Identification and functional characterization of ankyrin-repeat family protein ANKRA as a protein interacting with BKCa channel

Ankyrin-repeat family A protein (ANKRA) was originally cloned in mouse as an interacting protein to megalin, a member of low-density lipoprotein receptor superfamily. Here, we report that the isolation of rat ANKRA as a new binding partner for the alpha-subunit of rat large-conductance Ca2+-activated K+ channel (rSlo). We mapped the binding region of each protein by using yeast two-hybrid and in vitro binding assays. ANKRA expressed together with rSlo channels were colocalized near the plasma membrane and coimmunoprecipitated in transfected cells. We also showed that BKCa channel in rat cerebral cortex coprecipitated with rANKRA and colocalized in cultured rat hippocampal neuron. Although the coexpression of ANKRA did not affect the surface expression of rSlo, the gating kinetics of rSlo channel was significantly altered and the effects were highly dependent on the intracellular calcium. These results indicate that ANKRA could modulate the excitability of neurons by binding directly to endogenous BKCa channel and altering its gating kinetics in a calcium-dependent manner.     

Safety assessment of potential lactic acid bacteria Bifidobacterium longum SPM1205 isolated from healthy Koreans

The safety assessment of Bifidobacterium longum SPM1205 isolated from healthy Koreans and this strain's inhibitory effects on fecal harmful enzymes of intestinal microflora were investigated. The overall safety of this strain was investigated during a feeding trial. Groups of SD rats were orally administered a test strain or commercial reference strain B. longum 1 x 10(9) CFU/kg body weight/day for four weeks. Throughout this time, their feed intake, water intake and live body weight were monitored. Fecal samples were periodically collected to test harmful enzyme activities of intestinal microflora. At the end of the four-week observation period, samples of blood, liver, spleen, kidney, and gut tissues were collected to determine for hematological parameters and histological differences. The results obtained in this experiment demonstrated that four weeks of consumption of this Bifidobacterium strain had no adverse effects on rat's general health status, blood biochemical parameters or histology. Therefore, it is likely to be safe for human use. Fecal harmful enzymes such as beta-glucosidase, beta-glucuronidase, tryptophanase and urease, were effectively inhibited during the administration of the B. longum SPM1205. These results suggested that this B. longum SPM 1205 could be used for humans as a probiotic strain.     

Prevalence of putative periodontopathogens in subgingival dental plaques from gingivitis lesions in Korean orthodontic patients

The objective of this study was to detect and compare the presence of periodontopathogens in the subgingival plaques of gingivitis lesions in adults who wore fixed orthodontic appliances, as opposed to adults who did not wear any orthodontic appliances. Thirty-six individuals participated in this study. Nineteen of these subjects did not wear any orthodontic appliances, and these subjects comprised the control group. The other 17 individuals had been wearing fixed orthodontic appliances for at least 3 months each. After a periodontal examination, we collected subgingival plaque samples from the gingivitis lesions of each patient. Using PCR based on 16S rDNA, we detected the presence of 6 putative periodontopathogenic species, Treponema denticola, Porphyromonas gingivalis, Tannerella forsythia (formerly Bacteroides forsythus), Prevotella nigrescens, Prevotella intermedia, and Actinobacillus actinomycetemcomitans. With regard to the presence of individual periodontopathogens, we found that T. forsythia, T. denticola, and P. nigrescens were significantly more common in the samples obtained from the orthodontic patients than in the samples obtained from the non-orthodontic patient controls. Our results indicate that the local changes associated with the wearing of fixed orthodontic appliances may affect the prevalence of periodontopathogens in subgingival dental plaques.     

Design of a description language for generating wrapper to collect biological data

The biological data are scattered in various areas with various formats and they are changing continuously. Therefore, data integration becomes an important issue to provide researcher a dynamic access of data. In the data integration process, the method of extracting heterogeneous data dynamically from the data source is an essential part. Data extraction method using wrapper can provide flexibility and extensibility to an integration system.     

A memory-efficient algorithm for multiple sequence alignment with constraints

MOTIVATION: Recently, the concept of the constrained sequence alignment was proposed to incorporate the knowledge of biologists about structures/functionalities/consensuses of their datasets into sequence alignment such that the user-specified residues/nucleotides are aligned together in the computed alignment. The currently developed programs use the so-called progressive approach to efficiently obtain a constrained alignment of several sequences. However, the kernels of these programs, the dynamic programming algorithms for computing an optimal constrained alignment between two sequences, run in (gamman2) memory, where gamma is the number of the constraints and n is the maximum of the lengths of sequences. As a result, such a high memory requirement limits the overall programs to align short sequences only. RESULTS: We adopt the divide-and-conquer approach to design a memory-efficient algorithm for computing an optimal constrained alignment between two sequences, which greatly reduces the memory requirement of the dynamic programming approaches at the expense of a small constant factor in CPU time. This new algorithm consumes only O(alphan) space, where alpha is the sum of the lengths of constraints and usually alpha < n in practical applications. Based on this algorithm, we have developed a memory-efficient tool for multiple sequence alignment with constraints. AVAILABILITY: http://genome.life.nctu.edu.tw/MUSICME.     

Rapid PCR confirmation of E. coli O157:H7 after evanescent wave fiber optic biosensor detection

Escherichia coli O157:H7 is an enteric pathogen of public health importance, which is monitored by several government agencies. Many rapid detection tests have been developed to identify foodstuff and water supplies contaminated by E. coli O157:H7. However, these methods can be time consuming (24-48 h) due to the need to culture the bacteria to confirm detection results. Fiber optic biosensors can rapidly detect pathogens from complex matrices, yet confirmation tests can take up to 10h to complete. In addition, fiber optic biosensors can also be used to reduce the impact of PCR inhibitors present in complex matrices such as food and water. This paper presents methodologies to reduce the time necessary for confirmation from 10 to about 2 h, by direct PCR of bacteria from the fiber optic waveguides without the need for culture or enrichment steps.