Category Archives: ADVANCES IN

SOLID SOFTWARE

After the sequencing with SOLiD, the original sequence of color coding will be accumulated. According to double-base coding matrix, the origi­nal color sequence can be decoded to get the base sequence if we knew the base types for one of any position in the sequence. Because of a kind of color corresponding four base pair, the color coding of the […]

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DISCUSSION

Oleaginous microalgae can accumulate large quantities of lipid under stress inducing growth conditions, making them a target organism for sustainable liquid biofuel production. In the present study, we induced TAG production and accumulation in N. oleoabundans through nitrogen deprivation, and investigated the expression of genes involved in TAG production at the transcriptome level. Mapping reads to the assembled and annotated […]

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INTEGRATION OF MULTIPLE ANNOTATION DATABASES

The Algal Functional Annotation Tool integrates annotation data from the biological knowledge bases listed in Table 1. Publically available flat files containing annotation data were downloaded and parsed for each individual resource. Chlamydomonas reinhardtii proteins were assigned KEGG pathway annotations by means of sequence similarity to proteins within the KEGG genes database [1]. MetaCyc [2], Reactome [28], and Panther [30] […]

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FUTURE DIRECTIONS

As with all tools that integrate data from multiple external sources, the power of analysis using the Algal Functional Annotation Tool is ultimately limited by the quality of the annotations within the primary databases. With the steady growth of knowledge in these annotation databases, the utility of the analyses provided is expected to increase in the future as more biologi­cal […]

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ILLUMINA GA/HISEQ SYSTEM

In 2006, Solexa released the Genome Analyzer (GA), and in 2007 the company was purchased by Illumina. The sequencer adopts the technol­ogy of sequencing by synthesis (SBS). The library with fixed adaptors is denatured to single strands and grafted to the flowcell, followed by bridge amplification to form clusters which contains clonal DNA fragments. Before sequencing, the library splices into […]

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TRANSCRIPTOME RESPONSE OF N. OLEOABUNDANS TO NITROGEN LIMITATION

A primary physiological response to nitrogen limitation is a decrease in cell growth, as observed with the three times reduction in N. oleoabun­dans growth rate. The transcript profile of nitrogen-starved N. oleoabundans clearly reflects the decrease in cell proliferation and stressed physiological status of the cells. Gene ontology terms related to cellular growth, photo­synthesis, and protein machinery are significantly suppressed […]

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ASSIGNMENT OF ANNOTATION FROM ARABIDOPSIS THALIANA

To extend the terms associated with C. reinhartdii genes, functional terms were inferred by homology to the annotation set of the plant Arabidop — sis thaliana (thale cress). Identification of orthologous proteins was based on sequence similarity and subsequent filtering of the results by retain­ing only mutual best hits between the two sets of protein sequences. The corresponding Arabidopsis thaliana […]

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TRANSCRIPTOMIC ANALYSIS OF THE OLEAGINOUS MICROALGA NEOCHLORIS OLEOABUNDANS REVEALS METABOLIC INSIGHTS INTO TRIACYLGLYCERIDE ACCUMULATION

HAMID RISMANI-YAZDI, BERAT Z. HAZNEDAROGLU, CAROL HSIN, and JORDAN PECCIA 12.1 BACKGROUND Important advantages of microalgae-based biofuels over first generation biofuels include algae’s greater solar energy conversion efficiency com­pared to land plants [1], the ability of oleaginous microalgae to utilize non-arable land and saline or waste-water, and their high content of energy dense neutral lipids that can be readily transesterified […]

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HISEQ SOFTWARE

HiSeq control system (HCS) and real-time analyzer (RTA) are adopted by HiSeq 2000. These two softwares could calculate the number and position of clusters based on their first 20 bases, so the first 20 bases of each se­quencing would decide each sequencing’s output and quality. HiSeq 2000 uses two lasers and four filters to detect four types of nucleotide (A, […]

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THE REGULATION OF FATTY ACID AND TAG BIOSYNTHESIS AND SUPPLY OF PRECURSORS

While under nitrogen deprivations, there has been considerable uncertain­ty expressed whether the increase in TAG content is due to a reduction in the mass of the cell, rather than increase in TAG production [2]. Both the measured increase in TAG content per cell dry weight reported here (which accounted for the loss of cell mass during nitrogen limitation), and the […]

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