Depth profiling of calcifications in breast tissue using picosecond Kerr-gated Raman spectroscopy

Breast calcifications are found in both benign and malignant lesions and their composition can indicate the disease state. Calcium oxalate (dihydrate) (COD) is associated with benign lesions, however calcium hydroxyapatite (HAP) is found mainly in proliferative lesions including carcinoma. The diagnostic practices of mammography and histopathology examine the morphology of the specimen. They can not reliably distinguish between the two types of calcification, which may indicate the presence of a cancerous lesion during mammography. We demonstrate for the first time that Kerr-gated Raman spectroscopy is capable of non-destructive probing of sufficient biochemical information from calcifications buried within tissue, and this information can potentially be used as a first step in identifying the type of lesion. The method uses a picosecond pulsed laser combined with fast temporal gating of Raman scattered light to enable spectra to be collected from a specific depth within scattering media by collecting signals emerging from the sample at a given time delay following the laser pulse. Spectra characteristic of both HAP and COD were obtained at depths of up to 0.96 mm, in both chicken breast and fatty tissue; and normal and cancerous human breast by utilising different time delays. This presents great potential for the use of Raman spectroscopy as an adjunct to mammography in the early diagnosis of breast cancer.     

Stochastic pairwise alignments and scoring methods for comparative protein structure modeling

Despite recent advances in fold recognition algorithms that identify template structures with distant homology to the target sequence, the quality of the target-template alignment can be a major problem for distantly related proteins in comparative modeling. Here we report for the first time on the use of ensembles of pairwise alignments obtained by stochastic backtracking as a means to improve three-dimensional comparative protein models. In every one of the 35 cases, the ensemble produced by the program probA resulted in alignments that were closer to the structural alignment than those obtained from the optimal alignment. In addition, we examined the lowest energy structure among these ensembles from four different structural assessment methods and compared these with the optimal and structural alignment model. The structural assessment methods consisted of the DFIRE, DOPE, and ProsaII statistical potential energies and the potential energy from the CHARMM protein force field coupled to a Generalized Born implicit solvent model. The results demonstrate that the generation of alignment ensembles through stochastic backtracking using probA combined with one of the statistical potentials for assessing three-dimensional structures can be used to improve comparative models.     

Label-free voltammetric detection of single-nucleotide mismatches recognized by the protein MutS

MutS, a protein involved in DNA mismatch repair, recognizes mispaired and unpaired bases in duplex DNA. We have previously used MutS in an electrochemical double-surface technique (DST) for in-vitro detection of point mutations in DNA. The DST involved binding of unlabeled MutS to DNA heteroduplexes at the surface of magnetic beads followed by a highly sensitive electrochemical determination of the protein by measurement of a catalytic protein signal (peak H) at mercury electrodes. Detection of MutS using a peak resulting from oxidation of tyrosine and tryptophan residues of the protein at a carbon-paste electrode (CPE) was also possible but was approximately three orders of magnitude less sensitive. In this work we present an optimized technique for ex-situ voltammetric determination of MutS at a CPE. Choice of optimum experimental conditions (pH of supporting electrolyte, square-wave voltammetry settings, etc.) resulted in substantial improvement of the sensitivity of the assay, enabling detection of approximately 140 pg (1.6 fmol protein monomer) MutS in a 5-μL sample. The sensitivity was increased further by acid hydrolysis of the protein before measurement. The hydrolyzed protein was detectable down to 5 pg (approx. 56 amol) MutS in 5 μL solution. By using the DST combined with determination of the bound unlabeled MutS at the CPE we demonstrated selective interactions of the protein with single-base mismatches and discrimination among different base mispairs in 30-mer or 95-mer DNA duplexes. In agreement with previous studies, binding of the protein to the 30-mer substrates followed the trend G:T>>C:A>A:A>C:T>homoduplex. The electrochemical data were confirmed by use of an independent technique—a quartz-crystal microbalance for real-time monitoring of MutS interactions with DNA duplexes containing different base mispairs. By using the electrochemical DST a G:T mismatch was detectable in up to 1000-fold excess of homoduplex DNA.     

Virtual Gires-Tournois etalons realized with phase-modulated wideband chirped fiber gratings

We propose and demonstrate novel virtual Gires-Tournois (GT) etalons based on fiber gratings. By introducing an additional phase modulation in wideband linearly chirped fiber Bragg gratings, we have successfully generated GT resonance with only one grating. This technique can simplify the fabrication procedure while retaining the normal advantages of distributed etalons, including their full compatibility with optical fiber, low insertion loss, and low cost. Such etalons can be used as dispersion compensation devices in optical transmission systems.     

Synthesis and study of mixed oxide inorganic pigment from Bi<Subscript>2</Subscript>O<Subscript>3</Subscript>–ZnO–CeO<Subscript>2</Subscript> system

Novel environment-friendly yellow mixed oxide inorganic pigment from Bi₂O₃–ZnO–CeO₂ system with the composition 23 mol% Bi₂O₃, 15 mol% ZnO and 62 mol% CeO₂ was successfully synthesized by a conventional solid-state reaction method. Comprehensive analyses were carried out to characterize the develop pigment powder including simultaneous TG–DTA thermal analysis, colour properties and particle size distribution. The results demonstrated that the optimum calcination for pigment synthesis was located at a range 800–950 °C. The colour of the studied mixed oxide pigment is connected with the calcination condition. The substitution of Zn²⁺ changes the colour from orange to yellow. The colour of the obtained samples was dependent on the calcination condition and the particle size distribution. The most saturated yellow hue was obtained at the calcination temperature of 950 °C for 2 h in a furnace of pure air and after its application into organic binder in mass tone. The value C of this sample was approx. 65. The mixed oxide pigments were also evaluated from the standpoint of their particle size distribution. Bi₂Ce₂O₇ is considered to be a non-toxic compound, and the other component (Zn²⁺ ions) is also the safe element. Therefore, the present mixed oxide could be an attractive candidate as a novel environment-friendly inorganic yellow pigment.     

Comparison of selected aroma compounds in cultivars of sea buckthorn (<Emphasis Type="Italic">Hippophae rhamnoides</Emphasis> L.)

Thirteen cultivars of sea buckthorn (Hippophae rhamnoides L.) berries: Aromat, Botanicky, Buchlovicky, Hergo, Krasavica, Leicora, Ljubitelna, Pavlovsky, Peterbursky, Sluni?ko, Trofinovsky, Vitaminnaja and Velkoosecky, were tested for the content of volatile aroma compounds using gas chromatography with the solid phase microextraction method during two consequent years (2012–2013). In total, 69 volatile compounds were identified: 26 alcohols, 12 aldehydes, 11 ketones, 9 acids and 11 esters. Based on principal component analysis, 18 most relevant compounds, best representing the variability of the whole system and suitable for the discrimination of the samples, were selected from all compounds identified. These compounds were then compared using the analysis of variance to confirm differences between the samples. Significant (p < 0.05) differences were found in the varieties in both years, Krasavica and Sluni?ko cultivars were found to be quite different from other varieties, being rich in the compounds identified and containing most of the selected compounds. Variability within the cultivars (between picking years) was low or not significant.     

Community genetics: a bridge between clinical genetics and public health

Clinical genetics and public health differ in their subjects; in who takes the initiative; in their aims, methods and outcome measures, and therefore in their ability to handle sensitive issues. They are seemingly incompatible. Nevertheless, they can be reconciled in community genetics. Community genetics combines the best from clinical genetics and public health. It shares with clinical genetics its aim of empowerment, its methods of information and support, its outcome measures and its possibility to handle sensitive issues. It has in common with public health its subjects; the origin of its initiatives, and non-reproductive prevention. In general, communities can be defined at different levels: geographically, linguistically, socially or genetically. Genetic communities can also be defined at different levels: on the basis of common heritage, on the basis of common practice, or on the basis of common problems.     

Changes in the proteome of extracellular vesicles shed by rat liver after subtoxic exposure to acetaminophen

To identify changes in extracellular vesicles (EVs) secreted by the liver following drug-induced liver injury (DILI), rats were treated with a subtoxic dose (500 mg/kg) of the analgesic drug, acetaminophen (APAP). EVs were collected by liver perfusion of sham and APAP-treated rats. Changes in EVs morphology were examined by transmission electron microscopic analysis of negatively stained vesicles. Results from morphometric analysis of EVs revealed striking differences in their size and distribution. Proteome composition of EVs collected by liver perfusion was determined by mass spectrometry using methods of sample preparation that enabled better detection of both highly hydrophobic proteins and proteins with complex post-translational modifications. The collection of EVs after liver perfusion is an approach that enables the isolation of EVs shed not only by isolated hepatocytes, but also by the entire complement of hepatic cells. EVs derived after DILI had a lower content of alpha-1-macroglobulin, ferritin, and members of cytochrome 450 family. Fibronectin, aminopeptidase N, metalloreductase STEAP4, integrin beta, and members of the annexin family were detected only in APAP-treated samples of EVs. These results show that the present approach can provide valuable insights into the response of the liver following drug-induced liver injury.     

Mechanisms Involved in Microbially Enhanced Oil Recovery

Microbial enhanced oil recovery (MEOR) represents a possible cost-effective tertiary oil recovery method. Although the idea of MEOR has been around for more than 75 years, even now little is known of the mechanisms involved. In this study, Draugen and Ekofisk enrichment cultures, along with Pseudomonas spp. were utilized to study the selected MEOR mechanisms. Substrates which could potentially stimulate the microorganisms were examined, and l-fructose, d-galacturonic acid, turnose, pyruvic acid and pyruvic acid methyl ester were found to be the best utilized by the Ekofisk fermentative enrichment culture. Modelling results indicated that a mechanism likely to be important for enhanced oil recovery is biofilm formation, as it required a lower in situ cell concentration compared with some of the other MEOR mechanisms. The bacterial cells themselves were found to play an important role in the formation of emulsions. Bulk coreflood and flow cell experiments were performed to examine MEOR mechanisms, and microbial growth was found to lead to possible alterations in wettability. This was observed as a change in wettability from oil wet (contact angle 154°) to water wet (0°) due to the formation of biofilms on the polycarbonate coupons.     

Lead Assays with Smartphone Detection Using a Monolithic Rod with 4-(2-Pyridylazo) Resorcinol

A monolithic rod of polyurethane foam–[4-(2-pyridylazo) resorcinol] (PUF–PAR) as a simple chemical sensor for lead assays with smartphone detection and image processing was developed. With readily available simple apparatus such as a plastic cup and a stirrer rod, the monolithic PUF rod was synthesized in a glass tube. The monolithic PUF–PAR rod could be directly loaded by standard/sample solution without sample preparation. A one-shot image in G/B value from a profile plot in ImageJ for a sample with triplicate results via a single standard calibration approach was obtained. A linear single standard calibration was: [G/B value] = −0.038[µg Pb²⁺] + 2.827, R² = 0.95 for 10–30 µg Pb²⁺ with a limit of quantitation (LOQ) of 33 µg L⁻¹. The precision was lower than 15% RSD. The proposed method was tested by an assay for Pb²⁺ contents in drinking water samples from Bangkok. The results obtained by the proposed method agree with those of ICP-OES and with 100–120% recovery, demonstrating that the method is useful for screening on-site water monitoring.