Silencing of Bruton's tyrosine kinase (Btk) using short interfering RNA duplexes (siRNA)

Tec family tyrosine kinases, Bruton's tyrosine kinase (Btk), Itk, Bmx, Tec, and Txk, are multi-domain proteins involved in hematopoietic signaling. Here, we demonstrate that human Btk protein can transiently be depleted using double-stranded short RNA interference (siRNA) oligonucleotides. Imaging and Western blotting analysis demonstrate that Btk expression is down regulated in heterologous systems as well as in hematopoietic lineages, following transfection or microinjection of Btk siRNA duplexes. The induction of histamine release, a pro-inflammatory mediator, in RBL-2H3 mast cells was reduced by 20-25% upon Btk down regulation. Similar, results were obtained when the Btk activity was inhibited using the kinase blocker LFM-A13. These results demonstrate a direct role of Btk for the efficient secretion of histamine in allergic responses.     

Down-regulation of human deoxyuridine triphosphate nucleotidohydrolase (dUTPase) using small interfering RNA (siRNA)

A small interfering double stranded RNA molecule (siRNA, 21 bp) corresponding to a portion (nucleotides 337 to 357) of domain 3 of the human dUTPase was synthesized and used to determine whether it could down-regulate dUTPase activity in human cells. Transfection of the siRNA into HeLa and HT29 cells resulted in a 56 +/- 3.6% decrease in dUTPase activity, while transfection of SW620 cells resulted in a 27 +/- 6% decrease in dUTPase activity when compared to non-treated controls.     

Conjugate for efficient delivery of short interfering RNA (siRNA) into mammalian cells

Cholesterol enrichment of rat liver mitochondria (CHM) impairs atractyloside-induced mitochondrial permeability transition (MPT) due to decreased membrane fluidity. In this study we addressed the effect of cholesterol enrichment on MPT induced by reactive oxygen species (ROS). Superoxide anion generated by xanthine plus xanthine oxidase triggered mitochondrial swelling and cytochrome c release in CHM, which was prevented by butylated hydroxytoluene, an anti-voltage-dependent anion channel antibody, or cyclosporin A. Furthermore, hydrogen peroxide generated by the combination of ganglioside GD3 and mitochondrial GSH depletion elicited mitochondrial swelling and release of cytochrome c, Smac/Diablo and apoptosis-inducing factor in control mitochondria and CHM. Thus, ROS induce MPT and apoptosome activation regardless of decreased mitochondrial membrane dynamics due to cholesterol enrichment.     

Phospholipase A2 sensitive liposomes for delivery of small interfering RNA (siRNA)

Small interfering RNA (siRNA) is potent and highly specific for gene silencing and there is currently a lot of enthusiasm for developing siRNA into a drug. However, for most therapeutic applications of siRNA, delivery systems are needed. These delivery systems have multiple requirements and should on one hand ideally be stable carriers protecting the siRNA from degradation and on the other hand assist the siRNA in overcoming membrane barriers for intracellular delivery to the cytosol. Long-circulating liposomes, which are sensitive to secretory phospholipase A(2) (sPLA(2)) are feasible delivery systems for systemic administration of drugs due to their passive targeting to pathological tissue via the enhanced permeability and retention (EPR) effect and their site-specific, enzyme-triggered release of encapsulated drug in response to sPLA(2) which exists locally at elevated levels at, e.g,. sites of inflammation. However, recent data suggest that endosomal membrane destabilizing approaches could be addressed to design sPLA(2)-sensitive liposomes as successful delivery systems for siRNA to the RNA interference pathway in the cytoplasm upon systemic administration.     

In silico designing of insecticidal small interfering RNA (siRNA) for Helicoverpa armigera control

Helicoverpa armigera, a polyphagous lepidopteron insect pest causes severe yield loss in cotton, legumes, tomato, okra and other crops. Application of chemical pesticides although effective, has human health and environmental safety concerns. Moreover, development of resistance against most of the available pesticides is compelling to look for alternative strategies. Adoption of Bt transgenic crops have resulted in reduction in pesticide consumption and increasing crop productivity. However, sustainability of Bt transgenic crops is threatened by the emergence of insect resistance. In the present study potential insecticidal siRNA were identified in six H. armigera horrhonal pathway genes. Out of over 2000 computationally identified siRNA, 16 most promising siRNA were selected that address the biosafety concerns and have high potential of targeted gene silencing. These siRNA will be useful for chemical synthesis, in insect feeding assays and knockdown the target H. armigera hormone biosynthesis, consequently obstructing the completion of insect life cycle. The siRNA have a great potential of deployment to control H. annrmigera alone as well as with Bt for insect resistance management.     

Application of small interfering RNA (siRNA) for modulation of airway epithelial gene expression

Small interfering RNA (siRNA) was developed as a novel tool to inhibit gene function in human disease. The aim of the present study was to modify the function of NF-kappaB in airway epithelial cells by application of siRNA. 1HAEo cells were transfected with siRNA directed to the p65 subunit of NF- kappaB (siRNA.p65). Application of siRNA.p65 caused decreased levels of p65 mRNA or protein after 72 hours, as determined by quantitative RT-PCR or Western blot analysis. The tumor necrosis factor- alpha (TNF-alpha)-induced release of interleukin-6 (IL-6) and IL-8 was significantly inhibited by the application of siRNA.p65. Well-differentiated primary cells were resistant to transfection with siRNA.p65. However, when undifferentiated primary cells were transfected, an effect of the siRNA could still be observed when the cells were differentiated in an air-liquid interface culture system. In conclusion, siRNA can be used to regulate the activity of NF-kappaB in airway epithelial cells.     

Short interfering RNA (siRNA), a novel therapeutic tool acting on angiogenesis

The formation of new blood vessels, uncontrolled cell expansions and invasions are the common feature of cancer, neovascular inflammatory and ocular diseases, such as age-related macular degeneration (AMD). Short interfering RNA (siRNA) and short-hairpin RNA (shRNA) have recently helped extend our understanding of the mechanisms regulating angiogenesis and tumor developments. Moreover, the early success of these tools has reinforced the therapeutic hopes of preventing endogenous or exogenous gene translation. In vivo experiments using several animal tumor models and human pre-clinical trials augured many benefits to control protein expression and cell signaling. The high specificity of siRNA and shRNA to target a protein is crucial to design a new generation of therapeutic agents. At the present, several investigations are focused on the understanding of both gene function and the proof-of-concept for siRNA-mediated anti-angiogenesis. Taken together, in vitro and in vivo studies shed light on the efficiency of siRNA as a new alternative therapeutic agent.     

A new copper(II) complex of unsymmetrical tetradentate ligand generated in situ: synthesis and molecular structure

A new copper(II) complex with tetradentate unsymmetrical ligand was prepared by one-pot condensation of methyl-2-pyrrole carboxylate, diethylenetriamine and copper(II) sulfate. The complex was characterized by elemental analysis, electronic and IR spectral, as well as X-ray crystal structure determination. The X-ray structure of the molecule reveals the copper(II) center is in a square planar environment through coordination by two nitrogen atoms of the amine, one amide nitrogen atom and one nitrogen atom of the pyrrole moieties, respectively. The copper(II) complex is neutral due to deprotonation of the amide and pyrrole groups.     

Variations of the 3' protruding ends in synthetic short interfering RNA (siRNA) tested by microinjection in Drosophila embryos

Short interfering RNAs (siRNAs) are the processing product originating from long double-stranded RNAs (dsRNAs) that are cleaved by the RNase III-like ribonuclease Dicer. As siRNAs mediate cleavage of specific single-stranded target RNAs, they are essential intermediates of RNA interference (RNAi). When applied in synthetic form, siRNAs likewise can induce the silencing process in the absence of long dsRNAs. Here, we tested variations of a conventional synthetic siRNA that had been used successfully to silence the Drosophila notch gene. The variants had two 3 ' -terminal deoxynucleotides in their protruding single-stranded ends. In one case, the deoxynulceotides would match to the notch mRNA, whereas the other variant had nonmatching deoxy-T residues, representing a widely used siRNA design. siRNAs with different combinations of sense and antisense strands were injected into Drosophila embryos at two different concentrations. We found that the all-ribonucleotide siRNA gave the best inhibition of notch expression. The combination of two modified strands with 3 ' -terminal deoxynucleotides was effective, but if combined with a sense or antisense ribostrand, the efficacy dropped. The siRNAs with nonmatching 3 ' -terminal TT residues showed a reduced silencing potential, which became evident at low concentration. An siRNA with a nonmatching 3 ' -terminal ribonucleotide in the antisense strand retained most of its silencing potential in accordance with the hypothesis that primer extension for generation of ssRNA from single-stranded mRNA does not operate in Drosophila.     

Revision of the Euthalia phemius complex (Lepidoptera: Nymphalidae) based on morphology and molecular analyses

Adults of the Euthalia phemius complex, which is composed of three South‐East Asian nymphalid species, Euthalia phemius, Euthalia ipona, and Euthalia euphemia, were genetically analysed by examining mitochondrial and nuclear genes. The E. phemius complex was also examined morphologically, with particular emphasis on wing markings and male genitalia. No significant differences amongst the three species in the complex were detected with respect to either genetic distance or genital morphology. We therefore conclude that the three currently recognized Euthalia species belong to a single species. Accordingly, E. ipona is synonymized with E. phemius. Euthalia euphemia is treated as a subspecies of E. phemius. Type specimens of all taxa and a synonymic list for the E. phemius complex are also given. In addition, we briefly discuss the evolution and biogeography of the species complex. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 304–327.     

Dipeptide interactions with Zn(II)–cyclen artificial model for molecular recognition

The Zn(II)–cyclen–dipeptide ternary systems (where cyclen is abbreviated as L and dipeptide is glycylglycine (HL¹) or glycyl‐(S)‐alanine (HL²)) were investigated by potentiometry applying both “out‐of‐cell” and direct titrations and by ¹H NMR spectroscopy. Especially, the ¹H NMR study was found to be very efficient to estimate speciation in the systems. The results obtained under full equilibria indicated two main species, [Zn(L)(HL^1,2)]²⁺ and [Zn(L)(L^1,2)]⁺, in both the systems. In the [Zn(L)(HL^1,2)]²⁺ complex, presence of carbonyl‐carboxylate chelate was confirmed, and in the [Zn(L)(L^1,2)]⁺ species, the peptide coordination is re‐organized to carbonyl‐amine chelate or only terminal amino group is coordinated. Equilibrium constants describing [Zn(L)]²⁺–dipeptide interaction are relatively low, log K = 3.4 for Gly‐Gly and 4.1 for Gly‐(S)‐Ala, respectively. Nevertheless, the values are slightly higher than stability constants for interaction of Zn(II) with the dipeptides (i.e. [Zn(L^1,2)]⁺ species) where a chelate formation is expected. It indicates that interaction between Zn(II) ion in [Zn(L)]²⁺ and the dipeptides should be supported by some additional interactions. Potentiometry carried out under non‐equilibrum condition showed different species where these additional stabilizing forces play more important role. Copyright © 2015 John Wiley & Sons, Ltd.     

A molecular dynamics simulation of the flavin mononucleotide–RNA aptamer complex

We report on an unrestrained molecular dynamics simulation of the flavin mononucleotide (FMN)–RNA aptamer. The simulated average structure maintains both cross‐strand and intermolecular FMN–RNA nuclear Overhauser effects from the nmr experiments and has all qualitative features of the nmr structure including the G10–U12–A25 base triple and the A13–G24, A8–G28, and G9–G27 mismatches. However, the relative orientation of the hairpin loop to the remaining part of the molecule differs from the nmr structure. The simulation predicts that the flexible phosphoglycerol part of FMN moves toward G27 and forms hydrogen bonds. There are structurally long‐lived water molecules in the FMN binding pocket forming hydrogen bonds within FMN and between FMN and RNA. In addition, long‐lived water is found bridging primarily RNA backbone atoms. A general feature of the environment of long‐lived “structural” water is at least two and in most cases three or four potential acceptor atoms. The 2′‐OH group of RNA usually acts as an acceptor in interactions with the solvent. There are almost no intrastrand O2′H(n)⋮O4′(n + 1) hydrogen bonds within the RNA backbone. In the standard case the preferred orientation of the 2′‐OH hydrogen atoms is approximately toward O3′ of the same nucleotide. However, a relatively large number of conformations with the backbone torsional angle γ in the trans orientation is found. A survey of all experimental RNA x‐ray structures shows that this backbone conformation occurs but is less frequent than found in the simulation. Experimental nmr RNA aptamer structures have a higher fraction of this conformation as compared to the x‐ray structures. The backbone conformation of nucleotide n + 1 with the torsional angle γ in the trans orientation leads to a relatively short distance between 2′‐OH(n) and O5′(n + 1), enabling hydrogen‐bond formation. In this case the preferred orientation of the 2′‐OH hydrogen atom is approximately toward O5′(n + 1). We find two relatively short and dynamically stable types of backbone–backbone next‐neighbor contacts, namely C2′(H)(n)⋮O4′(n + 1) and C5′(H)(n + 1)⋮O2′(n). These interactions may affect both backbone rigidity and thermodynamic stability of RNA helical structures. © 1999 John Wiley & Sons, Inc. Biopoly 50: 287–302, 1999     

Exploring the interactions of a Tb(III)–quercetin complex with serum albumins (HSA and BSA): spectroscopic and molecular docking studies

Serum albumins (human serum albumin (HSA) and bovine serum albumin (BSA), two main circulatory proteins), are globular and monomeric macromolecules in plasma that transport many drugs and compounds. In the present study, we investigated the interactions of the Tb(III)–quercetin (Tb–QUE) complex with HSA and BSA using common spectroscopic techniques and a molecular docking study. Fluorescence data revealed that the inherent fluorescence emission of HSA and BSA was markedly quenched by the Tb–QUE complex through a static quenching mechanism, confirming stable complex formation (a ground‐state association) between albumins and Tb–QUE. Binding and thermodynamic parameters were obtained from the fluorescence spectra and the related equations at different temperatures under biological conditions. The binding constants (K_b) were calculated to be 0.8547 × 10³ M^?1 for HSA and 0.1363 × 10³ M^?1 for BSA at 298 K. Also, the number of binding sites (n) of the HSA/BSA–Tb–QUE systems was obtained to be approximately 1. Thermodynamic data calculations along with molecular docking results indicated that electrostatic interactions have a main role in the binding process of the Tb–QUE complex with HSA/BSA. Furthermore, molecular docking outputs revealed that the Tb–QUE complex has high affinity to bind to subdomain IIA of HSA and BSA. Binding distances (r) between HSA–Tb–QUE and BSA–Tb–QUE systems were also calculated using the Forster (fluorescence resonance energy transfer) method. It is expected that this study will provide a pathway for designing new compounds with multiple beneficial effects on human health from the phenolic compounds family such as the Tb–QUE complex.     

Copper(II) assisted hydrolysis of 2,4,6-tris(pyrazol-1-yl)-1,3,5-triazine. Crystal and molecular structure of catena-[CuL(H2O)Cl]n (L = 2,4-dione-1,3,5-(1H)-triazin-1-amido)

This article describes the partial hydrolysis of the multidentate ligand 2,4,6-tris(pyrazol-1-yl)-1,3,5-triazine in the presence of copper(II), to give the anionic ligand 2,4-dione-1,3,5-(1H)-triazin-1-amido, which was isolated as the cupric complex catena-[CuL(H₂O)Cl]_n, where L is the amido ligand. No other hydrolysis products were isolated or identified.The complex defines a zigzag 1D covalent chain, along the b cell axis, through apical copper-oxygen bonds (Cu-N-C-O···Cu bridges).     

pH- and DNA-induced dual molecular light switches based on a novel ruthenium(II) complex

A novel Ru(II) complex, [Ru(bpy)₂(btppz)]Cl₂, where bpy = 2,2′-bipyridine and btppz = benzo[h]tripyrido[3,2-a:2′,3′-c:2″,3″-j]phenazine, has been synthesized and characterized. The pH effects on UV-visible (UV-vis) absorption and emission spectra of the complex have been studied and ground- and excited-state ionization constants of the complex have been derived. The calf thymus DNA (ct-DNA) binding properties of the complex were investigated with UV-vis absorption and luminescence spectrophotometric titrations, steady-state emission quenching by [Fe(CN)₆]⁴⁻, DNA competitive binding with ethidium bromide, DNA melting experiments, reverse salt titrations and viscosity measurements. The complex was demonstrated to act as dual molecular switches: pH-induced “on-off” emission switch with an on-off intensity ratio of ∼54 which is favorably compared with those reported for structurally analogous Ru(II) complexes, and a DNA molecular light switch with a luminescence enhancement factor of 22 as it intercalatively bound to the DNA.     

Guidelines for model adaptation: A study of the transferability of a general seagrass ecosystem Dynamic Bayesian Networks model

In general, it is not feasible to collect enough empirical data to capture the entire range of processes that define a complex system, either intrinsically or when viewing the system from a different geographical or temporal perspective. In this context, an alternative approach is to consider model transferability, which is the act of translating a model built for one environment to another less well‐known situation. Model transferability and adaptability may be extremely beneficial—approaches that aid in the reuse and adaption of models, particularly for sites with limited data, would benefit from widespread model uptake. Besides the reduced effort required to develop a model, data collection can be simplified when transferring a model to a different application context. The research presented in this paper focused on a case study to identify and implement guidelines for model adaptation. Our study adapted a general Dynamic Bayesian Networks (DBN) of a seagrass ecosystem to a new location where nodes were similar, but the conditional probability tables varied. We focused on two species of seagrass (Zostera noltei and Zostera marina) located in Arcachon Bay, France. Expert knowledge was used to complement peer‐reviewed literature to identify which components needed adjustment including parameterization and quantification of the model and desired outcomes. We adopted both linguistic labels and scenario‐based elicitation to elicit from experts the conditional probabilities used to quantify the DBN. Following the proposed guidelines, the model structure of the general DBN was retained, but the conditional probability tables were adapted for nodes that characterized the growth dynamics in Zostera spp. population located in Arcachon Bay, as well as the seasonal variation on their reproduction. Particular attention was paid to the light variable as it is a crucial driver of growth and physiology for seagrasses. Our guidelines provide a way to adapt a general DBN to specific ecosystems to maximize model reuse and minimize re‐development effort. Especially important from a transferability perspective are guidelines for ecosystems with limited data, and how simulation and prior predictive approaches can be used in these contexts.