FASTPAT: a fast and efficient algorithm for string searching in DNA sequences

A new string searching algorithm is presented aimed at searchingfor the occurrence of character patterns in longer charactertexts. The algorithm, specifically designed for nucleic acidsequence data, is essentially derived from the Boyer –Moore method (Comm. ACM, 20, 762 – 772, 1977). Both patternand text data are compressed so that the natural 4-letter alphabetof nucleic acid sequences is considerably enlarged. The stringsearch starts from the last character of the pattern and proceedsin large jumps through the text to be searched. The data compressionand searching algorithm allows one to avoid searching for patternsnot present in the text as well as to inspect, for each pattern,all text characters until the exact match with the text is found.These considerations are supported by empirical evidence andcomparisons with other methods.     

WORDUP: an efficient algorithm for discovering statistically significant patterns in DNA sequences.

We present here a fast and sensitive method designed to isolate short nucleotide sequences which have non-random statistical properties and may thus be biologically active. It is based on a first order Markov analysis and allows us to detect statistically significant sequence motifs from six to ten nucleotides long which are significantly shared (or avoided) in the sequences under investigation. This method has been tested on a set of 521 sequences extracted from the Eukaryotic Promoter Database (2). Our results demonstrate the accuracy and the efficiency of the method in that the sequence motifs which are known to act as eukaryotic promoters, such as the TATA-box and the CAAT-box, were clearly identified. In addition we have found other statistically significant motifs, the biological roles of which are yet to be clarified.     

SIMD parallelization of the WORDUP algorithm for detecting statistically significant patterns in DNA sequences

The development of new techniques in sequencing nucleic acidshas produced a great amount of sequence data and has led tothe discovery of new relationships. In this paper, we studya method for parallelizing the algorithm WORDUP, which detectsthe presence of statistically significant patterns in DNA sequences.WORDUP implements an efficient method to identify the presenceof statistically significant oligomers in a nonhomologous groupof sequences. It is based on a modified version of the Boyer-Moorealgorithm, which is one of the fastest algorithms for stringmatching available in the literature. The aim of the parallelversion of WORDUP presented here is to speed up the computationaltime and allow the analysis of a greater set of longer nucleotidesequences, which is usually impractical with sequential algorithms.     

<Emphasis Type="Italic">Bifidobacterium adolescentis</Emphasis> (DSM 20083) and <Emphasis Type="Italic">Lactobacillus casei</Emphasis> (Lafti L26-DSL): Probiotics Able to Block the In Vitro Adherence of Rotavirus in MA104 Cells

Rotavirus is the leading worldwide cause of gastroenteritis in children under five years of age. Even though there are some available vaccines to prevent the disease, there are limited strategies for challenging diarrhea induced by rotavirus infection. For this reason, researchers are constantly searching for other approaches to control diarrhea by means of probiotics. In order to demonstrate the ability of some probiotic bacteria to interfere with the in vitro rotavirus infection in MA104 cells, strains of Lactobacillus sp. and Bifidobacterium sp. were tested in MA104 cells before the viral infection. As a preliminary assay, a blocking effect treatment was performed with viable bacteria. In this screening assay, four of initial ten bacteria showed a slight reduction of the viral infection (measured by percentage of infection). L. casei (Lafti L26-DSL), L. fermentum(ATCC 9338), B. adolescentis (DSM 20083), and B. bifidum (ATCC 11863) were used in further experiments. Three different treatments were tested in order to evaluate protein-based metabolites obtained from mentioned bacteria: (i) cell exposure to the protein-based metabolites before viral infection, (ii) exposure to protein-based metabolites after viral infection, and (iii) co-incubation of the virus and protein-based metabolites before viral infection to the cell culture. The best effect performed by protein-based metabolites was observed during the co-incubation assay of the virus and protein-based metabolites before adding them into the cell culture. The results showed 25 and 37% of infection in the presence of L. casei and B. adolescentis respectively. These results suggest that the antiviral effect may be occurring directly with the viral particle instead of making a blocking effect of the cellular receptors that are needed for the viral entrance.     

In Vitro Assessment of Probiotic Potential of Saccharomyces Cerevisiae DABRP5 Isolated from Bollo Batter,a Traditional Goan Fermented Food

Bollo is a traditional Goan fermented food in which coarse wheat/wheat and finger millet is leavened with toddy. We here isolated 42 yeast strains from Bollo batter. Initial screening of the isolates with probiotic properties yielded four yeast isolates (DABRP1, DABRP2, DABRP5 and DABRP12). These isolates exhibited tolerance to high bile salt concentration and acidic pH and resistance to various antibiotics, which indicated their probiotic nature. All these yeast isolates were identified as Saccharomyces cerevisiae through D1D2-LSU-rDNA sequencing. These yeast isolates also showed higher percent hydrophobicity towards chloroform followed by n-hexadecane and o-xylene indicating their mucosal surface-adhesive property. To evaluate the safety of the isolates for them to be called as generally recognized as safe, the pathogenic behavior of the isolates determined through the in vitro hemolysis assay and evaluation of DNase and gelatinase activities. None of the isolates exhibited hemolysis or produced DNase or gelatinase and thus were considered potentially safe. In terms of beneficial effects, the most potent isolate S. cerevisiae DABRP5 showed antibacterial activity against the test pathogens. It also showed excellent antioxidant activity with DPPH free radical scavenging activity of 68.85 ± 0.69%, anti-inflammatory activity with 60.39 ± 0.34% inhibition of protein denaturation, and antidiabetic activity with 71.75 ± 0.45% inhibition of α-amylase activity. The isolate produced α-amylase, lipase, and β-galactosidase. The probiotic potential of the isolate S. cerevisiae DABRP5 was similar to that of the reference strain (Saccharomyces boulardii CNCM I-745) used in this study. The results thus indicate that yeast isolates from Bollo batter have probiotic potential.

     

Youthful Vigor and Mature Realism in Ceramic Studies

The Emergence of Pottery: Technology and Innovation in Ancient Societies. William K. Barnett and John W. Hoopes. eds. Smithsonian Series in Archaeological Inquiry. Washington, DC: Smithsonian Institution Press, 1996. 286 pp.
The Social Dynamics of Pottery Style in the Early Puebloan Southwest. Michelle Hegmon. Cortez, CO. Crow Canyon Archaeological Center (distributed by University of Arizona Press), 1995. 272 pp.