Capillary and microelectrophoretic separations of ligase detection reaction products produced from low-abundant point mutations in genomic DNA

Capillary gel electrophoresis (CGE) and polymer-based microelectrophoretic platforms were investigated to analyze low-abundant point mutations in certain gene fragments with high diagnostic value for colorectal cancers. The electrophoretic separations were carried out on single-stranded DNA (ssDNA) products generated from an allele-specific ligation assay (ligase detection reaction, LDR), which was used to screen for a single base mutation at codon 12 in the K-ras oncogene. The presence of the mutation generated a ssDNA fragment that was >40 base pairs (bp) in length, while the primers used for the ligation assay were <30 bp in length. Various separation matrices were investigated, with the success of the matrix assessed by its ability to resolve the ligation product from the large molar excess of unligated primers when the mutant allele was lower in copy number compared to the wild-type allele. Using CGE, LDR product models (44 and 51 bp) could be analyzed in a cross-linked polyacrylamide gel with a 1000-fold molar excess of LDR primers (25 bp) in approximately 45 min. However, when using linear polyacrylamide gels, these same fragments could not be detected due to significant electrokinetic biasing during injection. A poly(methylmethacrylate) (PMMA) microchip of 3.5 cm effective column length was used with a 4% linear polyacrylamide gel to analyze the products generated from an LDR. When the reaction contained a 100-fold molar excess of wild-type DNA compared to a G12.2D mutant allele, the 44 bp ligation product could be effectively resolved from unligated primers in under 120 s, nearly 17 times faster than the CGE format. In addition, sample cleanup was simplified using the microchip format by not requiring desalting of the LDR prior to loading.     

Three‐Component Langmuir–Blodgett Films Consisting of Surfactant,Clay Mineral,and Lysozyme: Construction and Characterization

The Langmuir–Blodgett (L–B) technique has been employed for the construction of hybrid films consisting of three components: surfactant, clay, and lysozyme (Lys). The surfactants are octadecylammonium chloride (ODAH) and octadecyl ester of rhodamine B (RhB18). The clays include saponite and laponite. Surface pressure versus area isotherms indicate that lysozyme is adsorbed by the surfactant–clay L–B film at the air–water interface without phase transition. The UV‐visible spectra of the hybrid film ODAH–saponite–Lys show that the amount of immobilized lysozyme in the hybrid film is (1.3±0.2) ng mm^?2. The average surface area (Ω) per molecule of lysozyme is approximately 18.2 nm² in the saponite layer. For the multilayer film (ODAH–saponite–Lys)_n, the average amount of lysozyme per layer is (1.0±0.1) ng mm^?2. The amount of lysozyme found in the hybrid films of ODAH–laponite–Lys is at the detection limit of about 0.4 ng mm^?2. Attenuated total reflectance (ATR) FTIR spectra give evidence for clay layers, ODAH, lysozyme, and water in the hybrid film. The octadecylammonium cations are partially oxidized to the corresponding carbamate. A weak 1620 cm^?1 band of lysozyme in the hybrid films is reminiscent of the presence of lysozyme aggregates. AFM reveals evidence of randomly oriented saponite layers of various sizes and shapes. Individual lysozyme molecules are not resolved, but aggregates of about 20 nm in diameter are clearly seen. Some aggregates are in contact with the clay mineral layers, others are not. These aggregates are aligned in films deposited at a surface pressure of 20 mN m^?1.     

Limitations of the scalp-hair biologic monitor in assessing selenium status in epidemiological investigations

Scalp hair is routinely used to assess exposure to toxic trace elements and nutritional status of some required trace elements. The advantages and disadvantages of hair as a biologic monitor have been comprehensively discussed in the literature for many years. Among the concerns is distinguishing between exogenous and endogenous contributions. Nested in this issue is the longitudinal distribution of a trace element along the hair strand. The typical observation for many elements of interest is that the element concentration increases from the root end to the distal end; and this is attributed to continuing contamination from exogenous sources. In this study we used neutron activation analysis to measure 14 trace elements in 6 mm segments of full-length scalp hair from three healthy members of the same household having light-urban environmental exposure. To extend the data set for selenium, we included three adult female subjects with longer than average scalp hair. From these trace-element concentrations we calculated the root-to-distal end ratios as a profile diagnostic of trace-element distributions. Ratios fall into three diagnostic categories, >1, ≈1, and <1 corresponding to profiles having decreasing root-to-distal concentrations, unchanging concentrations, and increasing concentrations, respectively. Of the 14 elements measured, only Se has R > 1, Zn and S have R ≈ 1, and the remaining 11 elements all have R < 1 in the order: As > I > Hg ≈ Au ≈ Mg ≈ Mn ≈ Sb ≈ Ca > Cu > Al ≈ Ag. R _Se is greater than 1 and increases with hair length (P = 0.02) corresponding to a continuous longitudinal loss of Se in stark and puzzling contrast to the other elements measured. An analogous loss of Se in the nail monitor was not observed leading us to conclude that the nail is less prone to misclassification of selenium status in epidemiological studies.     

Pathogen detection using engineered bacteriophages

Bacteriophages, or phages, are bacterial viruses that can infect a broad or narrow range of host organisms. Knowing the host range of a phage allows it to be exploited in targeting various pathogens. Applying phages for the identification of microorganisms related to food and waterborne pathogens and pathogens of clinical significance to humans and animals has a long history, and there has to some extent been a recent revival in these applications as phages have become more extensively integrated into novel detection, identification, and monitoring technologies. Biotechnological and genetic engineering strategies applied to phages are responsible for some of these new methods, but even natural unmodified phages are widely applicable when paired with appropriate innovative detector platforms. This review highlights the use of phages as pathogen detector interfaces to provide the reader with an up-to-date inventory of phage-based biodetection strategies.     

Photodissociation dynamics of the reaction H2CO-->H+HCO via the singlet (S0) and triplet (T1) surfaces

We have explored the photodissociation dynamics of the reaction H(2)CO+hnu-->H+HCO in the range of 810-2600 cm(-1) above the reaction threshold. Supersonically cooled formaldehyde was excited into selected J(Ka,Kc) rotational states of six vibrational levels (1(1)4(1), 5(1), 2(2)6(1), 2(2)4(3), 2(3)4(1), and 2(4)4(1)) in the A((1)A2) state. The laser induced fluorescence spectra of the nascent HCO fragment provided detailed product state distributions. When formaldehyde was excited into the low-lying levels 1(1)4(1), 5(1), and 2(2)6(1), at E(avail)<1120 cm(-1), the product state distribution can be modeled qualitatively by phase space theory. These dynamics are interpreted as arising from a reaction path on the barrierless S0 surface. When the initial states 2(2)4(3) and 2(3)4(1) were excited (E(avail)=1120-1500 cm(-1)), a second type of product state distribution appeared. This second distribution peaked sharply at low N, Ka and was severely truncated in comparison with those obtained from the lower lying states. At the even higher energy of 2(4)4(1) (E(avail) approximately 2600 cm(-1)) the sharply peaked distribution appears to be dominant. We attribute this change in dynamics to the opening up of the triplet channel to produce HCO. The theoretical height of the barrier on the T1 surface lies between 1700 and 2100 cm(-1) and so we consider the triplet reaction to proceed via tunneling at the intermediate energies and proceed over the barrier at the higher energies. Considerable population was observed in the excited (0,0,1) state for all initial H(2)CO states that lie above the appearance energy. Rotational populations in the (0,0,1) state dropped more rapidly with (N,Ka) than did the equivalent populations in (0,0,0). This indicates that, although individual rotational states are highly populated in (0,0,1), the total v3=1 population might not be so large. Specific population was also measured in the almost isoenergetic Kc and J states. No consistent population preference was found for either asymmetry or spin-rotation component.     

Characterization of highly unusual NH+-O hydrogen bonding to ester ether oxygen atoms through spectroscopic and computational studies

We characterize a highly unusual, charged NH-O hydrogen bond formed within esters of 8-(dimethylamino)naphthalen-1-ol in which an ammonium ion serves as an intramolecular hydrogen bond donor to spatially proximate ester ether oxygen atoms. Infrared spectroscopic analysis of the ester carbonyl frequencies demonstrates significant blue-shifting when ether hydrogen bonding is possible, in stark contrast to the more commonly observed red shift that occurs upon hydrogen bonding to the ester carbonyl oxygen. The intrinsic behavior of the linkage (i.e., in which counterions and solvent effects are eliminated) is provided by vibrational predissociation spectroscopy of the isolated gas-phase cations complexed with weakly bound D(2) molecules.     

Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors

By conducting a structure-activity relationship study of the backbone of a series of oligoamide-foldamer-based α-helix mimetics of the Bak BH3 helix, we have identified especially potent inhibitors of Bcl-x(L). The most potent compound has a K(i) value of 94 nM in vitro, and single-digit micromolar IC(50) values against the proliferation of several Bcl-x(L)-overexpressing cancer cell lines.     

DNA reorientation on Au nanoparticles: label-free detection of hybridization by surface enhanced Raman spectroscopy

DNA sequences attached to Au nanoparticles via thiol linkers stand up from the surface, giving preferential enhancement of the adenine ring breathing SERS band. Non-specific binding via the nucleobases reorients the DNA, reducing this effect. This change in intensity on reorientation was utilised for label-free detection of hybridization of a molecular beacon.     

Evaporation of Lennard-Jones fluids

Evaporation and condensation at a liquid/vapor interface are ubiquitous interphase mass and energy transfer phenomena that are still not well understood. We have carried out large scale molecular dynamics simulations of Lennard-Jones (LJ) fluids composed of monomers, dimers, or trimers to investigate these processes with molecular detail. For LJ monomers in contact with a vacuum, the evaporation rate is found to be very high with significant evaporative cooling and an accompanying density gradient in the liquid domain near the liquid/vapor interface. Increasing the chain length to just dimers significantly reduces the evaporation rate. We confirm that mechanical equilibrium plays a key role in determining the evaporation rate and the density and temperature profiles across the liquid/vapor interface. The velocity distributions of evaporated molecules and the evaporation and condensation coefficients are measured and compared to the predictions of an existing model based on kinetic theory of gases. Our results indicate that for both monatomic and polyatomic molecules, the evaporation and condensation coefficients are equal when systems are not far from equilibrium and smaller than one, and decrease with increasing temperature. For the same reduced temperature T/T(c), where T(c) is the critical temperature, these two coefficients are higher for LJ dimers and trimers than for monomers, in contrast to the traditional viewpoint that they are close to unity for monatomic molecules and decrease for polyatomic molecules. Furthermore, data for the two coefficients collapse onto a master curve when plotted against a translational length ratio between the liquid and vapor phase.