A parallel computing algorithm for 16S rRNA probe design

A constrained interpolation profile (CIP) method has been developed to solve 2-D water entry problems. This paper presents the further development of the numerical method using staggered grids and a parallel computing algorithm. In this work, the multi-phase slamming problems, governed by the Navier-Stokes (N-S) equations, are solved by a CIP-based finite difference method. The interfaces between different phases (solid, water and air) are captured using density functions. A parallel computing algorithm based on the Message Passing Interface (MPI) method and the domain decomposition scheme was implemented to speed up the computations. The effect of decomposition scheme on the solution and the speed-up were studied. Validation studies were carried out for the water entry of various 2-D wedges and a ship section. The predicted slamming force, pressure distribution and free surface elevation are compared with experimental results and other numerical results.

Download Full-text

Differential sensitivity of 16S rRNA targeted oligonucleotide probes used for fluorescence in situ hybridization is a result of ribosomal higher order structure

Canadian Journal of Microbiology ◽

10.1139/m96-136 ◽

1996 ◽

Vol 42 (10) ◽

pp. 1061-1071 ◽

Cited By ~ 39

Author(s):

Marc E. Frischer ◽

Peter J. Floriani ◽

Sandra A. Nierzwicki-Bauer

Keyword(s):

In Situ Hybridization ◽

16S Rrna ◽

Fluorescence In Situ Hybridization ◽

Differential Sensitivity ◽

Probe Design ◽

Oligonucleotide Probes ◽

Whole Cells ◽

Gene Probes ◽

Wide Range

The use of 16S rRNA targeted gene probes for the direct analysis of microbial communities has revolutionized the field of microbial ecology, yet a comprehensive approach for the design of such probes does not exist. The development of 16S rRNA targeted oligonucleotide probes for use with fluorescence in situ hybridization (FISH) procedures has been especially difficult as a result of the complex nature of the rRNA target molecule. In this study a systematic comparison of 16S rRNA targeted oligonucleotide gene probes was conducted to determine if target location influences the hybridization efficiency of oligonucleotide probes when used with in situ hybridization protocols for the detection of whole microbial cells. Five unique universal 12-mer oligonucleotide sequences, located at different regions of the 16S rRNA molecule, were identified by a computer-aided sequence analysis of over 1000 partial and complete 16S rRNA sequences. The complements of these oligomeric sequences were chemically synthesized for use as probes and end labeled with either [γ-32P] ATP or the fluorescent molecule tetramethylrhodamine-5/-6. Hybridization sensitivity for each of the probes was determined by hybridization to heat-denatured RNA immobilized on blots or to formaldehyde fixed whole cells. All of the probes hybridized with equal efficiency to denatured RNA. However, the probes exhibited a wide range of sensitivity (from none to very strong) when hybridized with whole cells using a previously developed FISH procedure. Differential hybridization efficiencies against whole cells could not be attributed to cell wall type, since the relative probe efficiency was preserved when either Gram-negative or -positive cells were used. These studies represent one of the first attempts to systematically define criteria for 16S rRNA targeted probe design for use against whole cells and establish target site location as a critical parameter in probe design.Key words: 16S rRNA, oligonucleotide probes, in situ hybridization.

Download Full-text