MRI diffusion-based filtering: a note on performance characterisation

Frequently MRI data is characterised by a relatively low signal to noise ratio (SNR) or contrast to noise ratio (CNR). When developing automated Computer Assisted Diagnostic (CAD) techniques the errors introduced by the image noise are not acceptable. Thus, to limit these errors, a solution is to filter the data in order to increase the SNR. More importantly, the image filtering technique should be able to reduce the level of noise, but not at the expense of feature preservation. In this paper we detail the implementation of a number of 3D diffusion-based filtering techniques and we analyse their performance when they are applied to a large collection of MR datasets of varying type and quality

Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, <i>Nannochloropsis oceanica</i> CCMP1779

Utilization of microalgae has been hampered by limited tools for creating loss-of-function mutants. Furthermore, modified strains for deployment into the field must be free of antibiotic resistance genes and face fewer regulatory hurdles if they are transgene free. The oleaginous microalga, <i>Nannochloropsis oceanica</i> CCMP1779, is an emerging model for microalgal lipid metabolism. We present a one-vector episomal CRISPR/Cas9 system for <i>N. oceanica</i> that enables the generation of marker-free mutant lines. The CEN/ARS6 region from <i>Saccharomyces cerevisiae</i> was included in the vector to facilitate its maintenance as circular extrachromosal DNA. The vector utilizes a bidirectional promoter to produce both Cas9 and a ribozyme flanked sgRNA. This system efficiently generates targeted mutations, and allows the loss of episomal DNA after the removal of selection pressure, resulting in marker-free nontransgenic engineered lines. To test this system, we disrupted the nitrate reductase gene (<i>NR</i>) and subsequently removed the CRISPR episome to generate nontransgenic marker-free nitrate reductase knockout lines (NR-KO)

Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, <i>Nannochloropsis oceanica</i> CCMP1779

Utilization of microalgae has been hampered by limited tools for creating loss-of-function mutants. Furthermore, modified strains for deployment into the field must be free of antibiotic resistance genes and face fewer regulatory hurdles if they are transgene free. The oleaginous microalga, <i>Nannochloropsis oceanica</i> CCMP1779, is an emerging model for microalgal lipid metabolism. We present a one-vector episomal CRISPR/Cas9 system for <i>N. oceanica</i> that enables the generation of marker-free mutant lines. The CEN/ARS6 region from <i>Saccharomyces cerevisiae</i> was included in the vector to facilitate its maintenance as circular extrachromosal DNA. The vector utilizes a bidirectional promoter to produce both Cas9 and a ribozyme flanked sgRNA. This system efficiently generates targeted mutations, and allows the loss of episomal DNA after the removal of selection pressure, resulting in marker-free nontransgenic engineered lines. To test this system, we disrupted the nitrate reductase gene (<i>NR</i>) and subsequently removed the CRISPR episome to generate nontransgenic marker-free nitrate reductase knockout lines (NR-KO)

Nontransgenic Marker-Free Gene Disruption by an Episomal CRISPR System in the Oleaginous Microalga, <i>Nannochloropsis oceanica</i> CCMP1779

Utilization of microalgae has been hampered by limited tools for creating loss-of-function mutants. Furthermore, modified strains for deployment into the field must be free of antibiotic resistance genes and face fewer regulatory hurdles if they are transgene free. The oleaginous microalga, <i>Nannochloropsis oceanica</i> CCMP1779, is an emerging model for microalgal lipid metabolism. We present a one-vector episomal CRISPR/Cas9 system for <i>N. oceanica</i> that enables the generation of marker-free mutant lines. The CEN/ARS6 region from <i>Saccharomyces cerevisiae</i> was included in the vector to facilitate its maintenance as circular extrachromosal DNA. The vector utilizes a bidirectional promoter to produce both Cas9 and a ribozyme flanked sgRNA. This system efficiently generates targeted mutations, and allows the loss of episomal DNA after the removal of selection pressure, resulting in marker-free nontransgenic engineered lines. To test this system, we disrupted the nitrate reductase gene (<i>NR</i>) and subsequently removed the CRISPR episome to generate nontransgenic marker-free nitrate reductase knockout lines (NR-KO)

MOESM3 of Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata

Additional file 3: Figure S2. Incubation of N. oceanica cells in the environmental photobioreactor (ePBR)

MOESM6 of Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata

Additional file 6: Figure S5. Maps of the plasmids used for the generation of N. oceanica DGTT5-overexpressing strains

MOESM4 of Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata

Additional file 4: Figure S3. Cell growth and biomass in the environmental photobioreactor (ePBR)

MOESM1 of Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata

Additional file 1: Table S1. Lipid and fatty acid contents of Mortierella fungi incubated in different media (mg g−1 total dry weight)

MOESM8 of Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata

Additional file 8: Table S2. Predicted genes and proteins involved in fatty acid and glycerolipid synthesis in M. elongata AG77

MOESM7 of Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata

Additional file 7: Figure S6. Increasing triacylglycerol content in N. oceanica by the overexpression of N. oceanica DGTT5 encoding acyl-CoA:diacylglycerol acyltransferase DGTT5