imidazo4,5-f]1,10]phenanthroline (nip in 4), were prepared and characterized and their photocytotoxicity studied (Fc = ferrocenyl moiety). Complexes Cu(Ph-met)(B)](NO3) of the reduced Schiff base from benzaldehyde and L-methionine (Ph-metH) and B (phen in 5, dppz in 6) were prepared and used as control species. Complexes 1 and 5 were structurally characterized by X-ray crystallography. Complex 1 as a discrete monomer has a CuN3OS core with the thiomethyl group as the axial ligand. Complex 5 has a polymeric structure with a CuN3O2 core in the solid state. Complexes 5 and 6 are formulated as Cu(Ph-met)(B)(H2O)] (NO3) in an aqueous phase based on the mass spectral data. Complexes 1-4 showed the Cu(II)-Cu(I) and Fc(+)-Fc redox couples at similar to 0.0 and similar to 0.5 V vs SCE, respectively, in DMF-0.1 M (Bu4N)-N-n](ClO4). A Cu(II)-based weak d-d band near 600 nm and a relatively strong ferrocenyl band at similar to 450 nm were observed in DMF-Tris-HCl buffer (1:4 v/v). The complexes bind to calf thymus DNA, exhibit moderate chemical nuclease activity forming (OH)-O-center dot radical species, and are efficient photocleavers of pUC19 DNA in visible light of 454, 568, and 647 rim, forming (OH)-O-center dot radical as the reactive oxygen species. They are cytotoxic in HeLa (human cervical cancer) and MCF-7 (human breast cancer) cells, showing an enhancement of cytotoxicity upon visible light irradiation. Significant change in the nuclear morphology of the HeLa cells was observed with 3 in visible light compared to the nonirradiated sample. Confocal imaging using 4 showed its nuclear localization within the HeLa cells.

Use of Vertex Index in Structure-Activity Analysis and Design of Molecules

The last few decades have witnessed application of graph theory and topological indices derived from molecular graph in structure-activity analysis. Such applications are based on regression and various multivariate analyses. Most of the topological indices are computed for the whole molecule and used as descriptors for explaining properties/activities of chemical compounds. However, some substructural descriptors in the form of topological distance based vertex indices have been found to be useful in identifying activity related substructures and in predicting pharmacological and toxicological activities of bioactive compounds. Another important aspect of drug discovery e. g. designing novel pharmaceutical candidates could also be done from the distance distribution associated with such vertex indices. In this article, we will review the development and applications of this approach both in activity prediction as well as in designing novel compounds.

A variant peptide of buffalo colostrum beta-lactoglobulin inhibits angiotensin I-converting enzyme activity

beta-lactoglobulin is a rich source of bioactive peptides. The LC-MS separated tryptic peptides of buffalo colostrum beta-lactoglobulin (BLG-col) were computed based on MS-MS fragmentation for de novo sequencing. Among the selected peptides (P1-P8), a variant was detected with methionine at position 74 instead of glutamate. The sequences of two peptides were identical to hypocholesterolemic peptides whereas the remaining peptides were in accordance with buffalo milk beta-lactoglobulin. Comparative sequence analysis of BLG-col to milk beta-lactoglobulin was carried out using CLUSTALW2 and a molecular model for BLG-col was constructed (PMDB ID-PM0076812). The synthesized variant pentapeptide (IIAMK, m/z-576 Da) was found to inhibit angiotensin I-converting enzyme (ACE) with an IC50 of 498 +/- 2 mu M, which was rationalized through docking simulations using Molgrow virtual docker. (C) 2012 Elsevier Masson SAS. All rights reserved.

Synthesis of benzofuran based 1,3,5-substituted pyrazole derivatives: As a new class of potent antioxidants and antimicrobials-A novel accost to amend biocompatibility

In search for a new antioxidant and antimicrobial agent with improved potency, we synthesized a series of benzofuran based 1,3,5-substituted pyrazole analogues (5a-l) in five step reaction. Initially, o-alkyl derivative of salicyaldehyde readily furnish corresponding 2-acetyl benzofuran 2 in good yield, on treatment with 1,8-diaza bicyclo5.4.0]undec-7-ene (DBU) in the presence of molecular sieves. Further, aldol condensation with vanillin, Claisen-Schmidt condensation reaction with hydrazine hydrate followed by coupling of substituted anilines afforded target compounds. The structures of newly synthesized compounds were confirmed by IR, H-1 NMR, C-13 NMR, mass, elemental analysis and further screened for their antioxidant and antimicrobial activities. Among the tested compounds 5d and 5f exhibited good antioxidant property with 50% inhibitory concentration higher than that of reference while compounds 5h and 5l exhibited good antimicrobial activity at concentration 1.0 and 0.5 mg/mL compared with standard, streptomycin and fluconazole respectively. (C) 2012 Elsevier Ltd. All rights reserved.

Design and Synthesis of a Functional Derivative of the Triazinium Cation and Its Rhodium Complex that Shows Photoinduced DNA Cleavage Activity and Photocytotoxicity

The design and synthesis of an intensely blue rhodium(III) complex 3]+ of a new N,N-donor ligand, 8-(quinolin-8-ylamino)pyrido2,1-c]1,2,4]benzotriazin-11-ium, 2]+, which contains a planar pendant triazinium arm, is described. Structural characterization for 3]+ was carried out by using various spectroscopic techniques and single-crystal X-ray crystallography. The organometallic rhodium(III) compound shows a ligand-based reversible reduction at 0.65 V. The electrochemically reduced compound displays a single-line EPR spectrum that signifies the formation of ligand-based free radicals. Compound 3]+ shows a binding propensity to calf thymus DNA to give a Kapp value of 6.05X105 M1. The parent triazinium salt, pyrido2,1-c]1,2,4]benzotriazin-11-ium 1]+ and the ligand salt 2]+ exhibit photoinduced cleavage of DNA in UV-A light, whereas the reference Rh complex 3]+ photocleaves DNA with red light (647.1 nm). The compounds show photonuclease activities under both aerobic and anaerobic conditions. Mechanistic investigations under aerobic conditions with several inhibitors indicate the formation of hydroxyl radicals by means of a photoredox pathway. Under anaerobic conditions, it is believed that a photoinduced oxidation of DNA mechanism is operative. Compound 3]+ exhibits photocytotoxicity in HeLa cervical cancer cells to give IC50 values of (12+/-0.9) mu M in UV-A light at 365 nm and (31.4+/-1.1) mu M in the dark.

Stabilization and Structural Alteration of the G-Quadruplex DNA Made from the Human Telomeric Repeat Mediated by Troger's Base Based Novel Benzimidazole Derivatives

Ligand-induced stabilization of the G-quadruplex DNA structure derived from the single-stranded 3'-overhang of the telomeric DNA is an attractive strategy for the inhibition of the telomerase activity. The agents that can induce/stabilize a DNA sequence into a G-quadruplex structure are therefore potential anticancer drugs. Herein we present the first report of the interactions of two novel bisbenzimidazoles (TBBz1 and TBBz2) based on Troger's base skeleton with the G-quadruplex DNA (G4DNA). These Troger's base molecules stabilize the G4DNA derived from a human telomeric sequence. Evidence of their strong interaction with the G4DNA has been obtained from CD spectroscopy, thermal denaturation, and UV-vis titration studies. These ligands also possess significantly higher affinity toward the G4DNA over the duplex DNA. The above results obtained are in excellent agreement with the biological activity, measured in vitro using a modified TRAP assay. Furthermore, the ligands are selectively more cytotoxic toward the cancerous cells than the corresponding noncancerous cells. Computational studies suggested that the adaptive scaffold might allow these ligands to occupy not only the G-quartet planes but also the grooves of the G4DNA.

TURBULENT PUMPING OF MAGNETIC FLUX REDUCES SOLAR CYCLE MEMORY AND THUS IMPACTS PREDICTABILITY OF THE SUN'S ACTIVITY

Prediction of the Sun's magnetic activity is important because of its effect on space environment and climate. However, recent efforts to predict the amplitude of the solar cycle have resulted in diverging forecasts with no consensus. Yeates et al. have shown that the dynamical memory of the solar dynamo mechanism governs predictability, and this memory is different for advection- and diffusion-dominated solar convection zones. By utilizing stochastically forced, kinematic dynamo simulations, we demonstrate that the inclusion of downward turbulent pumping of magnetic flux reduces the memory of both advection- and diffusion-dominated solar dynamos to only one cycle; stronger pumping degrades this memory further. Thus, our results reconcile the diverging dynamo-model-based forecasts for the amplitude of solar cycle 24. We conclude that reliable predictions for the maximum of solar activity can be made only at the preceding minimum-allowing about five years of advance planning for space weather. For more accurate predictions, sequential data assimilation would be necessary in forecasting models to account for the Sun's short memory.

Synthesis, characterization and phosphotriesterase mimetic activity of some Zn(II) and Cu(II) complexes

We report here the synthesis and characterization of a few phenolate-based ligands bearing tert- amino substituent and their Zn(II) and Cu(II) metal complexes. Three mono/binuclear Zn(II) and Cu(II) complexes Zn(L1)(H2O)].CH3OH.H2O (1) (H (2) L1 = 6,6(')-(((2-dimethylamino)ethylazanediyl)bis(methylene))bis(2, 4-dimethylphenol), Zn-2(L2)(2)] (2) (H (2) L2 = 2,2(')-(((2-dimethylamino)ethyl)azanediyl)bis(methylene)bis(4- methylphenol) and Cu-2(L3)(2).CH2 Cl-2] (3) (H (2) L3 = (6,6(')-(((2-(diethylamino)ethyl)azanediyl)bis(methylene)) bis(methylene))bis(2,4-dimethylphenol) were synthesized by using three symmetrical tetradendate ligands containing N2O2 donor sites. These complexes are characterized by a variety of techniques including; elemental analysis, mass spectrometry, H-1, C-13 NMR spectroscopic and single crystal X-ray analysis. The new complexes have been tested for the phosphotriesterase (PTE) activity with the help of P-31 NMR spectroscopy. The P-31 NMR studies show that mononuclear complex Zn(L1)(H2O)].CH3OH.H2O (1) can hydrolyse the phosphotriester i.e., p-nitrophenyl diphenylphosphate (PNPDPP), more efficiently than the binuclear complexes Zn-2(L2)(2)] (2) and Cu-2(L3)(2).CH2Cl2] (3). The mononuclear Zn(II) complex (1) having one coordinated water molecule exhibits significant PTE activity which may be due to the generation of a Zn(II)-bound hydroxide ion during the hydrolysis reactions in CHES buffer at pH 9.0.

A Calcium-Dependent Plasticity Rule for HCN Channels Maintains Activity Homeostasis and Stable Synaptic Learning

Theoretical and computational frameworks for synaptic plasticity and learning have a long and cherished history, with few parallels within the well-established literature for plasticity of voltage-gated ion channels. In this study, we derive rules for plasticity in the hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, and assess the synergy between synaptic and HCN channel plasticity in establishing stability during synaptic learning. To do this, we employ a conductance-based model for the hippocampal pyramidal neuron, and incorporate synaptic plasticity through the well-established Bienenstock-Cooper-Munro (BCM)-like rule for synaptic plasticity, wherein the direction and strength of the plasticity is dependent on the concentration of calcium influx. Under this framework, we derive a rule for HCN channel plasticity to establish homeostasis in synaptically-driven firing rate, and incorporate such plasticity into our model. In demonstrating that this rule for HCN channel plasticity helps maintain firing rate homeostasis after bidirectional synaptic plasticity, we observe a linear relationship between synaptic plasticity and HCN channel plasticity for maintaining firing rate homeostasis. Motivated by this linear relationship, we derive a calcium-dependent rule for HCN-channel plasticity, and demonstrate that firing rate homeostasis is maintained in the face of synaptic plasticity when moderate and high levels of cytosolic calcium influx induced depression and potentiation of the HCN-channel conductance, respectively. Additionally, we show that such synergy between synaptic and HCN-channel plasticity enhances the stability of synaptic learning through metaplasticity in the BCM-like synaptic plasticity profile. Finally, we demonstrate that the synergistic interaction between synaptic and HCN-channel plasticity preserves robustness of information transfer across the neuron under a rate-coding schema. Our results establish specific physiological roles for experimentally observed plasticity in HCN channels accompanying synaptic plasticity in hippocampal neurons, and uncover potential links between HCN-channel plasticity and calcium influx, dynamic gain control and stable synaptic learning.

A possible connection between antidiabetic and antilipemic properties of psoralea corylifolia seeds and the trace elements present: a LIBS based study

Psoralea corylifolia (PC), a medicinal plant, is used in traditional medicine to treat diabetes. Purpose of the research was to examine the antidiabetic and antilipemic potential of PC and to determine the relationship between its antidiabetic potential and the trace elements present. Wistar rats (150-200 g) with fasting blood glucose (FBG) of 80-110 mg dl(-1)(sub-diabetic) and 150-200 mg dl(-1)(mild diabetic) were selected for the short term antidiabetic studies and severely diabetic rats (FBG > 300 mg dl(-1)) were chosen for the long term antidiabetic and hypolipemic studies of PC seed extract. Laser induced breakdown spectroscopy (LIBS) was used to detect trace elements in the PC extract and the intensity ratios of trace elements were estimated. The dose of 250 mg kg(-1) of PC extract was found to be the most effective in lowering blood glucose level (BGL) of normal, sub, mild and severely diabetic rats during FBG and glucose tolerance test (GTT) studies. Lipid profile studies on severely diabetic rats showed substantial reduction in total cholesterol, triglycerides, very low density lipoprotein, and low density lipoprotein and an increase in the total protein, body weight, high density lipoprotein, and hemoglobin after 28 days of treatment. Significant reduction in urine sugar and protein levels was also observed. LIBS analysis of the PC extract revealed the presence of Mg, Si, Na, K, Ca, Zn and Cl. The study validates the traditional use of PC in the treatment of diabetes and confirms its antilipemic potential. The antidiabetic activity of PC extract may partly be due to the presence of appreciable amounts of insulin potentiating elements like Mg, Ca, and K.

Case for multiple views of function in design based on a common definition

Functions are important in designing. However, several issues hinder progress with the understanding and usage of functions: lack of a clear and overarching definition of function, lack of overall justifications for the inevitability of the multiple views of function, and scarcity of systematic attempts to relate these views with one another. To help resolve these, the objectives of this research are to propose a common definition of function that underlies the multiple views in literature and to identify and validate the views of function that are logically justified to be present in designing. Function is defined as a change intended by designers between two scenarios: before and after the introduction of the design. A framework is proposed that comprises the above definition of function and an empirically validated model of designing, extended generate, evaluate, modify, and select of state-change, and an action, part, phenomenon, input, organ, and effect model of causality (Known as GEMS of SAPPhIRE), comprising the views of activity, outcome, requirement-solution-information, and system-environment. The framework is used to identify the logically possible views of function in the context of designing and is validated by comparing these with the views of function in the literature. Describing the different views of function using the proposed framework should enable comparisons and determine relationships among the various views, leading to better understanding and usage of functions in designing.

Synthetic glutathione peroxidase mimics: effect of nucleophilicity of the aryl thiol cofactor on the antioxidant activity

Catalytic activity of a series of potent amide- and amine-based organoselenium compounds are studied in the presence of various aromatic thiols having electron donating and electron withdrawing substituents on the phenyl ring. This study suggests that the antioxidant activities of the synthetic GPx mimics can be significantly increased by the incorporation of a suitable electron donating group on the phenyl ring of an aromatic thiol.