Category Archives: ADVANCES IN

FUNCTIONAL TERM ENRICHMENT TESTING

The hypergeometric distribution is commonly used to determine the sig­nificance of functional term enrichment within a list of genes. In this test, the occurrence of a functional term within a gene list is compared to the background level of occurrence across all genes in the genome to deter­mine the degree of enrichment. A p-value based on this test can be […]

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MAJOR BIOMOLECULE CONTENT AND COMPOSITION DIFFER BETWEEN THE NITROGEN REPLETE (+N) AND NITROGEN-LIMITED (-N) GROWTH ENVIRONMENTS

To track gene transcription in the oleaginous microalga N. oleoabundans, cells were first grown under+N and — N conditions as a method to pro­duce differential cellular enrichments of TAGs. Cells were harvested after 11 days. This sampling time corresponded to below detection level con­centrations for NO3- and a reduction in growth rate in the -N reactors (Fig­ure 1A, B). The […]

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LIPID TURNOVER

In our study, several genes encoding enzymes involved in the intracel­lular breakdown of fatty acids and lipids are significantly repressed under — N (Table 3). Repressing p-oxidation is a clear strategy for maintaining a higher concentration of fatty acids within a cell. In contrast, most of the identified lipases (with the exception of triacylglycerol lipases) are overexpressed during nitrogen limitation. […]

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DYNAMIC VISUALIZATION OF KEGG PATHWAY MAPS

Individual pathway maps from KEGG provide information on protein localization within the cell, compartmentalization into different cellular components, or of reactions within a larger metabolic process. Visualiza­tion of proteins from gene lists onto pathway maps is useful for their in­terpretation. The Algal Functional Annotation Tool utilizes the publicly available KEGG application programming interface (API) for pathway highlighting. The information linking […]

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DE NOVO TRANSCRIPTOME ASSEMBLY, ANNOTATION, AND EXPRESSION

In order to produce statistically reliable and comparable RNA-Seq data, cDNA library construction and sequencing was performed for each of the duplicate+N reactors, and each of the duplicate — N reactors. Over 88 mil­lion raw sequencing reads were generated and subjected to quality score and length based trimming; resulting in a high quality (HQ) read data set of 87.09 million […]

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BIOREACTOR EXPERIMENTS

N. oleoabundans (UTEX # 1185) was obtained from the Culture Collec­tion of Algae at the University of Texas (UTEX, Austin, TX, USA). Batch cultures were started by inoculation with 106 log growth phase cells into 1 liter glass flasks filled with 750 ml of Modified Bold-3 N medium [49] without soil extract. The concentration of nitrogen in the medium was […]

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INTEGRATION OF EXPRESSION DATA

The expression levels of C. reinhardtii genes have been experimentally characterized under numerous conditions using high-throughput methods such as RNA-seq [[26,27], unpublished data (Castruita M., et al.)]. These expression data were compiled and analyzed to determine which genes are over — and under-expressed in each experimental condition. The expres­sion data was preprocessed to normalize the counts for uniquely mappable reads […]

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LIPID CONTENT IN MICROALGAE

Many microalgae are capable of accumulating a large amount of lipids in the cells [10]. On average, the lipid contents typically range from 10 to 30% of dry weight (Table 3). Depending on the specific algae species and their cultivation conditions, however, microalgal lipid production may range widely from 2 to 75% [2]. In some extreme cases, it can reach […]

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