Charles Plessy @charles_plessy@mastodon.technology

Speed fluctuations of bacterial replisomes. I am co-author in this #bioRxiv preprint. In this work, three #OIST units joined their forces to produce experimental data of #DNA abundance in exponentially growing Escherichia coli, and to formulate a #theory that permits to infer the #dynamics of replisomes from the DNA abundance distribution. Big congratulations to my colleagues Deepak and Simone who lead that work.

Just gave a presentation on R packaging this morning in a mini-course at #OIST. Our slides are here: https://github.com/Rafael-Ayala/R-packages-minicourse #rstats

In #PNAS today, an article from the University of #Birmingham, using the BstNI enzyme to nick a #DNA oligonucleotide annealed to the #RNA of the SARS-CoV-2 #virus (causing #COVID19) produce the trigger for detection under 10 min with an #isothermal exponential amplification system called #EXPAR. https://www.pnas.org/content/118/35/e2100347118

The #Interdisciplinary #Postdoctoral Scholar #Fellowship (IPSF) program provides a unique opportunity to advance researchers' academic careers by conducting full-time #interdisciplinary research and training at the #Okinawa Institute for #Science and #Technology (#OIST). Follow this link to apply: https://apply.interfolio.com/75577

Scientists are being judged – and too much – on their publication list, and on their contribution to these publications. Often, there is more than one person who was essential to the work.

I disagree with the negative image given to co-first authorship in this career feature article in the Nature journal. Co-first authorship is a win, not a loss. Employers who consider shared authorship as lessening someone's contribution are wrong. https://www.nature.com/articles/d41586-021-01574-y

Learn more about the #PhDProgram at the #Okinawa Institute of #Science and #Technology Graduate University (#OIST) in our #NetCafé today! https://groups.oist.jp/grad/event/oist-cafe-online-202106

Join us to study #plankton genomes!

Our research unit is #hiring a post-doctoral researcher to study #Plankton #genomics at #OIST (#Okinawa Institute of Science and Technology Graduate University). https://www.oist.jp/careers/postdoctoral-researcher-plankton-genomics-luscombe-unit

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.