Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements

It has been shown that the activity of the hammerhead ribozyme at microM magnesium ion concentrations is markedly increased by the inclusion of loops in helices I and II. We have studied the effect of such loops on the magnesium ion-induced folding of the ribozyme, using fluorescence resonance energy transfer. We find that with the loops in place, folding into the active conformation occurs in a single step, in the microM range of magnesium ion concentration. Disruption of the loop-loop interaction leads to a reversion to two-step folding, with the second stage requiring mM concentrations of magnesium ion. Sodium ions also promote the folding of the natural form of the ribozyme at high concentrations, but the folding occurs as a two-stage process. The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions.     

Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures

Tertiary stabilizing motifs (TSMs) between terminal loops or internal bulges facilitate folding of natural hammerhead ribozymes (hRz) under physiological conditions. However, both substrate and enzyme strands contribute nucleotides to the TSMs of trans-cleaving hRz, complicating the design of hRz that exploit TSMs to target specific mRNA. To overcome this limitation, we used SELEX to identify new, artificial TSMs that are less sensitive to sequence context. Nucleotides in loop II or in a bulge within the ribozyme strand of stem I were randomized, while the interaction partner was held constant. All nucleotides of the substrate pair with the ribozyme, minimizing their possible recruitment into the TSM, as such recruitment could constrain choice of candidate target sequences. Six cycles of selection identified cis-acting ribozymes that were active in 100 microM MgCl2. The selected motifs partially recapitulate TSMs found in natural hRz, suggesting that the natural motifs are close to optimal for their respective contexts. Ribozyme "RzB" showed enhanced thermal stability by retaining trans-cleavage activity at 80 degrees C in 10 mM MgCl2 and at 70 degrees C in 2 mM MgCl2. A variant of ribozyme "RzB" with a continuously paired stem 1 rapidly lost activity as temperature was increased. The selected motifs are modular, in that they permit trans-cleavage of several substrates in submillimolar MgCl2, including two substrates derived from the U5 genomic region of HIV-1. The new, artificial tertiary stabilized hRz are thus nearly independent of sequence context and enable for the first time the use of highly active hRz targeting almost any mRNA at physiologically relevant magnesium concentrations.     

Functional Coupling of ATP-binding Cassette Transporter Abcb6 to Cytochrome P450 Expression and Activity in Liver

Although endogenous mechanisms that negatively regulate cytochrome P450 (P450) monooxygenases in response to physiological and pathophysiological signals are not well understood, they are thought to result from alterations in the level of endogenous metabolites, involved in maintaining homeostasis. Here we show that homeostatic changes in hepatic metabolite profile in Abcb6 (mitochondrial ATP-binding cassette transporter B6) deficiency results in suppression of a specific subset of hepatic P450 activity. Abcb6 null mice are more susceptible to pentobarbital-induced sleep and zoxazolamine-induced paralysis, secondary to decreased expression and activity of Cyp3a11 and Cyp2b10. The knock-out mice also show decrease in both basal and xeno-inducible expression and activity of a subset of hepatic P450s that appear to be related to changes in hepatic metabolite profile. These data, together with the observation that liver extracts from Abcb6-deficient mice suppress P450 expression in human primary hepatocytes, suggest that this mouse model may provide an opportunity to understand the physiological signals and the mechanisms involved in negative regulation of P450s.     

Mining of genomic databases to identify novel biodesulfurizing microorganisms

The commercialization of the biocatalytic desulfurization process does not seem to be realistic in the near future because of the low desulfurization rate of the known microorganisms. Hence, the future development will depend on either genetically modifying the currently available bacteria or identifying novel biodesulfurizers. In this study an in silico method to identify new biodesulfurizing microorganisms was adopted. By screening the available genomic databases, 13 novel desulfurizing microorganisms belonging to 12 genera were identified. Several of these could be of immense utility as they have both environment pollutant and industrial waste degrading capability.     

Non-Smad transforming growth factor-β signaling regulated by focal adhesion kinase binding the p85 subunit of phosphatidylinositol 3-kinase

TGF-β modulates numerous diverse cellular phenotypes including growth arrest in epithelial cells and proliferation in fibroblasts. Although the Smad pathway is fundamental for the majority of these responses, recent evidence indicates that non-Smad pathways may also have a critical role. Here we report a novel mechanism whereby the nonreceptor tyrosine focal adhesion kinase (FAK) functions as an adaptor necessary for cell type-specific responses to TGF-β. We show that in contrast to Smad actions, non-Smad pathways, including c-Abl, PAK2, and Akt, display an obligate requirement for FAK. Interestingly, this occurs in Src null SYF cells and is independent of FAK tyrosine phosphorylation, kinase activity, and/or proline-rich sequences in the C-terminal FAT domain. FAK binds the phosphatidylinositol 3-kinase (PI3K) p85 regulatory subunit following TGF-β treatment in a subset of fibroblasts but not epithelial cells and has an obligate role in TGF-β-stimulated anchorage-independent growth and migration. Together, these results uncover a new scaffolding role for FAK as the most upstream component regulating the profibrogenic action of TGF-β and suggest that inhibiting this interaction may be useful in treating a number of fibrotic diseases.     

Flubendiamide affects visual and locomotory activities of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> for three successive generations (P,F<Subscript>1</Subscript> and F<Subscript>2</Subscript>)

Flubendiamide is widely used in agricultural fields to exterminate a broad spectrum of pests (lepidopteran insects) by disrupting their muscle function. The main objective of this study was to find the effects of flubendiamide on a non-target organism, Drosophila melanogaster (dipteran insect). In the present study, different sub-lethal concentrations of Flubendiamide caused a significant (P?<?0.05) decrease in acetylcholinesterase activity and increase in cytochrome P450 activity in adult D. melanogaster. Phototaxis and climbing behaviours were found to significantly (P?<?0.05) alter in exposed flies. The observed alteration in phototaxis and climbing behaviours were not restricted to P generation, but were found to be transmitted to subsequent generations (F₁ and F₂ generation) that had never been directly exposed to the test chemical during their life time. It is only their predecessors (P generation) who have been affronted with different concentrations of Flubendiamide. Humans and Drosophilids share almost 60% genomic similarity and 75% disease gene resemblance. Moreover, most of the circuits governing the behaviours studied involve the inhibition and excitation of neurotransmitters, which are conserved in humans and flies. Thus, the present findings suggest that chronic flubendiamide exposure might induce alteration in neurotransmission leading to discrepancy in the behavioural responses (vision and flight) in other beneficial insects and insect-dependent organisms.     

Photoluminescence and electron paramagnetic resonance properties of a potential phototherapic agent: MMgF4:Gd3+ (M = Ba,Sr) sub‐microphosphors

Novel narrow band UVB‐emitting phosphors, BaMgF₄:Gd³⁺ and SrMgF₄:Gd³⁺ phosphors, were synthesized using a co‐precipitation synthesis method. X‐Ray diffraction analysis was carried out to confirm compound formation, phase purity and crystallinity of the phosphor. At 274 nm excitation, phosphors show a sharp narrow band emission at 313 nm that can be assigned to ⁶P_7/2 → ⁸S_7/2 transition of the Gd³⁺ ion. With increasing dopant concentration, intensity enhances and then decreases after a certain concentration, which is an indication of concentration quenching taking place in the phosphor. Scanning electron microscopy images of the phosphor show agglomerated particles in the sub‐micron range. Particles range in size from 600 to 800 nm. Electron paramagnetic resonance studies of the phosphors were carried out to detect radicals present in the prepared phosphor. With narrow band UVB emission, phosphor seems to be a good candidate for UV phototherapy application. Copyright © 2016 John Wiley & Sons, Ltd.