The determination of tissue-specific DNA methylation patterns in forensic biofluids using bisulfite modification and pyrosequencing

The goal of this study is to explore the application of epigenetic markers in the identification of biofluids that are commonly found at the crime scene. A series of genetic loci were examined in order to define epigenetic markers that display differential methylation patterns between blood, saliva, semen, and epithelial tissue. Among the different loci tested, we have identified a panel of markers, C20orf117, ZC3H12D, BCAS4, and FGF7, that can be used in the determination of these four tissue types. Since methylation modifications occur at cytosine bases that are immediately followed by guanine bases (CpG sites), methylation levels were measured at CpG sites spanning each marker. Up to 11 samples of each tissue type were collected and subjected to bisulfite modification to convert unmethylated CpG-associated cytosine bases to thymine bases. The bisulfite modified DNA was then amplified via nested PCR using a primer set of which one primer was biotin labeled. Biotinylated PCR products were in turn analyzed and the methylation level at each CpG site was quantitated by pyrosequencing. The percent methylation values at each CpG site were determined and averaged for each tissue type. The results indicated significant methylation differences between the tissue types. The methylation patterns at the ZC3H12D and FGF7 loci differentiated sperm from blood, saliva, and epithelial cells. The C20orf117 locus differentiated blood from sperm, saliva, and epithelial cells and saliva was differentiated from blood, sperm, and epithelial cells at a fourth locus, BCAS4. The results of this study demonstrate the applicability of epigenetic markers as a novel tool for the determination of biofluids using bisulfite modification and pyrosequencing.     

Reveal Listeria 2.0 test for detection of Listeria spp. in foods and environmental samples

A Performance Tested Method validation study was conducted for a new lateral flow immunoassay (Reveal Listeria 2.0) for detection of Listeria spp. in foods and environmental samples. Results of inclusivity testing showed that the test detects all species of Listeria, with the exception of L. grayi. In exclusivity testing conducted under nonselective growth conditions, all non-listeriae tested produced negative Reveal assay results, except for three strains of Lactobacillus spp. However, these lactobacilli are inhibited by the selective Listeria Enrichment Single Step broth enrichment medium used with the Reveal method. Six foods were tested in parallel by the Reveal method and the U.S. Food and Drug Administration/Bacteriological Analytical Manual (FDA/BAM) reference culture procedure. Considering data from both internal and independent laboratory trials, overall sensitivity of the Reveal method relative to that of the FDA/BAM procedure was 101%. Four foods were tested in parallel by the Reveal method and the U.S. Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS) reference culture procedure. Overall sensitivity of the Reveal method relative to that of the USDA-FSIS procedure was 98.2%. There were no statistically significant differences in the number of positives obtained by the Reveal and reference culture procedures in any food trials. In testing of swab or sponge samples from four types of environmental surfaces, sensitivity of Reveal relative to that of the USDA-FSIS reference culture procedure was 127%. For two surface types, differences in the number of positives obtained by the Reveal and reference methods were statistically significant, with more positives by the Reveal method in both cases. Specificity of the Reveal assay was 100%, as there were no unconfirmed positive results obtained in any phase of the testing. Results of ruggedness experiments showed that the Reveal assay is tolerant of modest deviations in test sample volume and device incubation time.     

Heat and mass transmission of an Oldroyd-B nanofluid flow through a stratified medium with swimming of motile gyrotactic microorganisms and nanoparticles

Journal of Thermal Analysis and Calorimetry - This paper focuses on the research of motile microorganism rates in the bioconvective Oldroyd-B nanoliquid flow over a vertical stretching sheet with...     

Bicyclo[2.1.1]hexan-2-one as a new probe for the study of π-facial selectivity in nucleophilic additions. A comment

The cation complexation model performs better than the hydride model and is at par with the transition state model at the HF/6-31G* and B3LYP/6-31G* levels. Electrostatic effects that rely on the residual charges on C5 and C6 of the title substrate and that are believed to contribute to the overall performance of the hydride model also perform poorly.     

Voltammetric determination of catechol and hydroquinone using nitrogen-doped multiwalled carbon nanotubes modified with nickel nanoparticles

Nitrogen-doped multiwalled carbon nanotubes modified with nickel nanoparticles (Ni/N-MWCNT) were prepared by a thermal reduction process starting from urea and Ni(II) salt in an inert atmosphere. The nanocomposite was deposited on a screen printed electrode and characterized by X-ray diffraction, scanning and transmission electron microscopy, nitrogen adsorption, X-ray photoelectron spectroscopy, and thermogravimetric analyses. The performance of the composite was investigated by cyclic voltammetry, differential pulse voltammetry and chronoamperometry. The numerous active metal sites with fast electron transfer properties result in enhanced electrocatalytic activity towards the individual and simultaneous detection of catechol (CC) and hydroquinone (HQ), best at 0.21 V for CC and 0.11 V for HQ (vs. Ag/AgCl). For both targets the detection limit (S/N of 3) was 9 nM (CC) and 11 nM (HQ), and the Ni/N-MWCNT-electrode showed linear response from 0.1–300 μM CC, and 0.3–300 μM HQ. The electrode is selective over many potentially interfering ions. It was applied to the analysis of spiked water samples and gave satisfactory recoveries. It also is sensitive for CC (5.396 μA·μM^?1 cm^?2) and HQ (5.1577 μA·μM^?1 cm^?2), highly active, durable, acceptably repeatable and highly reproducible.

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Graphical abstract Voltammetric determination of catechol and hydroquinone using nitrogen-doped multiwalled carbon nanotubes modified with nickel nanoparticles.

     

Calamitic liquid crystals of 1,2,3-triazole connected to azobenzene: synthesis,characterisation and anisotropic properties

Azobenzene-based calamitic liquid crystals, 4-((4-(4-methoxymethyl-1,2,3-triazol-1-yl)phenyl)diazenyl)phenylalkanoates have been isolated and their structures were characterised. The structure–property correlation with respect to the different alkanoyloxy terminal chain (–COOC_nH_2n+1 where n adopts odd numbers ranging from 3 to 15) has also been given attention in the present study. In this series, all compounds exhibit smectogenic properties. The lower homologues shows enantiotropic SmA phase as well as monotropic SmC phase. The higher homologues exhibit homeotropic alignment of smectic phases. These compounds possess very high anisotropic inclination in which the mesomorphic region covers nearly 80°C.     

Simple replication methods for producing nanoslits in thermoplastics and the transport dynamics of double-stranded DNA through these slits

Mixed-scale nano- and microfluidic networks were fabricated in thermoplastics using simple and robust methods that did not require the use of sophisticated equipment to produce the nanostructures. High-precision micromilling (HPMM) and photolithography were used to generate mixed-scale molding tools that were subsequently used for producing fluidic networks into thermoplastics such as poly(methyl methacrylate), PMMA, cyclic olefin copolymer, COC, and polycarbonate, PC. Nanoslit arrays were imprinted into the polymer using a nanoimprinting tool, which was composed of an optical mask with patterns that were 2-7 μm in width and a depth defined by the Cr layer (100 nm), which was deposited onto glass. The device also contained a microchannel network that was hot embossed into the polymer substrate using a metal molding tool prepared via HPMM. The mixed-scale device could also be used as a master to produce a polymer stamp, which was made from polydimethylsiloxane, PDMS, and used to generate the mixed-scale fluidic network in a single step. Thermal fusion bonding of the cover plate to the substrate at a temperature below their respective T(g) was accomplished by oxygen plasma treatment of both the substrate and cover plate, which significantly reduced thermally induced structural deformation during assembly: ～6% for PMMA and ～9% for COC nanoslits. The electrokinetic transport properties of double-stranded DNA (dsDNA) through the polymeric nanoslits (PMMA and COC) were carried out. In these polymer devices, the dsDNA demonstrated a field-dependent electrophoretic mobility with intermittent transport dynamics. DNA mobilities were found to be 8.2 ± 0.7 × 10(-4) cm(2) V(-1) s(-1) and 7.6 ± 0.6 × 10(-4) cm(2) V(-1) s(-1) for PMMA and COC, respectively, at a field strength of 25 V cm(-1). The extension factors for λ-DNA were 0.46 in PMMA and 0.53 in COC for the nanoslits (2-6% standard deviation).     

Designing highly specific biosensing surfaces using aptamer monolayers on gold

To build highly specific surfaces using aptamer affinity reagents, the effects of linker and coadsorbents were investigated for maximizing target binding and specificity for aptamer-based self-assembled monolayers (SAMs) supported on gold. An aptamer that binds the protein thrombin was utilized as a model system to compare different mixed monolayer systems toward maximizing binding and selectivity to the immobilized aptamer. Important factors used to optimize binding characteristics of thrombin to the aptamer-based monolayer films include changes in design elements of the linker and different coadsorbent thiols. Binding events measured by surface plasmon resonance (SPR) and ellipsometry showed that the binding performance of the aptamer SAMs depends principally on the linker and to a lesser extent on the coadsorbent. SAMs formed with HS-(CH2)6-OP(O)2O-(CH2CH2O)6-TTTTT-aptamer exhibited a 4-fold increase in binding capacity versus SAMs made using HS-(CH2)6-TTTTT-aptamer. Furthermore, SAMs made using HS-(CH2)6-OP(O)2O-(CH2CH2O)6-TTTTT-aptamer showed nearly complete specificity for thrombin versus bovine serum albumin (BSA, less than 2% bound), while a SAM incorporating a random DNA fragment (HS-(CH2)6-OP(O)2O-(CH2CH2O)6-TTTTT-RANDOM) showed little binding of thrombin. Irrespective of the aptamer-linker system, use of HS-(CH2)11(OCH2CH2)3OH, referred to as EG(3), as a coadsorbent enhanced binding of thrombin by approximately 2.5-fold compared to that of HS-(CH2)6-OH (mercaptohexanol, MCH).