Fluorescence-based nucleic acid detection and microarrays

Recent analytical innovations for nucleic acid detection have revolutionized the biological sciences. Single nucleic acid sequence detection methods have been expanded to incorporate multiplexed detection strategies. A variety of nucleic acid detection formats are now available that can address high throughput genomic interrogation. Many of these parallel detection platforms or arrays, employ fluorescence as the signaling method. Fluorescence-based assays offer many advantages, including increased sensitivity, safety and multiplexing capabilities, as well as the ability to measure multiple fluorescence properties. Multiplexed microarray platforms provide parallel detection capabilities capable of measuring thousands of simultaneous responses. This review will discuss both single target detection and microarray applications with a focus on gene expression and pathogenic microorganism (PM) detection.     

Macroscopic mass and energy balance of a pilot plant anaerobic bioreactor operated under thermophilic conditions

Intensive poultry production generates over 100,000 t of litter annually in West Virginia and 9×10⁶ t nationwide. Current available technological alternatives based on thermophilic anaerobic digestion for residuals treatment are diverse. A modification of the typical continuous stirred tank reactor is a promising process being relatively stable and owing to its capability to manage considerable amounts of residuals at low operational cost. A 40-m³ pilot plant digester was used for performance evaluation considering energy input and methane production. Results suggest some changes to the pilot plant configuration are necessary to reduce power consumption although maximizing biodigester performance.     

Cucurbit[6]uril pseudorotaxanes: distinctive gas-phase dissociation and reactivity

Cucurbit[6]uril forms a doubly charged complex with 1,4-butanediammonium cation that is observed using electrospray ionization Fourier transform mass spectrometry. Such 1:1 complexes are not observed for the smaller cucurbit[5]uril, which forms a 2:1 ammonium:cucurbituril complex instead. The 1:1 complex with cucurbit[6]uril is difficult to fragment via collisional activation; when it does fragment, both breakup of the cucurbituril cage and loss of the amine are observed. Further, the complex reacts with tert-butylamine via slow adduction. In contrast, nonrotaxane analogues (such as doubly charged 2:1 complexes of either protonated 1,4-butanediamine or protonated ethylenediamine with cucurbit[6]uril) fragment via easy loss of the intact amine upon collisional activation and react with tert-butylamine via rapid displacement of the original amine. On the basis of stoichiometry, fragmentation behavior, and reactivity, we conclude that the doubly charged complex of cucurbit[6]uril with 1,4-butanediammonium is a gas-phase pseudorotaxane.     

Preparation and crystal structure ofexo-2,exo-6-dihydroxy-2,6-dimethyl-9-oxabicyclo[3.3.1]nonane

In a further exploration of the structural factors causing alicyclic diols such asexo-2,exo-6-dihydroxy-2,6-dimethylbicyclo[3.3.1]nonane (1) to adopt the helical tubuland inclusion host structure, the title compound (8) has been synthesized and its crystal structure determined. This 9-oxa analogue of (1) has a totally different structure [C₁₀H₁₈O₃; orthorhombic;P2₁2₁2;a 18.989(4),b 19.064(3),c 14.256(3) Å;Z 20; with finalR 0.065] due to involvement of the ether oxygen atom in the hydrogen bonding network. The structure of the diol (8) approximatesP¯42₁ c symmetry, and 16 of the 20 molecules per cell create a hostlike structure of this symmetry, which consists of tightly bound hydrogen bonded pillars parallel toc. The remaining guestlike molecules occupy inequivalent pseudo ¯4 sites separated byc/2 to form weakly bound columns parallel toc. Hydrogen bonds also occur between the pillars and columns. An ordered structure with sensible intermolecular contacts can be formed inP2₁2₁2₁ with thec axis doubled. A difference betweena andb axial lengths correlates with a difference in occupancies of pseudo-¯4-related sites for the guest-like component of the structure.     

Electron transfer reactions of cytochrome c at metal electrodes

The heterogeneous electron transfer reactions of cytochromec occurring at platinum, gold and mercury electrodes are shown to be quasi-reversible. In each case the electrodes have not been modified and the cytochromec samples are native. This work extends previous work and demonstrates that biological molecule electron transfer reactions can be studied at clean metal surfaces to gain fundamental knowledge of the mechanisms of these reactions.     

Enantioselective, chirally templated sol-gel thin films

Enantioselective surfactant-templated thin films were fabricated through the sol-gel (SG) process. The enantioselectivity is general in the sense that it discriminates between pairs of enantiomers not used for the imprinting process. The chiral cationic surfactant (-)-N-dodecyl-N-methylephedrinium bromide (1) was used as the surfactant template, and after its extraction chiral domains were created. The chiral discriminative feature of these films was examined by challenging with pure enantiomer solutions for rebinding. Selective adsorption was shown using (R)- and (S)-propranolol, (R)-2 and (S)-2, respectively, and (R)- and (S)-2,2,2-trifluoro-1-(9-anthryl)ethanol, (R)-3 and (S)-3, respectively, as the chiral probes. The selective adsorption was measured by fluorescence analysis, and the chiral selectivity factors were found to be 1.6 for 2 and 2.25 for 3. In both cases, (R)-enantiomer was adsorbed preferably. The resulting material was characterized by transmission electron microscopy, by diffraction, and by surface area measurements, and was found to be semicrystalline with short-range ordered domains (50 A) of hexagonal symmetry.     

Diamond and diamond-like carbon from a preceramic polymer

The synthesis of poly(hydridocarbyne), one of a class of carbon-based random network polymers and a structural isomer of polyacetlyene, is reported. The network backbone of this polymer is primarily composed of tetrahedrally hybridized carbon atoms, each bearing one hydride substituent and linked via three carbon-carbon single bonds into a three-dimensional random network of fused rings. This atomic-level carbon network backbone confers unusual properties on the polymer, including facile thermal decomposition to form diamond or diamond-like carbon high-quality films at atmospheric pressure, by direct deposition or by chemical vapor deposition (CVD), without the use of hydrogen or any other reagent.     

Amber‐Woody Scent: Alcohols with Divergent Structure Present Common Olfactory Characteristics and Sharp Enantiomer Differentiation

Only one out of the four possible trans isomers of the important perfumery alcohol Norlimbanol^® ( 1 ) possesses a very strong amber‐woody smell, the isomer 1A with (1′R,3S,6′S) absolute configuration. Its enantiomer 1B is almost odorless and devoid of amber‐woody character, whereas the diastereoisomers 1C and 1D are considerably weaker and perceptible only by the most‐sensitive persons. The same is true for a whole series of perceptual analogs of 1 , including β‐alkoxy alcohols. These ethers belong to two structural classes: [(2,2,6‐trimethylcyclohexyl)oxy]‐ (see 3, 4 , and 16 ) or {[2‐(tert‐butyl)cyclohexyl]oxy}alkan‐2‐ol derivatives (see 19 and 20 ; Table). A superimposition model allowing for good overlap of the respective hydroxylated side chains offers a tentative explanation for the shared perceptual characteristics of the two classes (Fig. 5). The lipophilic cyclohexane moieties present only a minimal overlap in this model, suggesting that quite larger molecules might possess the same smell. (S)‐Configured β‐alkoxy alcohols can conveniently be obtained on a larger scale by enantioselective reduction of the corresponding ketones (Scheme 9).     

MPW1K Performs Much Better than B3LYP in DFT Calculations on Reactions that Proceed by Proton-Coupled Electron Transfer (PCET)

DFT calculations have been performed with the B3LYP and MPW1K functional on the hydrogen atom abstraction reactions of ethenoxyl with ethenol and of phenoxyl with both phenol and alpha-naphthol. Comparison with the results of G3 calculations shows that B3LYP seriously underestimates the barrier heights for the reaction of ethenoxyl with ethenol by both proton-coupled electron transfer (PCET) and hydrogen atom transfer (HAT) mechanisms. The MPW1K functional also underestimates the barrier heights, but by much less than B3LYP. Similarly, comparison with the results of experiments on the reaction of phenoxyl radical with alpha-naphthol indicates that the barrier height for the preferred PCET mechanism is calculated more accurately by MPW1K than by B3LYP. These findings indicate that the MPW1K functional is much better suited than B3LYP for calculations on hydrogen abstraction reactions by both HAT and PCET mechanisms.     

Liquid Densities and Excess Molar Volumes for Binary Systems (Ionic Liquids + Methanol or Water) at 298.15, 303.15 and 313.15 K,and at Atmospheric Pressure

Binary excess molar volumes, V _m ^E, have been evaluated from density measurements, using a vibrating tube densimeter over the entire composition range for binary liquid mixtures of ionic liquids 1-ethyl-3-methyl-imidazolium diethyleneglycol monomethylethersulphate [EMIM]⁺[CH₃(OCH₂CH₂)₂OSO₃]⁻ or 1-butyl-3-methyl-imidazolium diethyleneglycol monomethylethersulphate [BMIM]⁺[CH₃(OCH₂CH₂)₂OSO₃]⁻ or 1-methyl-3-octyl-imidazolium diethyleneglycol monomethylethersulphate [MOIM]⁺[CH₃(OCH₂CH₂)₂OSO₃]⁻+methanol and [EMIM]⁺[CH₃(OCH₂CH₂)₂OSO₃]⁻+water at 298.15, 303.15 and 313.15 K. The V _m ^E values were found to be negative for all systems studied. The V _m ^E results are explained in terms of intermolecular interactions and packing effects. The experimental data were fitted by the Redlich-Kister polynomial.