Fringe—A Java-based finite fringe analysis package

A package for analysing two-dimensional finite fringe interferograms is described. Through a combination of automatic and interactive routines, an interferogram can be processed to extract the phase shift imparted on the recording light by a transparent object. The package consists of routines to condition and pad the original image for Fourier transform analysis, to filter the image and obtain the phase, to unwrap the phase, and to remove the background phase ramp. A sample image recorded using holographic interferometry is successfully analysed.Program summaryProgram title: FRINGECatalogue identifier: AEMM_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEMM_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 134006No. of bytes in distributed program, including test data, etc.: 4029801Distribution format: tar.gzProgramming language: Java.Computer: Personal Computers.Operating system: Mac OS X, Windows XP, Linux and any other system that can run Java Jar files.RAM: 1GB recommendedClassification: 18.Nature of problem: A standalone multi-platform program to perform analysis of finite fringe interferograms.Solution method: Fourier filtering approach with phase unwrapping and background subtraction.Restrictions: Designed to analyse square images.Running time: Interactive processing takes several minutes. Minimal cpu time.     

Quantification of Mixtures of C2 and C3 Hydroxy Acids and Products of Glycerol Oxidation by High-Performance Liquid Chromatography and Quantitative 13C NMR

The aim of this study was to develop an improved general method for detecting and quantifying mixtures of hydroxy acids and other products of glycerol oxidation in aqueous media, to prevent the confusions that can occur due to similarities and interactions between these compounds depending on media conditions. Standard potential products of glycerol oxidation—glycerol, glyceraldehyde, dihydroxyacetone, glyceric acid, lactic acid, glycolic acid, glyoxylic acid, oxalic acid, tartronic acid, and mesoxalic acid—were analyzed by high-performance liquid chromatography (HPLC) and quantitative ¹³C nuclear magnetic resonance (NMR), in mixtures of known composition. The results obtained were concordant with the known compositions tested. HPLC was more accurate than quantitative ¹³C NMR for simple mixtures, but ¹³C NMR was required for complex mixtures containing dihydroxyacetone and glycerol, oxalic acid and mesoxalic acid, or glyoxylic acid and tartronic acid, pairs of compounds not well separated or detected by HPLC. As proof-of-concept, an unknown mixture generated by glycerol oxidation was analyzed by HPLC and quantitative ¹³C NMR. The results obtained were concordant and allowed accurate determination of the composition of the sample, which contained mesoxalic acid as the major product, with oxalic acid, tartronic acid, and glyceric acid as by-products.     

Discovery of Ubonodin,an Antimicrobial Lasso Peptide Active against Members of the Burkholderia cepacia Complex

We report the heterologous expression, structure, and antimicrobial activity of a lasso peptide, ubonodin, encoded in the genome of Burkholderia ubonensis. The topology of ubonodin is unprecedented amongst lasso peptides, with 18 of its 28 amino acids found in the mechanically bonded loop segment. Ubonodin inhibits RNA polymerase in vitro and has potent antimicrobial activity against several pathogenic members of the Burkholderia genus, most notably B. cepacia and B. multivorans, causative agents of lung infections in cystic fibrosis patients.     

Dichotomous feedback: a signal sequestration-based feedback mechanism for biocontroller design

We introduce a new design framework for implementing negative feedback regulation in synthetic biology, which we term ‘dichotomous feedback’. Our approach is different from current methods, in that it sequesters existing fluxes in the process to be controlled, and in this way takes advantage of the process’s architecture to design the control law. This signal sequestration mechanism appears in many natural biological systems and can potentially be easier to realize than ‘molecular sequestration’ and other comparison motifs that are nowadays common in biomolecular feedback control design. The loop is closed by linking the strength of signal sequestration to the process output. Our feedback regulation mechanism is motivated by two-component signalling systems, where a second response regulator could be competing with the natural response regulator thus sequestering kinase activity. Here, dichotomous feedback is established by increasing the concentration of the second response regulator as the level of the output of the natural process increases. Extensive analysis demonstrates how this type of feedback shapes the signal response, attenuates intrinsic noise while increasing robustness and reducing crosstalk.     

Oregano: chemical analysis and evaluation of its antimalarial, antioxidant, and cytotoxic activities

Abstract: GC‐FID and GC‐MS analysis of essential oil from oregano leaves (Origanum compactum) resulted in the identification of 46 compounds, representing more than 98% of the total composition. Carvacrol was the predominant compound (36.46%), followed by thymol (29.74%) and p‐cymene (24.31%). Serial extractions with petroleum ether, ethyl acetate, ethanol, and water were performed on aerials parts of Origanum compactum. In these extracts, different chemical families were characterized: polyphenols (gallic acid equivalent 21.2 to 858.3 g/kg), tannins (catechin equivalent 12.4 to 510.3 g/kg), anthocyanins (cyanidin equivalent 0.38 to 5.63 mg/kg), and flavonoids (quercetin equivalent 14.5 to 54.7 g/kg). The samples (essential oil and extracts) were subjected to a screening for antioxidant (DPPH and ABTS assays) and antimalarial activities and against human breast cancer cells. The essential oil showed a higher antioxidant activity with an IC₅₀= 2 ± 0.1 mg/L. Among the extracts, the aqueous extract had the highest antioxidant activity with an IC₅₀= 4.8 ± 0.2 mg/L (DPPH assay). Concerning antimalarial activity, Origanum compactum essential oil and ethyl acetate extract showed the best results with an IC₅₀ of 34 and 33 mg/mL, respectively. In addition, ethyl acetate extract (30 mg/L) and ethanol extract (56 mg/L) showed activity against human breast cancer cells (MCF7). The oregano essential oil was considered to be nontoxic.     

Influence of titania on zirconia promoted Cu/SiO2 catalysts for methanol synthesis from CO/H2 and CO2/H2

The effects of adding mixtures of titania and zirconia on the methanol synthesis activity and selectivity of Cu/SiO₂ were investigated. The synthesis of methanol from both CO/H₂ and CO₂/H₂ mixtures was examined at 0.65 MPa and temperatures between 448 and 573 K. For CO hydrogenation, the addition of ZrO₂ alone increased the methanol synthesis activity of Cu/SiO₂ by up to three-fold. Substitution of a portion of the ZrO₂ by TiO₂ decreased the methanol synthesis activity of the catalyst relative to that observed when only ZrO₂ is added. ZrO₂ addition also enhanced the methane synthesis activity by as much as seven fold. In the case of CO₂ hydrogenation, the maximum methanol synthesis activity is achieved when a 50/50 wt% mixture of ZrO₂ and TiO₂ is added to Cu/SiO₂. Neither the presence of the oxide additive nor its composition had any effect on the activity of the reverse water–gas-shift reaction, which suggests that this reaction proceeds only on Cu. The observed effects of ZrO₂ and TiO₂ on the catalytic activity of methanol synthesis from CO and CO₂, and methane synthesis from CO, are interpreted in terms of the strength and concentration of acidic and basic groups on the surface of the dispersed oxide.     

An in situ infrared study of NO reduction by C3H8 over Fe‐ZSM‐5

The interactions of NO, O₂ and NO₂ with Fe‐ZSM‐5, as well as the reduction of NO by C₃H₈ in the presence of O₂, have been investigated using in situ infrared spectroscopy. The sample of Fe‐ZSM‐5 (Fe/Al =0.56) was prepared by solid‐state ion exchange. NO adsorption in the absence of O₂ produces only mono‐ and dinitrosyl species associated with Fe²⁺ cations. Adsorbed NO₂/NO₃ species are formed via the reaction of adsorbed O₂ with gas‐phase NO or by the adsorption of gas‐phase NO₂. The reduction of NO in the presence of O₂ begins with the reaction of gas‐phase C₃H₈ with adsorbed NO₂/NO₃ species to form a nitrogen‐containing polymeric species. A reaction pathway is proposed for the catalyzed reduction of NO by C₃H₈ in the presence of O₂. This revised version was published online in July 2006 with corrections to the Cover Date.     

Replication-Deficient Lymphocytic Choriomeningitis Virus-Vectored Vaccine Candidate for the Induction of T Cell Immunity against Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) represents a major burden to global health, and refined vaccines are needed. Replication-deficient lymphocytic choriomeningitis virus (rLCMV)-based vaccine vectors against cytomegalovirus have proven safe for human use and elicited robust T cell responses in a large proportion of vaccine recipients. Here, we developed an rLCMV vaccine expressing the Mtb antigens TB10.4 and Ag85B. In mice, rLCMV elicited high frequencies of polyfunctional Mtb-specific CD8 and CD4 T cell responses. CD8 but not CD4 T cells were efficiently boosted upon vector re-vaccination. High-frequency responses were also observed in neonatally vaccinated mice, and co-administration of rLCMV with Expanded Program of Immunization (EPI) vaccines did not result in substantial reciprocal interference. Importantly, rLCMV immunization significantly reduced the lung Mtb burden upon aerosol challenge, resulting in improved lung ventilation. Protection was associated with increased CD8 T cell recruitment but reduced CD4 T cell infiltration upon Mtb challenge. When combining rLCMV with BCG vaccination in a heterologous prime-boost regimen, responses to the rLCMV-encoded Mtb antigens were further augmented, but protection was not significantly different from rLCMV or BCG vaccination alone. This work suggests that rLCMV may show utility for neonatal and/or adult vaccination efforts against pulmonary tuberculosis.     

Performance of solar driven methanol–water combined ejector–absorption cycle in the Athens area

The performance of a solar driven CH₄O-H₂O combined ejector– absorption unit, operating in conjunction with intermediate temperature solar collectors in Athens, is predicted along the five months (May–September) in case of the unit working as heat pump in an industrial area. The operation of the unit and the related thermodynamics are simulated by suitable computer codes and the required local climatological data are determined by statistical processings over a considerable number of years. It is found that the heat gain factor varies in the range from 2.1330 to 2.4481 for the above period of time. The maximum HGF of about 2.4481 is obtained in July at 14.25 hrs with corresponding specific heat gain power 915 W/m². The maximum Q_gain of about 1086 W/m² is obtained in June at 12.54 hrs with corresponding HGF 2.3572. Also the maximum value of HGF was estimated by correlation of three temperatures: generator temperature (85.0°C–97.2°C), condenser temperature (43.3°C–47.6°C) and evaporator temperature (12.6°C–25.4°C).     

Synthesis of Brightly PEGylated Luminescent Magnetic Upconversion Nanophosphors for Deep Tissue and Dual MRI Imaging

A method is developed to fabricate monodispersed biocompatible Yb/Er or Yb/Tm doped β‐NaGdF₄ upconversion phosphors using polyelectrolytes to prevent irreversible particle aggregation during conversion of the precursor, Gd₂O(CO₃)₂?H₂O:Yb/Er or Yb/Tm, to β‐NaGdF₄:Yb/Er or Yb/Tm. The polyelectrolyte on the outer surface of nanophosphors also provided an amine tag for PEGylation. This method is also employed to fabricate PEGylated magnetic upconversion phosphors with Fe₃O₄ as the core and β‐NaGdF₄ as a shell. These magnetic upconversion nanophosphors have relatively high saturation magnetization (7.0 emu g^?1) and magnetic susceptibility (1.7 × 10^?2 emu g^?1 Oe^?1), providing them with large magnetophoretic mobilities. The magnetic properties for separation and controlled release in flow, their optical properties for cell labeling, deep tissue imaging, and their T₁‐ and T₂‐weighted magnetic resonance imaging (MRI) relaxivities are studied. The magnetic upconversion phosphors display both strong magnetophoresis, dual MRI imaging (r₁ = 2.9 mM^?1 s^?1, r₂ = 204 mM^?1 s^?1), and bright luminescence under 1 cm chicken breast tissue.