Data management and analysis for high-throughput DNA sequencingprojects

The rapid advances in molecular biology have begun to shift many of the bottlenecks in genome research from the laboratory to the data analysis facility. The pace at which this has occurred creates a situation in which software development always has to catch up with the flow of data. Since such large-scale processes were not anticipated, the analysis infrastructure has not been fully established. Furthermore, most systems that have been built were designed by the biologists who collected the data. More recently, computer scientists, mathematicians, and engineers have taken an interest in this problem. This has had a positive effect, since it has created a tight synergy between the informatics and the biology. Several principles affected the design of the system developed at TIGR. Each of the sample preparation, sequencing, and analysis steps had to be managed, scheduled, and tracked. This information had to be made readily available to those who needed it for carrying out their tasks. Different skill levels of the users had to be taken into account. The degree of human intervention at each step had to be evaluated and built into the design. A mixed processing environment of Macintosh and Unix platforms had to be integrated. Most importantly, the system had to save time, reduce error, and ensure uniformity of the analysis and quality of the results. In the authors' experience, the tools they have built work well because of their early decisions as to which systems to use for development. The authors settled on a robust relational database management system (Sybase) and a portable development environment (C, C++)     

Skewed oligomers and origins of replication

In pigs, induction of embryonic degeneration, by exogenous oestrogens given early in gestation, has been long recognised. However, the underlying mechanisms responsible for this degeneration remain unclear. The present study was conducted to determine whether oestrogen-induced early porcine embryonic mortality was associated with changes in the levels of tumour necrosis factor-alpha (TNF-alpha) messenger RNA in the uterine endometrium. Prepubertal gilts were induced into oestrus with PG600 and artificially inseminated at their second natural oestrus and again 24 h later. After insemination, gilts were randomly assigned to treatment and given 0.5 ml intramuscular injections of either oestradiol valerate (10 mg ml-1) or corn oil on day 9 and 10 of gestation. The gilts were slaughtered on day 12, 15 or 18 of gestation. The reproductive tract was removed from each gilt and the uterine horns were flushed to check for the presence and integrity of embryos. Samples of uterine endometrial tissues were collected, snap-frozen in liquid nitrogen and stored at -80 degrees C. Total cellular RNA was isolated from frozen tissues using a guanidine isothiocyanate-cesium chloride method. The abundance of TNF-alpha messenger RNA was determined by Northern blot hybridisation analysis. Treatment of pregnant gilts with oestrogen resulted in severe fragmentation of embryos on days 15 (2/3) and 18 (2/2), confirming the embryocidal effect of exogenous oestrogen. Uterine TNF-alpha messenger RNA level was elevated in oestrogen-treated gilts compared with controls (P < 0.05). This observation of an association between increased levels of TNF-alpha mRNA in the uterus and embryonic degeneration in oestrogen-treated gilts suggests that TNF-alpha may be involved in mediating oestrogen-induced early embryonic mortality in the pig.