DNA detection and signal amplification via an engineered allosteric enzyme

Rapid, sensitive, and sequence-specific DNA detection can be achieved in one step using an engineered intrasterically regulated enzyme. The semi-synthetic inhibitor-DNA-enzyme (IDE) construct (left) rests in the inactive state but upon exposure to a complementary DNA sequence undergoes a DNA hybridization-triggered allosteric enzyme activation (right). The ensuing rapid substrate turnover provides the built-in signal amplification mechanism for detecting approximately 10 fmol DNA in less than 3 min under physiological conditions.     

Characterisation of flowability of cohesive powders by testing small quantities of weak compacts

Characterisation of flowability of small quantifies of cohesive powders is of great industrial interest, particularly for the pharmaceutical sec tors, where a limited amount of material is available or the material is not easily accessible. In this paper, ball indentation on a powder bed is evaluated for flow charaeterisation of small quantifies of cohesive powders at low levels of consolidation pressures. In parallel, the bulk powder is subjected to the common test method of unconfined direct compression. Analogous to indentation hardness testing, for which the indentation pressure is related to the flow stress, a constraint factor (C) is defined relating the unconfined yield stress and indentation pres sure. The constraint factors for the test powders have been evaluated, enabling an easy method to characterize the flow behaviour of cohesive powders.     

Self-assembling peptide nanotubes with antiviral activity against hepatitis C virus

Hepatitis C virus (HCV) infects chronically 3% of the world population and the current therapy against this pathogen is only partially effective. With the aim of developing novel antiviral strategies against HCV, we screened a D,L-α-peptide library using an?unbiased methodology based on a cell culture infection system for HCV. We found a family of highly?active amphiphilic eight-residue cyclic D,L-α-peptides that specifically blocked entry of all tested HCV genotypes into target cells at a postbinding step without affecting infection by other enveloped RNA viruses. Structure-activity relationship studies indicate that antiviral activity was dependent on cyclic D,L-α-peptide self-assembly processes and that, although they possess a net neutral charge,?they display a characteristic charge distribution. Our results indicate that supramolecular amphiphilic peptide structures constitute a class of highly selective HCV entry inhibitors.     

Nano ZSM-5 type ferrisilicates as novel catalysts for ethylbenzene dehydrogenation in the presence of N2O

Nanosized ZSM-5 type ferrisilicates were successfully prepared using hydrothermal process. Several parameters including gel initiative compositions (Na⁺ or K⁺ alkali system), SiO₂/Fe₂O₃ molar ratios and hydrothermal temperature were systematically investigated. The samples were characterized by XRD, TEM, SEM-EDS, BET surface area and ICP techniques. It was found that surface areas and the total pore volume increase with increasing in the SiO₂/Fe₂O₃ molar ratio at Na-FZ ferrisilicates. The catalytic performance of the synthesized catalysts was evaluated in ethylbenzene dehydrogenation to styrene in the presence of N₂O or steam at temperatures ranging from 400 °C to 660 °C under atmospheric pressure. The effects of gel initiative compositions, SiO₂/Fe₂O₃ molar ratio as well as the hydrothermal synthesis temperature on the catalytic performance of these catalysts have been addressed. It was shown that styrene yield significantly influenced by altering in the SiO₂/Fe₂O₃ ratio but was not greatly influenced by changes in hydrothermal synthesis temperatures. The comparison between performance of potassium and sodium containing catalysts was shown that the one with potassium has higher yield and selectivity toward styrene production at an optimum temperature of 610 °C.     

A highly membrane-active peptide in Flock House virus: implications for the mechanism of nodavirus infection.

BACKGROUND: Nodaviruses are among the simplest animal viruses, and are therefore attractive systems for deconvoluting core viral processes such as assembly, infection and uncoating. Membrane translocation of the single-stranded RNA genome of nodaviruses has been proposed to be mediated by direct lipid-protein interactions between a post-assembly autocatalytic cleavage product from the capsomere and the target membrane. To probe the validity of this hypothesis, we have synthesized a 21-residue Met-->Nle (norleucine) variant of the amino-terminal helical domain (denoted here as gamma1) of the cleavage peptide in Flock House nodavirus (FHV) and studied its ability to alter membrane structure and function. RESULTS: The synthetic peptide gamma1 increases membrane permeability to hydrophilic solutes, as judged by fluorescence experiments with liposome-encapsulated dyes and ion-conductance measurements. Furthermore, peptide orientation and location within lipid bilayers was determined using tryptophan-fluorescence-quenching experiments and attenuated total reflectance infrared spectroscopy. CONCLUSIONS: The helical domain of the FHV cleavage product partitions spontaneously into lipid bilayers and increases membrane permeability, consistent with the postulated mechanism for viral genome translocation. The existence of a membrane-binding domain in the FHV cleavage sequence suggests peptide-triggered disruption of the endosomal membrane as a prelude to viral uncoating in the host cytoplasm. A model for this interaction is proposed.     

A new approach to variable selection in least squares problems

The title Lasso has been suggested by Tibshirani (1996) as acolourful name for a technique of variable selection which requiresthe minimization of a sum of squares subject to an l₁ bound on the solution. This forces zero components in the minimizingsolution for small values of . Thus this bound can functionas a selection parameter. This paper makes two contributionsto computational problems associated with implementing the Lasso:(1) a compact descent method for solving the constrained problemfor a particular value of is formulated, and (2) a homotopymethod, in which the constraint bound becomes the homotopyparameter, is developed to completely describe the possibleselection regimes. Both algorithms have a finite terminationproperty. It is suggested that modified Gram-Schmidt orthogonalizationapplied to an augmented design matrix provides an effectivebasis for implementing the algorithms.     

Modular multi-level circuits from immobilized DNA-based logic gates

One of the fundamental goals of molecular computing is to reproduce the tenets of digital logic, such as component modularity and hierarchical circuit design. An important step toward this goal is the creation of molecular logic gates that can be rationally wired into multi-level circuits. Here we report the design and functional characterization of a complete set of modular DNA-based Boolean logic gates (AND, OR, and AND-NOT) and further demonstrate their wiring into a three-level circuit that exhibits Boolean XOR (exclusive OR) function. The approach is based on solid-supported DNA logic gates that are designed to operate with single-stranded DNA inputs and outputs. Since the solution-phase serves as the communication medium between gates, circuit wiring can be achieved by designating the DNA output of one gate as the input to another. Solid-supported logic gates provide enhanced gate modularity versus solution-phase systems by significantly simplifying the task of choosing appropriate DNA input and output sequences used in the construction of multi-level circuits. The molecular logic gates and circuits reported here were characterized by coupling DNA outputs to a single-input REPORT gate and monitoring the resulting fluorescent output signals.     

A combinatorial approach to the discovery of biocidal six-residue cyclic D,L-alpha-peptides against the bacteria methicillin-resistant Staphylococcus aureus (MRSA) and E. coli and the biofouling algae Ulva linza and Navicula perminuta

A combinatorial approach has been used to rapidly identify cyclic d,l-alpha-peptide hexamer sequences that exert biocidal activity towards both methicillin-resistant Staphylococcus aureus (MRSA) and E. coli bacteria, as well as the marine algae Ulva linza and Navicula perminuta. Evaluation of the effects against marine algae was facilitated by the development of a reliable, automated assay for toxicity, which should be of general utility for biofouling investigations. While the selective toxicity of cyclic D,L-alpha-peptides towards bacteria has been proven to be highly sensitive to minor changes in amino acid composition, this study demonstrates that this phenomenon extends to eukaryotic species as well, despite their significant structural differences. In performing toxicity assays on both prokaryotic and eukaryotic organisms in parallel, we have discovered examples of six-residue cyclic D,L-alpha-peptide sequences with either broad-spectrum or highly selective biocidal activities. Sequence [KWFFFH] (underlined amino acid abbreviations represent D-amino acid residues) was found to display 100-fold selectivity towards U. linza, demonstrating that the approach described herein may help lead to the development of new biofouling tools which are not generally toxic to all organisms, but rather specifically target microbial agents of interest.