Interactive DNA sequence and structure design for DNA nanoapplications

DNA sequence and structure design is very important for DNA nanoapplications. A computer-aided design tool is needed for exploring DNA sequence and structure of interests before experimental synthesis, which is a time- and labor-consuming process. In this paper, an interactive DNA sequence and structure design software tool called DNA shop is proposed and implemented. The visualization tool can generate DNA structures by specifying, selecting, and moving DNA sequences around and display corresponding structures. Using the tool, DNA sequence and structure can be visually inspected in three-dimensional space before experimental studies.     

Analysis of electromagnetic radiation from a video output amplifierinside a monitor by using FDTD method

The finite-difference time-domain (FDTD) method is used to analyze the electromagnetic compatibility and interference (EMC and EMI) problems due to the electromagnetic radiation from a video output amplifier located inside a computer monitor. The multiple grid technique is implemented in the FDTD method to improve the computational efficiency. The video output amplifier is modeled by a rectangular iron container with an equivalent dipole antenna located at the center of one opened wall facing the cathode-ray-tube (CRT). The coupled electric fields inside and outside the monitor are calculated. It is found that higher values of coupled electric fields occur near the monitor screen. It is also found that the coupled electric fields outside the CRT region drop sharply in amplitude. Simulation results of coupled electric fields at a distance of 3 m from the monitor screen also comply with the FCC regulations. Calculation results also agree with the experimental data for coupled electric fields outside the monitor screen at a measured distance of 3 m     

The yeast PRP19 protein is not tightly associated with small nuclear RNAs, but appears to associate with the spliceosome after binding of U2 to the pre-mRNA and prior to formation of the functional spliceosome

We have previously shown that the yeast PRP19 protein is associated with the spliceosome during the splicing reaction by immunoprecipitation studies with anti-PRP19 antibody. We have extended such studies by using extracts depleted of specific splicing factors to investigate the step of the spliceosome assembly process that PRP19 is involved in. PRP19 was not associated with the splicing complexes formed in U2- or U6-depleted extracts but was associated with the splicing complex formed in heat-inactivated prp2 extracts. This finding indicates that PRP19 becomes associated with the splicing complexes after or concomitant with binding of the U6 small nuclear ribonucleoprotein particle (snRNP) to the precursor RNA and before formation of the functional spliceosome. We further analyzed whether PRP19 is an integral component of snRNPs. We have constructed a strain in which an epitope of nine amino acid residues recognized by a well-characterized monoclonal antibody, 12CA5, is linked to the carboxyl terminus of the wild-type PRP19 protein. Immunoprecipitation of the splicing extracts with anti-PRP19 antibody or precipitation of the extracts prepared from the epitope-tagged strain with the 12CA5 antibody did not precipitate significant amounts of snRNAs. Addition of micrococcal nuclease-treated extracts to the PRP19-depleted extract restored its splicing activity. These results indicate that PRP19 is not tightly associated with any of the snRNAs required for the splicing reaction. No non-snRNP protein factor has been demonstrated to participate in either step of the spliceosome assembly pathway that PRP19 might be involved in. Thus, PRP19 represents a novel splicing factor.     

Quantum nondemolition filters

This is the second of two papers concerned with the formulation of a continuous-time quantum-mechanical filter. In the first paper, the invertibility of a quantum system coupled to a weak time-dependent classical field was studied. The physical system is modelled as an infinite-dimensional bilinear system. Necessary and sufficient conditions for invertibility were derived under the assumption that the output observable is a quantum nondemolition observable (QNDO), characterized by the classical property that its expected value is equal to its measured value. In this paper necessary and sufficient conditions are developed for an observable to qualify as a QNDO; if in addition the criteria for invertibility are met, the given observable defines a quantum nondemolition filter (QNDF). The associated filtering algorithm thus separates cleanly into the choice of output observable (a QNDO) and the choice of procedure for processing the measurement outcomes. This approach has the advantage over previous schemes that no optimization is necessary. Applications to demodulation of optical signals and to the detection and monitoring of gravitational waves are envisioned.Research supported in part by the National Science Foundation under Grant Nos. ECS-8017184, INT-7902976 and DMR-8008229 and by the Department of Energy under Contract No. DE-AC01-79ET-29367.     

Physicochemical properties of dry matter and starch from potatoes grown in Canada

In this study dry matter and starch were isolated from three potato cultivars (AC Stempede Russet, Russet Burbank and Karnico) grown at two locations (Fredericton and Benton) in New Brunswick, Canada. The chemical composition including total starch, dietary fibre, free glucose and protein content in potato dry matter and apparent amylose and total phosphorus content in potato starch were determined. Differential scanning calorimetry (DSC) was used to determine the thermal properties of gelatinization and retrogradation of potato dry matter and starch. The pasting properties of potato dry matter and starch were investigated by rapid visco analyzer (RVA). The resistant starch measurement method was employed to evaluate the digestibility in vitro of native and gelatinized potato starch. Molecular characteristics including chain length and chain length distribution of potato starch were also analyzed using high performance anion exchange chromatography (HPAEC). The analytical results suggest that differences in chemical composition and molecular chain length of potato starch may contribute to different functional properties of potato dry matter and starch of individual cultivars.