Determining Nannochloropsis cell wall and more
Nannochloropsis’ whole cells were recently analysed using 13C-SS-NMR spectroscopy (reference n 1). Cells were grown autotrophically in a sodium [13C] bicarbonate environment and harvested during the exponential phase.
Quantitative spectra of 13C labelled cells of Nannochloropsis oculata were analysed for resonance picks which are characteristic of carbohydrates and lipids, thus providing, among other interesting observations, useful insights on the cell wall composition of the microalga.
Need nice pics and images for your presentation?
A collection of microalgae cultures at CSIRO Marine Research. Image released by CSIRO under Creative Commons Attribution license http://scienceimage.csiro.au/tag/algae/i/1938/microalgae-collection/
The Commonwealth Scientific and Industrial Research Organization (CSIRO) has just released its Scientific Image Library under a Creative Commons Licence.
Among the many available pictures and images a small section is also dedicated to the microalgal collection of the institute. Following this link you can browse and freely download useful high quality images for lectures, reports and blog posts.
Do not forget that various collection of high quality images released under Creative Common licence already exist and some of them contain images and pictures of microalgae. For instance The Wikimedia Commons Scientific Images Collection. Don’t forget that you can easily upload your pictures and images of Nannochloropsis to the wikimedia commons collection too, as I did some time ago: https://en.wikipedia.org/wiki/File:NannochloropsisMinusNitrogenNileRed.jpg
New data on lipid accumulation in Nannochloropsis
We have already discussed in a previous post two possible models of cellular metabolism that can account for oil accumulation
and that are in agreement with the profile of transcript and protein abundance in Nannochloropsis‘ cultures that accumulate lipids. New experimental data became recently available for the scientific community concerning this issue. Jing Li and coworkers performed a time course experiment, tracking simultaneously transcript abundance and lipid content of Nannochloropsis cultures grown in N sufficient (+N) and N depleted (-N) media. The data and their analysis were published on Plant Cell (doi: http://dx.doi.org/10.1105/tpc.113.121418). Full reference is reported at the end of this post (reference n 1).
Access to N.gaditana B-31 data through the NCBI
After manual review by the NCBI experts, the genomic data of Nannochloropsis gaditana B-31 are now indexed in the NCBI databases and are accessible through the NCBI web interface and through the NCBI search tools (e.g. blast).
The genomes of the nucleus and of the organelles and the complete annotation of the genomic sequences are registered as bioproject PRJNA170989 ID: 170989, and can be accessed through the following links:
http://www.ncbi.nlm.nih.gov/bioproject/170989 ;
http://www.ncbi.nlm.nih.gov/nuccore/585113370
The sequencing data used to assembly of the genomes were also submitted to the NCBI SRA database and are available for consulting and download. You can find the data of: a fragment library of Nannochloropsis gaditana B-31 whole genomic DNA (i.e. includes DNA from the nucleus and from the organelles) sequenced using 454FLX Titanium XL sequencing kit, 2 half plates (http://www.ncbi.nlm.nih.gov/sra/SRX390591); a mate pair library of Nannochloropsis gaditana B-31 whole genomic DNA with an insert size of 1.5-3Kb sequenced using the SOLiD 3 Plus sequencing kit, half plate (http://www.ncbi.nlm.nih.gov/sra/SRX390674); a mate pair library of Nannochloropsis gaditana B-31 whole genomic DNA with an insert size of 3-5Kb sequenced using the SOLiD 3 Plus sequencing kit, half plate (http://www.ncbi.nlm.nih.gov/sra/SRX390681). Note that details about the biosamples and about the experiments are linked o the data.
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New features on the Bibliography section
We added a new feature to the Bibliography: “Altmetric donuts” close to each publication listed in the page.
What are the Article Level metrics (Altmetric) ?
Altmetrics give a measure of the digital impact and reach of an article by combining a selection of online indicators (both scholarly and non-scholarly) . They do this by tracking, collecting and measuring large amounts of data collected from all of the places where people talk about science online – for example, blogs, Twitter, Facebook, Google+, message boards and mainstream newspapers and magazines. Altmetric allows authors and publishers to see what people are saying about a scholarly paper and can tell them how much attention a paper is receiving relative to their peers.
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Proteomics and transcriptomics findings on lipids accumulation in Nannochloropsis
Confocal microscopy image of Nannochloropsis cell grown in nitrogen deprivation. Lipid droplets are in yellow and chloroplast is in red. From “Going ultra deep to unravel the secret recipe of biofuel” by Elisa Corteggiani Carpinelli
What is the mechanism by which Nannochloropsis cells synthesise and accumulate lipids in certain culturing conditions? And moreover is there a key control that we can manipulate to improve lipid yields and overcome the tradeoff between lipid production and growth? This is probably the “holy grail” of Nannochloropsis research. The general feeling is that we do not have an answer yet, but at least we have some clues to start our quest.
FTP area updated
We updated our FTP area, now including datasets from other Nannochloropsis species and strains and the list of families of orthologous proteins obtained from the comparison of N. gaditana and N. oceeanica predicted proteins.
Families of orthologous proteins: file type
N.gaditanaB-31|Naga_100019g47.1 N.gaditanaCCMP526|Nga20827 nudix hydrolase;
Even though the differences and the imprecisions of the various gene predictions probably play a major role in the determination of the differences among the two species, a close look at the lists of proteins that are putatively assigned as characteristic of each species my reserve interesting surprises!
References
- Corteggiani Carpinelli, E. et al. “Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion.” Molecular Plant (2014) 7 (2): 323-335.doi: 10.1093/mp/sst120
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Proteomics and transcriptomics findings on Nitrogen stress respons in Nannochloropsis
Nannochloropsis cultivated in normal growth condition and deprived of a nitrogen source continues growing for at least 4–5 days.
Analyses of the gene expression and of the protein abundance in nitrogen scarcity, reveal that Nannochloropsis activates mechanisms for nitrogen assimilation and redistribution to allow survival through a partial reorganisation of the cellular metabolism.
This figure reports the model of the response to nitrogen deprivation elaborated by Corteggiani Carpinelli et al. (2013).
DEGRADATIVE PROCESSES
Various genes involved in controlled degradation of proteins are over-expressed in the cells grown in nitrogen deprivation, including: cullin (Naga_100070g1), which is responsible for protein ubiquitination; ubiquitin-specific protease (Naga_100587g2); proteases (Naga_100611g3, Naga_100098g23, Naga_100015g80.1); endopeptidase Naga_101780g1); aminopeptidase (Naga_100024g51) and two autophagy-related proteins (Naga_101823g1 and Naga_100732g4), which are likely involved in the formation of cytosolic sequestering vesicles used for degradation and recycling of cellular components.
The proteomic study shows that the relative abundance of one subunit of the protein degrading complex (Proteasome subunit alpha) increases in nitrogen starvation supporting the evidence that processes of protein degradation are activated in response to nitrogen starvation. The analysis of protein abundance also suggests that in nitrogen starvation autophagy is induced. Indeed the abundance of a receptor-mediated endocytosis protein slightly increases and also that of two vacuolar proton pump subunits. These data, together with morfological observations, support the hypothesis that upon nitrogen deprivation the organelles are degraded in the vacuoles through a process of controlled autophagy.
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