Exploratory analysis of excitation-emission matrix fluorescence spectra with self-organizing maps—A tutorial

Large datasets are common in chemical and environmental engineering applications and tools for their analysis are in great demand. Here, the outputs of a series of fluorescence spectroscopy analyses are utilised to demonstrate the application of the self-organising map (SOM) technique for data analysis. Fluorescence spectroscopy is a well-established technique of organic matter fingerprinting in water. The technique can provide detailed information on the physico-chemical properties of water. However, analysis of fluorescence spectra requires the application of robust statistical and computational data pre-processing and analysis tools.This paper presents a tutorial for training engineering postgraduate researchers in the use of SOM techniques using MATLAB^®. Via a tutorial, the application of SOM to fluorescence spectra and, in particular, the characterisation of organic matter removal in water treatment, is presented. The tutorial presents a step-by-step example of the application of SOM to fluorescence data analysis and includes the source code for MATLAB^®, together with presentation and discussion of the results. With this tutorial we hope to popularise this robust pattern recognition technique for fluorescence data analysis and large data sets in general, and also to provide educational practitioners with a novel tool with which to train engineering students in SOM.     

Bright two-photon emission and ultra-fast relaxation dynamics in a DNA-templated nanocluster investigated by ultra-fast spectroscopy

Metal nanoclusters have interesting steady state fluorescence emission, two-photon excited emission and ultrafast dynamics. A new subclass of fluorescent silver nanoclusters (Ag NCs) are NanoCluster Beacons. NanoCluster Beacons consist of a weakly emissive Ag NC templated on a single stranded DNA ("Ag NC on ssDNA") that becomes highly fluorescent when a DNA enhancer sequence is brought in proximity to the Ag NC by DNA base pairing ("Ag NC on dsDNA"). Steady state fluorescence was observed at 540 nm for both Ag NC on ssDNA and dsDNA; emission at 650 nm is observed for Ag NC on dsDNA. The emission at 550 nm is eight times weaker than that at 650 nm. Fluorescence up-conversion was used to study the dynamics of the emission. Bi-exponential fluorescence decay was recorded at 550 nm with lifetimes of 1 ps and 17 ps. The emission at 650 nm was not observed at the time scale investigated but has been reported to have a lifetime of 3.48 ns. Two-photon excited fluorescence was detected for Ag NC on dsDNA at 630 nm when excited at 800 nm. The two-photon absorption cross-section was calculated to be ～3000 GM. Femtosecond transient absorption experiments were performed to investigate the excited state dynamics of DNA-Ag NC. An excited state unique to Ag NC on dsDNA was identified at ～580 nm as an excited state bleach that related directly to the emission at 650 nm based on the excitation spectrum. Based on the optical results, a simple four level system is used to describe the emission mechanism for Ag NC on dsDNA.     

Survey of acceptor dopants in SrTiO3: Factors limiting room temperature hole concentration

Unintentional impurities often found in strontium titanate (doped or undoped) have hindered efforts to study individual impurities experimentally. To fill this gap, a computational survey of acceptor-type point defects of common intentional or unintentional impurities (Al, Cu, Fe, K, Mg, Mn, N, Na, Ni, and Zn) is presented. Utilizing defect formation energies from density functional theory using hybrid exchange correlation functionals in a grand canonical model of the defect chemistry, the equilibrium Fermi level (μ_e) was calculated as a function of processing conditions for pure SrTiO₃, SrTiO₃ individually doped with each impurity, and SrTiO₃ co-doped with Al and N. Above a certain concentration, each impurity reduced the maximum predicted hole concentration relative to the intrinsic case. Al, Mg, Zn, K, and Na exhibited similar trends and behaved more like ideal acceptors while N, Ni, Fe, Mn, and Cu were all unique and pinned μ_e near or above the mid-gap in most conditions. Al/N:SrTiO₃ also exhibited similar trends at 800°C for all Al/N ratios, but more variation at 25°C. Additionally, the behavior of Al:SrTiO₃ was not recovered until Al/N = 10⁴. This suggests that to achieve SrTiO₃ with free holes at room temperature, the concentration of most impurities must be controlled.     

Mechanical and thermal properties of poly(ethylene terephthalate) fibers crosslinked with disulfonyl azides

A novel method for the crosslinking of poly(ethylene terephthalate) fibers is described using 1,6‐hexanedisulfonyl azide, 1,3‐benzenedisulfonyl azide, and 2,6‐naphthalenedisulfonyl azide. The azides are diffused into poly(ethylene terephthalate) fibers (Dacron) from perchloroethylene solution, and the fibers are heat treated to bring about decomposition of the sulfonyl azide and give rise to crosslinking. A study is made of the mechanical and thermal properties of the resultant fibers, which are changed considerably in comparison to the untreated fiber. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 83: 1517–1527, 2002     

Behavioral and electrophysiological activity of (Z,E)-7,9,11-dodecatrienyl formate,a mimic of the major sex pheromone component of carob moth,Ectomyelois ceratoniae

The behavioral and electrophysiological activity of a mimic [(Z,E)7,9,11-dodecatrienyl formate] of the major sex pheromone component [(Z,E) 9,11,13-tetradecatrienal] of carob moth was assessed. Wind-tunnel bioassays demonstrated that the formate was as effective as natural gland extracts, and significantly more effective than the trienal alone or than the trienal blended with two minor pheromone components, in evoking source contact. Dispensers containing the formate were as effective as trienal-containing blend lures in attracting males when placed at the same dosage in traps in date gardens. Single-cell recordings showed that at least two olfactory neurons, differentiated by spike amplitude, are located in the long trichoid hairs on male carob moth antennae. Dose-response relationships indicated that puffs from cartridges loaded with at least 0.1 g of the formate or of the trienal were necessary to elicit spiking by either the small or the large-spiking cell within a sensillum. Cross-adaptation studies demonstrated that both compounds stimulated the same large-spiking cell. The frequencies of spikes evoked from the large cell when stimulated by emissions from 0.1-g, 1-g, or 10-g cartridges of either the formate or the trienal were not significantly different, suggesting that the formate is an effective mimic of the trienal at the antennal receptor cell level.     

Identification of odors from overripe mango that attract vinegar flies,Drosophila melanogaster

Bioassays with a variety of overripe fruits, including mango, plum, pear, and grape, and their extracts showed that odors from overripe mango were most attractive to adult vinegar flies, Drosophila melanogaster. Combined gas chromatography–electroantennographic detection (GC-EAD) analyses of solid-phase microextraction (SPME) and Tenax extracts of overripe mango odors showed that several volatile compounds, including ethanol, acetic acid, amyl acetate, 2-phenylethanol, and phenylethyl acetate elicited significant EAG responses from antennae of female flies. Most of the volatile compounds in the extracts were identified by mass spectral and retention index comparisons with synthetic standards. In cage bioassays, lures with a blend of ethanol, acetic acid, and 2-phenylethanol in a ratio of 1:22:5 attracted six times more flies than any single EAG-active compound. This blend also attracted four times more flies than traps baited with overripe mango or unripe mango. However, in field trials, the blend was not as attractive as suggested by the laboratory bioassay.     

A study of the large strain deformation and failure behaviour of mixed biopolymer gels via in situ ESEM

A mixed biopolymer gel, consisting of a protein (gelatin) and polysaccharide (maltodextrin) mixture has been investigated. By controlling the composition it was possible to construct an ‘emulsion-like’ structure, with included spherical particles of one phase (maltodextrin) within a continuous matrix of the second (gelatin). Large strain deformation and failure behaviour of this system has been examined via in situ environmental scanning electron microscopy (ESEM). ESEM has been employed to explore the changes in the structure of the material, whilst allowing the sample to stay hydrated as it was subjected to tensile strain, thereby allowing simultaneous imaging and determination of stress-strain data of the native sample. Ductile behaviour was observed, which has been attributed to the stretching, tearing and fracture of gelatin ligaments and debonding at the interface between the maltodextrin particles and continuous gelatin matrix. Deformation and fracture of the maltodextrin particles during tensile testing was also observed. The interfacial fracture energy of the composite has been calculated following an elastomer composite-debonding model, although there are several limitations to this approach for the mixed gel. It was found in samples tested after different ageing times that the debonding stress and strain was decreasing with ageing leading to a lower interfacial fracture energy. Samples were also tested after successive loading cycles, which resulted in a mechanical strength decrease after each cycle.     

Lycopene from two food sources does not affect antioxidant or cholesterol status of middle-aged adults

Background

Epidemiological studies have reported associations between reduced cardiovascular disease and diets rich in tomato and/or lycopene. Intervention studies have shown that lycopene-containing foods may reduce cholesterol levels and lipid peroxidation, factors implicated in the initiation of cardiovascular disease. The objective of this study was to determine whether consumption of lycopene rich foods conferred cardiovascular protection to middle-aged adults as indicated by plasma lipid concentrations and measures of ex vivo antioxidants.

Methods

Ten healthy men and women consumed a low lycopene diet with no added lycopene (control treatment) or supplemented with watermelon or tomato juice each containing 20 mg lycopene. Subjects consumed each treatment for three weeks in a crossover design. Plasma, collected weekly was analyzed for total cholesterol, high density lipoprotein cholesterol (HDL-C) and triglyceride concentrations and for the antioxidant biomarkers of malondialdehyde formation products (MDA), plasma glutathione peroxidase (GPX) and ferric reducing ability of plasma (FRAP). Data were analyzed using Proc Mixed Procedure and associations between antioxidant and lipid measures were identified by Pearson's product moment correlation analysis.

Results

Compared to the control diet, the lycopene-containing foods did not affect plasma lipid concentrations or antioxidant biomarkers. Women had higher total cholesterol, HDL-C and triglyceride concentrations than did the men. Total cholesterol was positively correlated to MDA and FRAP while HDL-C was positively correlated to MDA and GPX. GPX was negatively correlated to triglyceride concentration.

Conclusions

The inclusion of watermelon or tomato juice containing 20 mg lycopene did not affect plasma lipid concentrations or antioxidant status of healthy subjects. However, plasma cholesterol levels impacted the results of MDA and FRAP antioxidant tests.     

Mass Spectrometry-Based Proteomics for Pre-Eclampsia and Preterm Birth

Pregnancy-related complications such as pre-eclampsia and preterm birth now represent a notable burden of adverse health. Pre-eclampsia is a hypertensive disorder unique to pregnancy. It is an important cause of maternal death worldwide and a leading cause of fetal growth restriction and iatrogenic prematurity. Fifteen million infants are born preterm each year globally, but more than one million of those do not survive their first month of life. Currently there are no predictive tests available for diagnosis of these pregnancy-related complications and the biological mechanisms of the diseases have not been fully elucidated. Mass spectrometry-based proteomics have all the necessary attributes to provide the needed breakthrough in understanding the pathophysiology of complex human diseases thorough the discovery of biomarkers. The mass spectrometry methodologies employed in the studies for pregnancy-related complications are evaluated in this article. Top-down proteomic and peptidomic profiling by laser mass spectrometry, liquid chromatography or capillary electrophoresis coupled to mass spectrometry, and bottom-up quantitative proteomics and targeted proteomics by liquid chromatography mass spectrometry have been applied to elucidate protein biomarkers and biological mechanism of pregnancy-related complications. The proteomes of serum, urine, amniotic fluid, cervical-vaginal fluid, placental tissue, and cytotrophoblastic cells have all been investigated. Numerous biomarkers or biomarker candidates that could distinguish complicated pregnancies from healthy controls have been proposed. Nevertheless, questions as to the clinically utility and the capacity to elucidate the pathogenesis of the pre-eclampsia and preterm birth remain to be answered.