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
20 years after reading the famous "Maniatis" book on molecular cloning, I read an actual article from him for the first time.
"Scientists rename human genes to stop Microsoft Excel from misreading them as dates" https://www.theverge.com/2020/8/6/21355674/human-genes-rename-microsoft-excel-misreading-dates
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
Centromere-specific antibody-mediated karyotyping of Okinawan Oikopleura dioica suggests the presence of three chromosomes.
The Okinawa Institute of Science and Technology Graduate University hires to fight #COVID and develop #DNA sequencing technologies !
#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.
Mankind is still losing genes of olfaction.
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
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
A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo
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
Tagmentation of DNA/RNA hybrids!
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)...
Researcher at OIST, Okinawa, Japan — Debian Developer. My private account is @charles_plessy on framapiaf.org.
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