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.
The N704/S507 index pair considered harmful on MiSeq seqeuencers.
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
Relatives of rubella virus [found] in diverse mammals.
Biosynthesis of medicinal tropane alkaloids in yeast
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
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
Researcher at OIST, Okinawa, Japan — Debian Developer. My private account is @charles_plessy on framapiaf.org.
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