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Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina

Algal Research

Lane, Todd L.; Lane, Pamela L.; Williams, Kelly P.; Wilkenfeld, Joshua S.; Solberg, Owen D.; Fuqua, Zachary B.; Cornelius, Nina G.; Gillespie, Shaunette; Samocha, Tzachi M.; Carney, Laura T.

Productivity of algal mass culture can be severely reduced by contaminating organisms. It is, therefore, important to identify contaminants, determine their effect on productivity and, ultimately, develop countermeasures against such contamination. In the present study we utilized microbiome analysis by second-generation sequencing of small subunit rRNA genes to characterize the predator and pathogen burden of open raceway cultures of Nannochloropsis salina. Samples were analyzed from replicate raceways before and after crashes. In one culture cycle, we identified two algivorous species, the rotifer Brachionus and gastrotrich Chaetonotus, the presence of which may have contributed to the loss of algal biomass. In the second culture cycle, the raceways were treated with hypochlorite in an unsuccessful attempt to interdict the crash. Our analyses were shown to be an effective strategy for the identification of the biological contaminants and the characterization of intervention strategies.

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TYPE Journal Article YEAR 2016
DOIOSTIScopus

Peregrine: A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material

RNA Biology

Langevin, Stanley A.; Bent, Zachary B.; Solberg, Owen D.; Curtis, Deanna J.; Lane, Pamela L.; Williams, Kelly P.; Schoeniger, Joseph S.; Lane, Todd L.; Sinha, Anupama S.

Use of second generation sequencing (SGS) technologies for transcriptional profiling (RNA-Seq) has revolutionized transcriptomics, enabling measurement of RNA abundances with unprecedented specificity and sensitivity and the discovery of novel RNA species. Preparation of RNA-Seq libraries requires conversion of the RNA starting material into cDNA flanked by platform-specific adaptor sequences. Each of the published methods and commercial kits currently available for RNA-Seq library preparation suffers from at least one major drawback, including long processing times, large starting material requirements, uneven coverage, loss of strand information and high cost. We report the development of a new RNA-Seq library preparation technique that produces representative, strand-specific RNA-Seq libraries from small amounts of starting material in a fast, simple and cost-effective manner. Additionally, we have developed a new quantitative PCR-based assay for precisely determining the number of PCR cycles to perform for optimal enrichment of the final library, a key step in all SGS library preparation workflows. © 2013 Landes Bioscience.

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TYPE Journal Article YEAR 2013
OSTIScopus
Results 26–50 of 71
Results 26–50 of 71