Yeast/E. coli shuttle vectors with multiple unique restriction sites

Two yeast/E. coli shuttle vectors have been constructed. The two vectors, YEp351 and YEp352, have the following properties: (1) they can replicate autonomously in Saccharomyces cerevisiae and in E. coli; (2) they contain the beta-lactamase gene and confer ampicillin resistance to E. coli; (3) they contain the entire sequence of pUC18; (4) all ten restriction sites of the multiple cloning region of pUC18 including EcoRI, SacI, KpnI, SmaI, BamHI, XbaI, SalI, PstI, SphI and HindIII are unique in YEp352; these sites are also unique in YEp351 except for EcoRI and KpnI, which occur twice; (5) recombinant plasmids with DNA inserts in the multiple cloning region of YEp351 and YEp352 can be recognised by loss of beta-galactosidase function in appropriate E. coli hosts; (6) YEp351 and YEp352 contain the yeast LEU2 and URA3 genes, respectively, allowing for selection of these auxotrophic markers in yeast and E. coli; (7) both plasmids are retained with high frequency in yeast grown under non-selective conditions indicative of high plasmid copy number. The above properties make the shuttle vectors suitable for construction of yeast genomic libraries and for cloning of DNA fragments defined by a large number of different restriction sites. The two vectors have been further modified by deletion of the sequences necessary for autonomous replication in yeast. The derivative plasmids YIp351 and YIp352 can therefore be used to integrate specific sequences into yeast chromosomal DNA.     

Crossover to Fermi-Liquid Behavior at Lowest Temperatures in Pure CeNi2Ge2

We present a low temperature study of the nearly antiferromagnetic heavy Fermion compound CeNi₂Ge₂ including specific heat measurements in magnetic fields up to 13 T, resistivity, magnetization, DC- and AC- susceptibility measurements down to 30 mK. The results show that, although the system is close to a quantum critical point, CeNi₂Ge₂ exhibits Fermi-liquid behavior below approximately 300 mK. At higher temperatures hyperscaling indicates the existence of strong coupling spin fluctuations responsible for the observed non-Fermi-liquid properties.     

Selective optical detection of aromatic vapors

A sensitive layer system of amorphous Teflon AF on silver has been coated on a glass substrate. With a monochromatic light source the reflectivity of the layer system as a function of the angle of incidence exhibits the surface-plasmon resonance as well as a set of leaky-mode resonances. These optical resonance phenomena are sensitive to small refractive-index changes that may be induced by diffusion of particles into the Teflon AF layer. On the basis of this effect, the aromatic vapors benzene; toluene; and o-, p-, and m-xylene have been investigated with different vapor concentrations. By selection of a distinct angle at a particular resonance, dynamic measurements can be performed. Assuming a diffusion process in accordance with Fick's law, the diffusion profile can be calculated as a function of time. As described by the Lorentz-Lorenz relation a refractive-index profile is induced that consequently interacts with the electromagnetic fields of the optical modes. With the function of the diffusion-induced refractive-index profile the shift of the resonance lines can be calculated from the measured reflectivity change as a function of time. The characteristic diffusion coefficients of the particular vapor allow for a distinction between the different types of aromate, even between the different xylenes.     

Robust DNA microarray image analysis

DNA microarrays are an increasingly important tool that allow biologists to gain insight into the function of thousands of genes in a single experiment. Common to all array-based approaches is the necessity to analyze digital images of the scanned DNA array. The ultimate image analysis goal is to automatically quantify every individual array element (spot), providing information about the amount of DNA bound to a spot. Irrespective of the quantification strategy, the preliminary information to extract about a spot includes the mapping between its location in the digital image and its possibly distorted position in the spot array (gridding). We present a gridding approach divided into a spot-amplification step (matched filter), a rotation estimation step (Radon transform), and a grid spanning step. Quantification of the spots is performed by robustly fitting of a parametric model to pixel intensities with the help of M-estimators. The main advantage of parametric spot fitting is its ability to cope with overlapping spots. If the goodness-of-fit is too bad, a semiparametric spot fitting is employed. We show that our approach is superior to simple quantification strategies such as averaging of the pixel intensities. The system was extensively tested on 1740 images resulting from two DNA libraries.Received: 15 June 2001, Accepted: 21 July 2002, Published online: 3 June 2003 Correspondence to: Norbert Brändle     

Deformation-morphology correlations in electrically conductive carbon nanotube—thermoplastic polyurethane nanocomposites

Addition of small amounts (0.5-10 vol%) of multiwall carbon nanotubes (CNT) to thermoplastic elastomer Morthane produced polymer nanocomposites with high electrical conductivity (σ∼1-10 S/cm), low electrical percolation (?∼0.005) and enhancement of mechanical properties including increased modulus and yield stress without loss of the ability to stretch the elastomer above 1000% before rupture. In situ X-ray scattering during deformation indicated that these mechanical enhancements arise not only from the CNTs, but also from their impact on soft-segment crystallization. The deformation behavior after yielding of the nanocomposites, irrespective of CNT concentration, is similar to the unfilled elastomer, implying that the mechanistics of large deformation is mainly governed by the matrix. The relative enhancement of the Young's modulus of the nanocomposites is comparable to other elastomeric nanocomposites, implying that to the first order specific chemical details of the elastomeric system is unimportant.     

Current status of the Cincinnati GCL test plots

This paper describes the design, layout, construction and current status on the performance of fourteen full scale test plots targeted at assessing the internal shear strength of GCLs in landfill cover applications. Five different commercially available GCLs from four manufacturers were used in the study. Each test plot is two geosynthetic clay line roll widths wide, with lengths of 29m (95 ft) on the 3(H)-to-1(V) (horizontal-to-vertical) slopes and 20m (67 ft) on the 2(H)-to-1(V) (horizontal-to-vertical) slopes. The plots are being monitored with numerous deformation ‘telltales’ as well as subgrade and GCL moisture gages.

Two slides occurred shortly after construction. Both involved the upper surfaces of the GCLs against the overlying textured geomembranes. The slides were clearly the result of bentonite lubricated interfaces and (although of interest) did not relate to the internal shear strength focus and goals of the project.

Upon inducing internal shear stress in the GCLs by cutting all of the overlying geosynthetics, the deformations have been small except for one plot. This plot involved a unreinforced bentonite GCL, sandwiched between two geomembranes. It was sampled and found to have a large region of unexpected and excessively high moisture content. Subsequently, the test plot slid, the interface being the upper geomembrane against the bentonite of the GCL. The test plot was constructed a second time and the current response is more in keeping with the anticipated behaviour. Other than these slides, however, all of the other GCL plots appear to be stable.

If the internal stability of the GCLs continue, it can be assumed that the 2(H)-to-1(V) slopes have a factor-of-safety of 1.0 or greater. This being the case, the 3(H)-to-1(V) slopes have a factor-of-safety of 1.5 or greater. While this hypothesis is still being substantiated, it speaks well for the internal shear strength of the GCLs used in the study when properly installed. The project is ongoing as of, the writing of this paper.     

Perfluorinated acids in Arctic snow: new evidence for atmospheric formation

Perfluorinated acids (PFAs) are ubiquitously found in water and biota, including remote regions such as the High Arctic. Under environmental conditions, PFAs exist mainly as anions and are not expected to be subject to long-range atmospheric transport in the gas phase. Fluorinated telomer alcohols (FTOHs) are volatile and can be atmospherically oxidized to form perfluorocarboxylic acids. Analogously, fluorosulfamido alcohols can be oxidized to form perfluorooctane sulfonate (PFOS). High Arctic ice caps experience contamination solely from atmospheric sources. By examining concentrations of PFAs in ice cap samples, it is possible to determine atmospheric fluxes to the Arctic. Ice samples were collected from high Arctic ice caps in the spring of 2005 and 2006. Samples were concentrated using solid-phase extraction and analyzed by LC-MS-MS. PFAs were observed in all samples, dating from 1996 to 2005. Concentrations were in the low-mid pg L(-1) range and exhibited seasonality, with maximum concentrations in the spring-summer. The presence of perfluorodecanoic acid (PFDA) and perfluoroundecanoic acid (PFUnA) on the ice cap was indicative of atmospheric oxidation as a source. Ratios of PFAs to sodium concentrations were highly variable, signifying PFA concentrations on the ice cap were unrelated to marine chemistry. Fluxes of the PFAs were estimated to the area north of 65 degrees N for the 2005 season, which ranged from 114 to 587 kg year(-1) for perfluorooctanoic acid (PFOA), 73 to 860 kg year(-1) for perfluorononanoic acid (PFNA), 16 to 84 kg year(-1) for PFDA, 26 to 62 kg year(-1) for PFUnA, and 18 to 48 kg year(-1) for PFOS. The PFOA and PFNA fluxes agreed with FTOH modeling estimations. A decrease in PFOS concentrations through time was observed, suggesting a fast response to changes in production. These data suggest that atmospheric oxidation of volatile precursors is a primary source of PFAs to the Arctic.