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1.  OMACC: an Optical-Map-Assisted Contig Connector for improving de novo genome assembly 
BMC Systems Biology  2013;7(Suppl 6):S7.
Genome sequencing and assembly are essential for revealing the secrets of life hidden in genomes. Because of repeats in most genomes, current programs collate sequencing data into a set of assembled sequences, called contigs, instead of a complete genome. Toward completing a genome, optical mapping is powerful in rendering the relative order of contigs on the genome, which is called scaffolding. However, connecting the neighboring contigs with nucleotide sequences requires further efforts. Nagarajian et al. have recently proposed a software module, FINISH, to close the gaps between contigs with other contig sequences after scaffolding contigs using an optical map. The results, however, are not yet satisfying.
To increase the accuracy of contig connections, we develop OMACC, which carefully takes into account length information in optical maps. Specifically, it rescales optical map and applies length constraint for selecting the correct contig sequences for gap closure. In addition, it uses an advanced graph search algorithm to facilitate estimating the number of repeat copies within gaps between contigs. On both simulated and real datasets, OMACC achieves a <10% false gap-closing rate, three times lower than the ~27% false rate by FINISH, while maintaining a similar sensitivity.
As optical mapping is becoming popular and repeats are the bottleneck of assembly, OMACC should benefit various downstream biological studies via accurately connecting contigs into a more complete genome.
PMCID: PMC4029551  PMID: 24564959
de novo genome assembly; gap closer; optical map; contig graph
2.  Effect of culture conditions on growth, lipid content, and fatty acid composition of Aurantiochytrium mangrovei strain BL10 
AMB Express  2012;2:42.
This study explored the influence of various culture conditions on the biomass, lipid content, production of docosahexaenoic acid (DHA), and fatty acid composition of Aurantiochytrium mangrovei strain BL10. The variables examined in this study include the species and concentration of salt, the concentrations of the two substrates glucose and yeast extract, the level of dissolved oxygen, the cerulenin treatment, and the stages of BL10 growth. Our results demonstrate that BL10 culture produces maximum biomass when salinity levels are between 0.2 and 3.0%. Decreasing salinity to 0.1% resulted in a considerable decrease in the biomass, lipid content, DHA production, and DHA to palmitic acid (PA) (DHA/PA) ratio, signifying deterioration in the quality of the oil produced. The addition of 0.9% sodium sulfate to replenish salinity from 0.1% to 1.0% successfully recovered biomass, lipid content and DHA production levels; however, this also led to a decrease in DHA/PA ratio. An increase in oxygen and cerulenin levels resulted in a concomitant decrease in the DHA to docosapentaenoic acid (DPA) (DHA/DPA) ratio in BL10 oil. Furthermore, the DHA/DPA and DHA/PA ratios varied considerably before and after the termination of cell division, which occurred around the 24 hour mark. These results could serve as a foundation for elucidating the biochemistry underlying the accumulation of lipids, and a definition of the extrinsic (environmental or nutritional) and intrinsic (cell growth stage) factors that influence lipid quality and the production of DHA by BL10.
PMCID: PMC3485123  PMID: 22883641
Lipid; Polyunsaturated fatty acid (PUFA); Docosahexaenoic acid (DHA); Aurantiochytrium mangrovei; Thraustochytrid

Results 1-2 (2)