Charles Plessy @charles_plessy@mastodon.technology

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

In #PNAS today: “Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes”, from Rausell, collaborators and Abel, of the #Necker hospital and other research institutions, shows that among 166 genes that appear to be often lost or non-functional in people's genomes, 41 are #olfactory receptors. Quel dommage. https://www.pnas.org/content/117/24/13626

#Aphids have a specific gene family, called "Ya" by its discoverers, which they inject as #RNA in their host plant in a way that increases their performance. Published this week in #PNAS by Chen, Singh, and their colleagues from the Department of #Crop #Genetics, John Innes Centre, #Norwich, UK. https://www.pnas.org/content/117/23/12763

Impressive laser sheet imaging and 3D modelling of giant Bathochordaeus tunicates living in the deep #sea. Here is a link to the news article at the #Monterey Bay Aquarium Research Institute https://www.mbari.org/deep-piv-3d-flow/

I just remembered how awesome is #RIKEN's #ZENBU #genome browser and its #stream processing module. https://zenbu-wiki.gsc.riken.jp/zenbu/wiki/index.php/Data_Stream_Processing

Oxford #Nanopore Technologies is releasing "LamPORE", an assay for sequencing the SARS coronavirus 2. The "LamP" in the name means that the method is "isothermal", which in practice means that only a heat block is needed to process the sample instead of an expensive PCR machine. This is one more step forward having virus detection at the "point of care" instead of in laboratories. Even before #COVID-19, the industry has been working hard for this in the past decades (for flu, etc.) https://nanoporetech.com/covid-19/lampore

Kudos to Li and coll. from the Chinese Academy of Sciences, who submitted to peer review on November 6 2019 an article with a method to reduce the cost of sequencing #coronavirus in bats, where they wrote "Active surveillance is both urgent and essential to predict and mitigate the emergence of bat-origin CoV in humans and livestock." https://msphere.asm.org/content/5/1/e00807-19

#RIKEN and other research institutes in #Japan are developing faster tests to detect the #coronavirus. https://japantoday.com/category/tech/Riken-Kanagawa-Pref-create-test-to-detect-coronavirus-in-30-minutes

Webpage of #Japan's ministry of health “About #Coronavirus Disease 2019 (#COVID-19) ”. https://www.mhlw.go.jp/stf/seisakunitsuite/bunya/newpage_00032.html

This is an article published this week by Nakamori, Panigrahi and their collaborators in Nature Genetics, where they show a small drug designed to force (CAG)n repeats to form stable hairpins, which causes these repeats to reduce their size. This is important because expansion of these repeats is part of the mechanism causing Huntington's disease. https://www.nature.com/articles/s41588-019-0575-8

In #PNAS today: researchers from Beijing and their collaborators have managed to use the Tn5 transposase to "tagment" #DNA/#RNA hybrids (https://www.pnas.org/content/117/6/2886). When we tried in my previous laboratory, we either could not make it work or did not realise it works, because as seen in the paper's supplemental figures 9 and 10, the difference of the size profile before and after reaction is easy to miss (compared with DNA/DNA tagmentation)...