Automated sample preparation method for suspension arrays using renewable surface separations with multiplexed flow cytometry fluorescence detection

In this paper, we describe a new method of automated sample preparation for multiplexed biological analysis systems that use flow cytometry fluorescence detection. In this approach, color-encoded microspheres derivatized to capture particular biomolecules are temporarily trapped in a renewable surface separation column to enable perfusion with sample and reagents prior to delivery to the detector. This method provides for separation of the biomolecules of interest from other sample matrix components as well as from labeling solutions. After sample preparation, the beads can be released from the renewable surface column and delivered to a flow cytometer for direct on-bead analysis one bead at a time. Using mixtures of color-encoded beads derivatized for various analytes yields suspension arrays for multiplexed analysis. Development of this approach required a new technique for automated capture and release of the color-encoded microspheres within a fluidic system. We developed a method for forming a renewable filter and demonstrate its use for capturing microspheres that are too small to be easily captured in previous flow cells for renewable separation columns. The renewable filter is created by first trapping larger beads in the flow cell, and then smaller beads are captured either within or on top of the bed of larger beads. Both the selective microspheres and filter bed are automatically emplaced and discarded for each sample. A renewable filter created with 19.9 μm beads was used to trap 5.6 μm optically encoded beads with trapping efficiencies of 99%. The larger beads forming the renewable filter did not interfere with the detection of color-encoded 5.6 μm beads by the flow cytometer fluorescence detector. The use of this method was demonstrated with model reactions for a variety of bioanalytical assay types including a one-step capture of a biotinylated label on Lumavidin beads, a two-step sandwich immunoassay, and a one-step DNA binding assay. A preliminary demonstration of multiplexed detection of two analytes using color-encoded beads was also demonstrated. The renewable filter for creating separation columns containing optically encoded beads provides a general platform for coupling renewable surface methods for sample preparation and analyte labeling with flow cytometry detectors for suspension array multiplexed analyses.     

Intercepting bacterial indole signaling with flustramine derivatives

Indole signaling is one of the putative universal signaling networks in bacteria. We have investigated the use of desformylflustrabromine (dFBr) derivatives for the inhibition of biofilm formation through modulation of the indole-signaling network in Escherichia coli and Staphylococcus aureus . We have found dFBr derivatives that are 10-1000 times more active than indole itself, demonstrating that the flustramine family of indolic natural products represent a privileged scaffold for the design of molecules to control pathogenic bacterial behavior.     

3M Petrifilm Staph Express Count plate method for the enumeration of Staphylococcus aureus in selected types of meat, seafood, and poultry: collaborative study

The 3M Petrifilm Staph Express Count plate method was compared with AOAC Official Method 975.55 for the enumeration of Staphylococcus aureus in selected foods. Four foods--cooked, diced chicken; cured ham; smoked salmon; and pepperoni--were analyzed for S. aureus by 12 collaborating laboratories. For each food tested, the collaborators received 8 blind test samples consisting of a control sample, a low inoculation level, a medium inoculation level, and a medium inoculation level with background flora, each in duplicate. The mean log10 counts for the methods were comparable for all 4 foods. The repeatability and reproducibility variances of the 24 h Petrifilm Staph Express Count plate method were similar to those of the 72 h standard method.     

Uranyl coordination environment in hydrophobic ionic liquids: an in situ investigation

Different inner-sphere coordination environments are observed for the uranyl nitrate complexes formed with octyl-phenyl-N,N-diisobutylcarbamoylmethylphosphine oxide and tributyl phosphate in dodecane and in the hydrophobic ionic liquids (ILs) [C(4)mim][PF(6)] and [C(8)mim][N(SO(2)CF(3))(2)]. Qualitative differences in the coordination environment of the extracted uranyl species are implied by changes in peak intensity patterns and locations for uranyl UV-visible spectral bands when the solvent is changed. EXAFS data for uranyl complexes in dodecane solutions is consistent with hexagonal bipyramidal coordination and the existence of UO(2)(NO(3))(2)(CMPO)(2). In contrast, the complexes formed when uranyl is transferred from aqueous nitric acid solutions into the ILs exhibit an average equatorial coordination number of approximately 4.5. Liquid/liquid extraction results for uranyl in both ILs indicate a net stoichiometry of UO(2)(NO(3))(CMPO)(+). The concentration of the IL cation in the aqueous phase increases in proportion to the amount of UO(2)(NO(3))(CMPO)(+) in the IL phase, supporting a predominantly cation exchange mechanism for partitioning in the IL systems.     

Simultaneous isolation and label‐free identification of bacteria using contactless dielectrophoresis and Raman spectroscopy

The traditional bacterial identification method of growing colonies on agar plates can take several days to weeks to complete depending on the growth rate of the bacteria. Successfully decreasing this analysis time requires cell isolation followed by identification. One way to decrease analysis time is by combining dielectrophoresis (DEP), a common technique used for cell sorting and isolation, and Raman spectroscopy for cell identification. DEP‐Raman devices have been used for bacterial analysis, however, these devices have a number of drawbacks including sample heating, cell‐to‐electrode proximity that limits throughput and separation efficiency, electrode fouling, or inability to address sample debris. Presented here is a contactless DEP‐Raman device to simultaneously isolate and identify particles from a mixed sample while avoiding common drawbacks associated with other DEP designs. Using the device, a mixed sample of bacteria and 3 μm polystyrene spheres were isolated from each other and a Raman spectrum of the trapped bacteria was acquired, indicating the potential for cDEP‐Raman devices to decrease the analysis time of bacteria.     

Rearrangement of epoxynitriles: a convenient homologation of acyclic and cyclic ketones to carboxylic acids

A convenient two-step homologation of both aliphatic and aromatic ketones to the corresponding carboxylic acid has been developed. First ketones were converted to epoxynitriles with the Darzens reaction. Second, a Lewis acid mediated rearrangement of these epoxynitriles with lithium bromide was achieved to give homologated secondary alkanoic acids (as well as aryl-alkanoic) in good yields. The mechanism and the scope of the rearrangement reaction were investigated. This strategy constitutes a two-step homologation of ketones to secondary carboxylic acids.     

On the conformational stability and dimerization of phosphotransferase enzyme I from Escherichia coli

The activity of enzyme I (EI), the first protein in the bacterial PEP:sugar phosphotransferase system, is regulated by a monomer–dimer equilibrium where a Mg²⁺-dependent autophosphorylation by PEP requires the homodimer. Using inactive EI(H189A), in which alanine is substituted for the active-site His189, substrate binding effects can be separated from those of phosphorylation. Whereas 1 mM PEP (with 2 mM Mg²⁺) strongly promotes dimerization of EI(H189A) at pH 7.5 and 20 °C, 5 mM pyruvate (with 2 mM Mg²⁺) has the opposite effect. A correlation between the coupling of N- and C-terminal domain unfolding, measured by differential scanning calorimetry, and the dimerization constant for EI, determined by sedimentation equilibrium, is observed. That is, when the coupling between N- and C-terminal domain unfolding produced by 0.2 or 1.0 mM PEP and 2 mM Mg²⁺ is inhibited by 5 mM pyruvate, the dimerization constant for EI(H189A) decreases from >10⁸ to <5 × 10⁵ or 3 × 10⁷ M⁻¹, respectively. With 2 mM Mg²⁺ at 15–25 °C and pH 7.5, PEP has been found to bind to one site/monomer of EI(H189A) with K_A′10⁶ M⁻¹ (ΔG′=−33.7±0.2 kJ mol⁻¹ and ΔH=+16.3 kJ mol⁻¹ at 20 °C with ΔC_p=−1.4 kJ K⁻¹ mol⁻¹). The binding of PEP to EI(H189A) is synergistic with that of Mg²⁺. Thus, physiological concentrations of PEP and Mg²⁺ increase, whereas pyruvate and Mg²⁺ decrease the amount of dimeric, active, dephospho-enzyme I.     

Characterization of humic substances: Implications for trihalomethane formation

Humic substances are precursors of carcinogenic trihalomethanes (THMs) formed during disinfection by chlorination in water treatment processes. In an effort to understand the relationship between trihalomethane formation potential (THMFP) and physicochemical properties of humic substances, UV-visible absorbance, fluorescence in emission and synchronous scan modes, and NMR spectra were measured for several aquatic fulvic and humic acids. For comparison, a soil fulvic acid was also examined using these methods. The feasibility of the gradient modified spin-echo (GOSE) NMR experiment to selectively measure singlet resonances arising from isolated protons was examined. In addition, diffusion coefficients were measured for DMSO solutions of the fulvic acids using BPPLED and GOSE-edited pulse sequences. Although none of the methods tested produced results that correlated with THMFP, the GOSE intensities determined for different regions of the NMR spectra did reflect the relative abundance of different types of functional groups produced by lignin oxidation. In addition, the GOSE-edited diffusion results suggest that the isolated protons, those most reactive to chlorination, are more likely contained in the larger molecular weight fractions of fulvic acids.     

Spermine participates in oxidative damage of guanosine and 8-oxoguanosine leading to deoxyribosylurea formation

Oxidation of single- or double-stranded DNA containing a 7,8-dihydro-8-oxoguanosine lesion with the one-electron oxidant Na2IrCl6 in the presence of spermine led to formation of a covalent adduct that was analyzed by gel electrophoresis, HPLC, ESI-MS, and UV-vis. The adduct was labile to heat, exhibiting a t1/2 of 12 h at 37 degrees C, and the ultimate hydrolysis product was characterized as a deoxyribosylurea lesion. Data from model studies with 1,3-diaminopropane vs 1,4-diaminobutane are consistent with initial formation of a C5 spermine adduct from a dehydro-8-oxoguanosine intermediate, followed by rearrangement to a spiroaminal subject to slow hydrolysis at C4 of the purine. Spermine adducts could also be formed from oxidation of the analogous G-containing oligomer from reaction with singlet oxygen, albeit in lower yield. These results are surprising in light of the traditional view that spermine is radioprotective against DNA oxidation.