Charles Plessy @charles_plessy@mastodon.technology

Our research on the #genome of the #Oikopleura #zooplankton in #Okinawa is finally published in #BMC Genomics! https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07512-6

#Faculty positions open in "#Quantum Information Science and #Engineering", "#Artificial #Intelligence", "Molecular and #Cell #Biology" and other areas at #OIST, the #Okinawa Institute of #Science and #Technology Graduate University. Application deadline: April 30th. https://groups.oist.jp/facultypositions

Great to read advocacy the #Unix command-line in the scientific journal #Nature. By the way,

awk -F, '{ if ($4 > 50) print $0 }'

can be shortened to

awk -F, '$4 > 50''

Link to the article: https://www.nature.com/articles/d41586-021-00263-0

“Guidance on software citation created by the community for the community”, a blog post about the work of the #FORCE11 #Software #Citation Implementation Working Group.

https://blog.f1000.com/2021/01/26/guidance-on-software-citation-created-by-the-community-for-the-community/

4-figures pre-prints show the ambition of their authors but their most important information in in the “supplemental” material.

The Science festival of #OIST will be held online this January 30th.
https://sciencefest.oist.jp/

I was reading about "hardware-agnostic" code in a research article. According to Wiktionary, "agnostic" comes from Greek and stands for "ignorant". But Wiktionary also tells us that "ignorant" comes from Latin (via French) and means "unknowing". If we would replace words from our #vocabulary such as "agnostic" with simpler words like "unknowing", would it make #science more accessible to all? I do not know.

Good catch from Hirose and colleagues, published in the journal "DNA research" this year. This particular combination of #Illumina indexes might have partial self-complementarity that would be detrimental to cluster generation on #MiSeq DNA sequencers. https://academic.oup.com/dnaresearch/article/27/4/dsaa017/5893952

Our work on analysing the activity the of human papillomavirus (#HPV) in patient samples using quantitative cDNA sequencing was finally published ! Our “#nanoCAGE” method focuses on the start (5′) sequences of the molecules to precisely locate the DNA regions that are active during HPV infection. It also easily discriminates between different HPV variants, allowing us to study co-infections. https://doi.org/10.1038/s41598-020-75133-2

Importantly, part of this discovery started as an effort to study #coronavirus in #bat before the 2019 pandemic started. The other part of the discovery was made by studying sick animals in a #zoo. Published recently in Nature (https://doi.org/10.1038/s41586-020-2812-9).

Some essential medicines still can only be extracted natural plants. This causes problems of supply chain and industrial #farming. Srinivasan and Smolke, from Stanford University, published last month in Nature an engineered #yeast with no less than 34 #genome modifications, that achieves the #biosynthesis of hyoscyamine and scopolamine. They estimate that “sourcing sugar from sugarcane would require at least 10-fold less land”. https://www.nature.com/articles/s41586-020-2650-9

We finished to assemble the #genome of the local population of the #zooplankton #Oikopleura dioica near #OIST on the #Okinawa island. We used #Nanopore sequencers and it allowed to assemble whole chromosomes into single contigs. Our preprint is available in #bioRxiv: https://www.biorxiv.org/content/10.1101/2020.09.11.292656v1 Our results open the way to interesting comparisons with related populations, to better understand species #diversity in the #Ocean.

A #sociology study of #synthetic biologists using laboratory #automation. https://journals.sagepub.com/doi/10.1177/0162243919893757

A roadmap to the next major version of the #yeast #synthetic #genome: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02130-z

The article demonstrates trans-splicing of nematode and trypanosome splice leaders in mammalian cells. (https://doi.org/10.1038/360692a0). "Trans-splicing" is the molecular basis for the #operon gene structure in eukaryotic cells.

Receiving #ZIP archives from your favourite funding agency with filenames encoded in Shift_JIS? Thanks to "Ask Ubuntu" I found out that "The Unarchiver" https://theunarchiver.com/ can convert them on the fly. https://askubuntu.com/questions/935022/how-to-unzip-a-japanese-zip-file-and-avoid-mojibake-garbled-characters

#soft #robot https://www.pnas.org/content/117/30/17571

Our latest work is now available before peer-review on #F1000Research. #Oikopleura is the animal #plankton that we are studying at #OIST. Its #genome is tiny and therefore its chromosomes are difficult to visualise. For that reason, we needed to make these experiments to confirm their number.

#OIST's DNA #sequencing section hires one Testing and Sequencing Specialist and one R&D and Sequencing Specialist. #Okinawa is a very nice place to live, and has been relatively safe from covid with no cases for a month. And OISTs facilities are, in one word, fantastic.

https://www.oist.jp/careers/testing-and-sequencing-specialist

https://www.oist.jp/careers/rd-and-sequencing-specialist