Charles Plessy @charles_plessy@mastodon.technology

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)...

#Nature published a column about reading or replying to #emails on weekends (https://www.nature.com/articles/d41586-020-00275-2). In the past years, I started to follow a policy of not sending emails outside business hours (although this gives challenges for intercontinental communications). If I write a reply on weekends, I wait for Monday morning before sending it.

Another step forward #Nanopore #sequencing of #protein molecules: Cardozo and colls., from the Paul G. Allen School of Computer Science and Engineering, University of Washington; preprint on #bioRxiv in 2019: https://www.biorxiv.org/content/10.1101/837542v1

In this #PNAS article, Kriegman and colleagues from the #Vermont and #Tufts universities assembled artificial aggregates of #xenopus cells, and modeled them into shapes that were discovered through a computer screen for various functions. As the aggregates contain muscle cells (cardiomyocytes), some aggregates display locomotor behaviours... https://www.pnas.org/content/117/4/1853.abstract

#Video explaining how my colleagues cultivate our favorite #zooplankton Oikopleura dioica at #OIST. https://vimeo.com/376297883/e161292ddc

You live in #Tokyo and want to know about studying at #OIST, the #Okinawa Institute of Science and Technology Graduate University? Join the "OIST Café" tomorrow Saturday at 14h, in the #FabCafe. https://groups.oist.jp/grad/event/oist-cafe-10

Press releases should report scientific results in a humble way: a reminder in the journal EMBO reports. https://www.embopress.org/doi/full/10.15252/embr.201949600

Our latest work on the #mitochondrial #genetic #code in #tunicate animals is now on-line in #bioRxiv. In brief, we checked that the genetic code already described in ascidian mitochondria could be the same as for the last common ancestor of all tunicates, and found that in a subset of tunicates, the genetic code of mitochondria might have evolved later. https://www.biorxiv.org/content/10.1101/865725v1

I often heard that Python is great because in this language, “there is only one way to do it”, which means more readable etc. So I am trying to learn it. Today I read the changelog of Python 3.8, and found the walrus operator and the equal specifier for f-strings, and I feel at home like in the good old days with Perl :)

In EMBO reports this month, Hiraga and collaborators propose to that #synthetic #biology will pave the way for a better #biodegradation of PET, which is a major source of #microplastics.
https://www.embopress.org/doi/full/10.15252/embr.201949365

Ranting again on #PubPeer about authors who publish improvements of our method that are very similar to some of our own improvements that we already published to years ago, without giving us proper credit. https://pubpeer.com/publications/35AD2D17557278284574DF035EA1A1