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Determining Nannochloropsis cell wall and more

cell_wall_schemeNannochloropsis’ 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.

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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/

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

 

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).

NCBI banner

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) ?

Altmetric donut

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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FTP area updated

Misc-Download-iconWe 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.

We’re looking for new authors and contributors

BloggerBirdStackBooksAre you an expert about Nannochloropsis? Is your research focused on this organism?

Consider becoming a new author of this blog and contributing to the scientific discussion!

Why don’t you start with advertising your recent publication or commenting on the posts of this blog?

Is there any hot topic that you would like to discuss or any suggestion that you would like to ask to this scientific community?

Fill this form and we will be happy to consider you application as new author

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Thank you!

We currently have more than 1.000 unique visitors per month, accounting for roughly 18,000 pageviews per month. Visitors are spread across the four continents…  Thank you for keeping alive Nannochloropsis.org. We are doing our best to update this site and we are also preparing new resources (to be released soon).

This week’s visits

 

Annotation file available

Upon user request we uploaded the GFF version of Nannochloropsis gaditana annotation. This file is in standard GFF3 format, and features refers to the assembled genome (i.e. scaffolds).

You can download the file from the Nannochloropsis genome FTP area.

Paper online

Our paper “Chromosome scale genome assembly and transcriptome profiling of Nannochloropsis gaditana in nitrogen depletion” is online.
You can access it from the Publisher’s website.

Help us keeping Nannochloropsis web resource up to date and advertise your paper!

Now available an on line form to share your findings with the Nanncohloropsis scientific community!

By completing the on line form you will advertise your paper through our Bibliography page and you will signal to the “nannochloropsis.org” personell how to update the databases integrating your new findings!

We will integrate your data as soon as possibile. And we will be pleased to open a discussion on your new findings in this blog with your help!