Production and certification of NIST Standard Reference Material 2372 Human DNA Quantitation Standard

Modern highly multiplexed short tandem repeat (STR) assays used by the forensic human-identity community require tight control of the initial amount of sample DNA amplified in the polymerase chain reaction (PCR) process. This, in turn, requires the ability to reproducibly measure the concentration of human DNA, [DNA], in a sample extract. Quantitative PCR (qPCR) techniques can determine the number of intact stretches of DNA of specified nucleotide sequence in an extremely small sample; however, these assays must be calibrated with DNA extracts of well-characterized and stable composition. By 2004, studies coordinated by or reported to the National Institute of Standards and Technology (NIST) indicated that a well-characterized, stable human DNA quantitation certified reference material (CRM) could help the forensic community reduce within- and among-laboratory quantitation variability. To ensure that the stability of such a quantitation standard can be monitored and that, if and when required, equivalent replacement materials can be prepared, a measurement of some stable quantity directly related to [DNA] is required. Using a long-established conventional relationship linking optical density (properly designated as decadic attenuance) at 260 nm with [DNA] in aqueous solution, NIST Standard Reference Material (SRM) 2372 Human DNA Quantitation Standard was issued in October 2007. This SRM consists of three quite different DNA extracts: a single-source male, a multiple-source female, and a mixture of male and female sources. All three SRM components have very similar optical densities, and thus very similar conventional [DNA]. The materials perform very similarly in several widely used gender-neutral assays, demonstrating that the combination of appropriate preparation methods and metrologically sound spectrophotometric measurements enables the preparation and certification of quantitation [DNA] standards that are both maintainable and of practical utility. Figure NIST Standard Reference Material (SRM) 2372 Human Quantitation Standard     

Solution-Phase and Magnetic Approach towards Understanding Iron Gall Ink-like Nanoassemblies

Metal-containing tubes: The structures of several iron-containing C-methylpyrogallol[4]arene (PgC(1) ) nanoassemblies were studied in both the solid and solution phases. The nanoassemblies have a tubular architecture with the iron as part of the framework (see picture; gray C, red O, turquoise/blue Fe), and magnetic analysis suggests a canted or spiral arrangement of the iron centers.     

Colloidal deposition on remotely controlled charged micropatterned surfaces in a parallel-plate flow chamber

This article describes a method to influence colloid deposition by varying the zeta potential at microelectrodes with remotely applied electric potentials. Deposition experiments were conducted in a parallel-plate flow chamber for bulk substrates of glass, indium tin oxide (ITO), and ITO-coated glass microelectrodes in 10 and 60 mM potassium chloride solutions. Colloid deposition was found to be a function of solution chemistry and the small locally delivered electric surface potentials. Electric fields and physical surface heterogeneity can be ruled out as cause of the observed deposition. Results are reported using experimentally determined Sherwood numbers and compared to the predictions of a previously developed patch model. Minor deviations between predicted and experimental Sherwood numbers imply that physical and chemical interactions occur. Specifically, we propose that colloidal particles respond to local variations in surface potential through electrostatic interactions, altering particle streamlines flowing along the surface and ultimately the extent of deposition.     

Volatile compounds from the integument of White Leghorn Chickens (Gallus gallus domesticus L.): candidate attractants of ornithophilic mosquito species

Candidate kairomones of ornithophilic mosquito species are reported from GC/MS analysis of compounds from the skin on the back, the feet, and feathers from the back of White Leghorn chickens (Gallus gallus domesticus). Hexane and ether extracts of chicken feathers differ significantly in attractiveness of Culex spp. mosquitoes. The active (hexane) extracts contained an abundance of alcohols, ketones, and diones. The inactive (ether) extracts contained aldehydes, which also were in the hexane extracts. Analysis of hexane extracts from chicken feet, skin, and feathers demonstrated the qualitative similarity in the compounds collected with subtle differences observed in the quantitative amounts of these compounds. Aldehydes and carboxylic acids were detected in a concentrated ether extract of feathers in quantitatively similar ratios within each compound class for the corresponding series of C(6)-C(9 )aldehydes and acids.     

Generation and characterization of high affinity human monoclonal antibodies that neutralize staphylococcal enterotoxin B

Background

Staphylococcal enterotoxins are considered potential biowarfare agents that can be spread through ingestion or inhalation. Staphylococcal enterotoxin B (SEB) is a widely studied superantigen that can directly stimulate T-cells to release a massive amount of proinflammatory cytokines by bridging the MHC II molecules on an antigen presenting cell (APC) and the Vβ chains of the T-cell receptor (TCR). This potentially can lead to toxic, debilitating and lethal effects. Currently, there are no preventative measures for SEB exposure, only supportive therapies.

Methods

To develop a potential therapeutic candidate to combat SEB exposure, we have generated three human B-cell hybridomas that produce human monoclonal antibodies (HuMAbs) to SEB. These HuMAbs were screened for specificity, affinity and the ability to block SEB activity in vitro as well as its lethal effect in vivo.

Results

The high-affinity HuMAbs, as determined by BiaCore analysis, were specific to SEB with minimal crossreactivity to related toxins by ELISA. In an immunoblotting experiment, our HuMAbs bound SEB mixed in a cell lysate and did not bind any of the lysate proteins. In an in vitro cell-based assay, these HuMAbs could inhibit SEB-induced secretion of the proinflammatory cytokines (INF-γ and TNF-α) by primary human lymphocytes with high potency. In an in vivo LPS-potentiated mouse model, our lead antibody, HuMAb-154, was capable of neutralizing up to 100 μg of SEB challenge equivalent to 500 times over the reported LD₅₀ (0.2 μg), protecting mice from death. Extended survival was also observed when HuMAb-154 was administered after SEB challenge.

Conclusion

We have generated high-affinity SEB-specific antibodies capable of neutralizing SEB in vitro as well as in vivo in a mouse model. Taken together, these results suggest that our antibodies hold the potential as passive immunotherapies for both prophylactic and therapeutic countermeasures of SEB exposure.     

Neuropeptide delivery to the brain: a von Willebrand factor signal peptide to direct neuropeptide secretion

Background  

Multiple neuropeptides, sometimes with opposing functions, can be produced from one precursor gene. To study the roles of the different neuropeptides encoded by one large precursor we developed a method to overexpress minigenes and establish local secretion.     

Two‐group classification using the Bayesian data reduction algorithm

The Bayesian data reduction algorithm (BDRA) is compared to traditional classification methods as well as feed forward artificial neural networks through a rigorous experiment. The BDRA performs comparably to alternative techniques and approaches theoretical optimal classification rates. Furthermore, it has a fundamentally different method for determining class membership. This study is novel in that it explores how the BDRA relates to established techniques, how it might be used in an explanatory manner, and how best to use it. © 2009 Wiley Periodicals, Inc. Complexity, 2010     

Assessment of the in-vivo stereochemical integrity of aprepitant based on the analysis of human plasma samples via high-performance liquid chromatography with mass spectrometric detection

Achiral and chiral liquid chromatographic methods utilizing mass spectrometric detection were developed to investigate the possibility of inversion of configuration at any or all of the chiral centers of the neurokinin-1 (NK-1) receptor antagonist, aprepitant (5-[[2(R)-[1(R)-(3,5-bistrifluoromethyl phenyl)ethoxy]-3(S)-(4-fluorophenyl)morpholin-4-yl]methyl]-2,4-dihydro-[1,2,4]triazol-3-one), in-vivo, following administration of the compound to man. A structure such as aprepitant, that contains three chiral centers, may exist in eight stereochemical forms or, more specifically, as four diastereoisomeric pairs of enantiomers. The four diastereoisomers were separated from each other using a ProntoSil C18 AQ HPLC column (4.6 x 100 mm, 3 microm particles) with a mobile phase composed of acetonitrile--water (47:53, v/v%). Detection was via a single quadrupole mass spectrometer that was connected to the HPLC system via an APCI interface. Analysis of post-dose plasma samples under these conditions indicated that only aprepitant and or its enantiomer were present following oral administration of the drug. Aprepitant and its enantiomer were separated using a Chiralcel OD-H HPLC column with a mobile phase composed of hexane-isopropanol (80:20, v/v%); tandem mass spectrometric detection using an APCI interface was employed. Post-dose plasma samples analyzed using the Chiracel column were found to contain only aprepitant. The results of these experiments confirm that the products of inversion of configuration at any or all of the three chiral centers of aprepitant are not detectable in human plasma samples obtained following the administration of the drug.     

Detecting bacteria and determining their susceptibility to antibiotics by stochastic confinement in nanoliter droplets using plug-based microfluidics

This article describes plug-based microfluidic technology that enables rapid detection and drug susceptibility screening of bacteria in samples, including complex biological matrices, without pre-incubation. Unlike conventional bacterial culture and detection methods, which rely on incubation of a sample to increase the concentration of bacteria to detectable levels, this method confines individual bacteria into droplets nanoliters in volume. When single cells are confined into plugs of small volume such that the loading is less than one bacterium per plug, the detection time is proportional to plug volume. Confinement increases cell density and allows released molecules to accumulate around the cell, eliminating the pre-incubation step and reducing the time required to detect the bacteria. We refer to this approach as 'stochastic confinement'. Using the microfluidic hybrid method, this technology was used to determine the antibiogram - or chart of antibiotic sensitivity - of methicillin-resistant Staphylococcus aureus (MRSA) to many antibiotics in a single experiment and to measure the minimal inhibitory concentration (MIC) of the drug cefoxitin (CFX) against this strain. In addition, this technology was used to distinguish between sensitive and resistant strains of S. aureus in samples of human blood plasma. High-throughput microfluidic techniques combined with single-cell measurements also enable multiple tests to be performed simultaneously on a single sample containing bacteria. This technology may provide a method of rapid and effective patient-specific treatment of bacterial infections and could be extended to a variety of applications that require multiple functional tests of bacterial samples on reduced timescales.     

Characterization of conformational adsorbate changes on a tissue-derived substrate using Fourier transform infrared spectroscopy

Fourier transform infrared (FT-IR) spectroscopy is utilized to observe adsorbate interactions with a tissue-derived collagen scaffold extracted from the Bruch's membrane of pig eyes. The characterization includes conformational changes in isoleucine, polyisoleucine, collagen-binding peptide, RGD-tagged collagen-binding peptide, and laminin after adsorption onto the substrate. Isotopically labeled isoleucine is further utilized to understand changes in the biomolecular structure upon binding to a tissue-derived surface. The adsorbates associated with the collagen scaffold predominately through hydrophobic interactions and hydrogen bonding. The results of this study can be used to improve our understanding of surface chemistry changes during the engineering of biomimetic scaffolds before and after biomolecule adsorption.