Using Multiple Fickett Bands to Accelerate Biological Sequence Comparisons.

Most of the exact algorithms for biological sequence comparison obtain the optimal result by calculating dynamic programming (DP) matrices with quadratic time and space complexity. Fickett prunes the DP matrices by only computing values inside a band of size k, thus reducing time and space complexity to [Formula: see text]. Myers and Miller (MM) proposed a linear space algorithm that splits a sequence comparison into multiple comparisons of subsequences, using a divide-and-conquer approach. In this article, we propose a parallel strategy that combines the Fickett and MM algorithms, thus adding pruning capability to the MM algorithm. By using an appropriate Fickett band in each subsequence comparison, we can significantly reduce the number of cells computed in the DP matrices. Our strategy was integrated to stages 3 and 4 of CUDAlign, a state-of-the-art parallel tool for optimal biological sequence comparison, generating two implementations: Fickett-MM-4 and Fickett-MM-3-4. These implementations were used to compare real DNA sequences, reaching a speedup of 101.19 × in the 10 × 10 millions of base pairs comparison when compared with CUDAlign stages 3 and 4. In this case, the execution time was reduced from 71.42 to 0.7 seconds.

Expression of potassium channels is relevant for cell survival and migration in a murine bone marrow stromal cell line.

S17 is a clonogenic bone marrow stromal (BMS) cell line derived from mouse that has been extensively used to assess both human and murine hematopoiesis support capacity. However, very little is known about the expression of potassium ion channels and their function in cell survival and migration in these cells. Thus, the present study was designed to characterize potassium ion channels using electrophysiological and molecular biological approaches in S17 BMS cells. The whole-cell configuration of the patch clamp technique has been applied to identify potassium ion currents and reverse transcription polymerase chain reaction (RT-PCR) used to determine their molecular identities. Based on gating kinetics and pharmacological modulation of the macroscopic currents we found the presence of four functional potassium ion channels in S17 BMS cells. These include a current rapidly activated and inactivated, tetraethylammonium-sensitive, (IKV ) in most (50%) cells; a fast activated and rapidly inactivating A-type K + current (IK A -like); a delayed rectifier K + current (IK DR ) and an inward rectifier potassium current (IK IR ), found in, respectively 4.5%, 26% and 24% of these cells. RT-PCR confirmed the presence of mRNA transcripts for the alpha subunit of the corresponding functional ion channels. Additionally, functional assays were performed to investigate the importance of potassium currents in cell survival and migration. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide analyses revealed a reduction in cell viability, while wound healing assays revealed reduced migration potential in cells incubated with different potassium channel blockers. In conclusion, our data suggested that potassium currents might play a role in the maintenance of overall S17 cell ionic homeostasis directly affecting cell survival and migration.

The effect of prostaglandin F(2α) administration at the time of insemination on the pregnancy rate of dairy cows.

This paper addresses the question whether the pregnancy rate of dairy cows and heifers may be affected by administering prostaglandin F(2α) at the time of artificial insemination. A field trial involving 1031 dairy cows and heifers distributed to a large number of small dairy farms in an area of extensive farming in central Germany provided evidence that intramuscular administration of 25mg Dinoprost (Dinolytic(®)) at the time of insemination has no effect on pregnancy rate (61% of the cows and heifers were pregnant in both prostaglandin F(2α)-treated and saline control groups). On the other hand, deposition of 0.5mL of a 0.5mg/mL Dinoprost solution in the uterine lumen immediately after artificial insemination gave rise to a pregnancy rate of 66% as compared with 59% in saline controls. The increase in pregnancy rate of 229 prostaglandin F(2α)-treated animals (66% pregnant) over that of 226 saline controls (59% pregnant) amounted to 12%. This improvement was not statistically significant (P=0.12). Factors exerting a significant effect on pregnancy rate were parity (74% pregnancies in heifers versus 57% in cows, P<0.01 and 65% pregnancies in first parity-cows versus 55% in older cows, P<0.01) and season (57% during the barn season versus 64% during the pasture season, P<0.05), whereas length of service period, level of milk production and serum or milk progesterone level at the time of insemination did not. A follow-up trial involving more animals will have to be conducted aimed at confirming the promising results obtained by intrauterine PGF(2α) administration.

Nutritional and metabolic studies of distillable fractions from fresh and thermally oxidized corn oil and olive oil.

A semisynthetic diet containing 15% by weight of dietary fat was fed to six groups of male wistar rats for 28 days. Two groups received the distillable fraction of fresh corn oil (DCO) or fresh olive oil (DOO), two groups the distallable fractions of the thermally oxidized fats (OCO,OOO), and two groups received the respective fresh fats as controls (FCO, FOO). Substantial changes in the fatty acid composition occurred in the fats upon thermal oxidation. Only the rats that received OOO showed overt symptoms of heated fat toxicity. This was reflected in the histological scores of these animals with the liver sustaining the most numerous and severe lesions. Tissue fatty acid changes of any significance were confined largely to the polar liver lipid of the rats that were fed OCO or OOO. The results of this study would suggest that the relatively greater toxicity of OOO, compared to OCO, may in part be due to the high oleic:linoleic acid ratio of the fresh olive oil and in part to a higher tocopherol content of the corn oil.

Biochemical and histological effects of feeding thermally oxidized rapeseed oil and lard to rats.

Four groups of weanling rats were fed semisynthetic diets containing 15 percent by weight of dietary fats for 28 days. Two groups received thermally oxidized low-erucic acid rapeseed oil (OLE) or lard (OLA) and the other two groups received the respective fresh fats (FLE, FLA) as controls. Average daily feed consumption and feed efficiency were not affected by either OLE or OLA, however final body weights were depressed by the OLA in the diet. The relative heart weights and heart total lipids were significantly increased in both the OLE and OLA groups. A majority of the animals in both the OLE and OLA groups exhibited various gross symptoms attributable to heated fat toxicity such as seborrhea, diarrhea and polyuria. Excessive hair loss was noted in all the animals fed the heated fats. Tissue fatty acid changes due to OLA were confined largely to the polar liver lipids, whereas OLE produced dramatic changes in both the neutral heart lipids as well as in the neutral and polar liver lipids. Histological evaluation of the hearts, livers and kidneys indicated that OLA was very injurious to the kidneys, whereas OLE caused greater damage to both the hearts and livers.