<Multi_key> <1> <1> <1> : "′" Show more
I have put this line in the .XCompose file of my home directory to type the "prime" character with the UNIX compose key. In molecular biology, we use a lot this character to indicate the direction on a #DNA strand, which is either « 5′ » or « 3′ » in our jargon. While a single quote character (« ' ») is often used as an ersatz, I prefer to enjoy nice #typography. (BTW, do not forget « include "%L" » on top of the file.)
The edible ones are said to grow taller than 10 cm...
Earth Biogenome: an ambitious project to #sequence the #genome of all living species on #Earth (actually, only eukaryotes; that excludes bacteria and archaebacteria, but includes unicellular organisms like yeast). Estimated data production in 10 years: 20 petabytes, well within the capacity of scientific infrastructures. https://www.earthbiogenome.org/
🍄 One day later
Distance to nuclear speckeles measured by quantitative sequencing shows stronger transcription deeper in nucleus. Show more
Mapping 3D #genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. http://jcb.rupress.org/content/early/2018/08/27/jcb.201807108
Chen, ..., and Belmont (Univ. Illinois) just published TSA-Seq (Tyramide Signal Amplification-Sequencing). Distances between chromosome domains and nuclear #speckles are reproducible across experiments; transcriptional activity increases from periphery to center.
Using Debian packages on CentOS with the Environment Modules system Show more
I am user on a computer #cluster running #CentOS, where we have to install software by ourselves. We use the "Environment Modules" system (http://modules.sourceforge.net) to manage parallel installs of different versions. Since I am a #Debian developer, I want to use our packages when possible. In the simplest cases I just have to extract the contents with "ar p packagename.deb data.tar.xz | tar xfJ -" and then write the "modulefile".
Lots of questions about abuse/moderation on Mastodon and how it’s different from Twitter.
This article goes into detail and explains a lot of how it works here.
Some things seem different (e.g. no global search, no ‘retweet’ with comments). But once you read the rationale behind it it makes sense.
*definitely* worth reading if you’re planning on sitting around here for a while.
A yeast cell witn a single chromosome was created by Chinese researchers. Show more
#Yeast cells usually have 16 chromosomes (when they are haploid...). Shao, collaborators and Qin created a single-#chromosome yeast line, by merging all the chromosomes together using #CRISPR and homologous recombination technologies. The resulting cells are viable, but lose competition with wild type cells when cultured together. This is an impressive piece of #synthetic #biology. https://www.nature.com/articles/s41586-018-0382-x
Artificial DNA sequences used to study the shape of chromosomes. Show more
To better study the condensation of chromosomes during cell division, Muller, colleagues and Koszul have engineered an artificial region of 144,000 base pairs in a yeast #chromosome, where cleavage sites for the HiC method were evenly spaced, which ensured an "unbiased distribution of contact frequencies." Published in Molecular Systems Biology: http://msb.embopress.org/content/14/7/e8293
The scientific journal Molecular Systems Biology is introducing "Structured Methods for reproducible science", putting more effort on conveying useful reagent lists, and allowing writers to publish extensive bullet-point methods instead of the condensed narratives. Reformatting methods from bullet to condensed style was and still is a source of errors and typos. #openscience http://msb.embopress.org/content/14/7/e8556
Adiconis and co. published an analysis in Nature Methods showing that CAGE is the best method for 5'-end RNA-#sequencing. It is a nice benchmark with overall a strong design.
Our #nanoCAGE method was also tested and performed poorly in the hands of the authors. However, they used 7.5 μg of total #RNA as starting material, which is totally out of the range that we designed nanoCAGE for. Therefore, I have posted a response on #PubPeer explaining that fact.
When BLT is about beads and transposases and not bacon and tomatoes Show more
The #Nextera DNA Flex kits use bead-bound #Tn5 transposase to 1) standardise the size range of the #sequencing libraries and 2) standardise the amount yielded by the reaction (which is a crucial step before loading the #Illumina DNA sequencers). I had completely overlooked it for quite some time. I did not try it, but the idea is smart. I have not looked at the price either...
Needing a new laptop at work that can run #Microsoft Office, I was tempted to try again #Windows after more than a decade on OSX, because I am quite curious about the windows #subsystem for Linux. Unfortunately, the laptop that I wanted to buy was only available in Japanese, and despite we are in 2018 it seems that MS still sells "single-language pack" systems were English can not be installed. Thus, I am going for a Mac instead. And of course running #Linux on my main desktop. Sorry MS, you must do better!
Poster flash talks in conferences: nice idea, but it takes precious time, so I was unsure if it was worth doing it, but recently I realised that it is an excellent opportunity to show videos, which obviously can not be on the posters (at least for the moment...).
Ranting on #PubPeer about authors who did not seem to check that their introduction was still up to date before submitting their paper: https://pubpeer.com/publications/4EDEA0037B3F02198380AC1A5B3543
High-throughput homologous recombination mutagenesis in yeast with libraries of plasmids providing the DNA template for recombination and expressing a guide RNA for inducing the recombination with a CRISPR-Cas9 break: 3 papers in last week's issue of Nature Biotechnology. https://www.nature.com/nbt/volumes/36/issues/6
Transparency on scientific instruments Show more
Manuscripts co-authored by instrument makers are less trused by the readers, according to a poll of a thousand researchers made by Carsten Bergenholtz, Samuel C MacAulay, Christos Kolympiris and Inge Seim.
Since this is an incentive to hide the participation of companies to research projects, they then argue that receiving discounts on instruments in that context should be listed as potential conflict of interest.
Published in "EMBO reports": http://embor.embopress.org/content/19/6/e45853
"Preproducibility", a new word to foster reproducible research. Show more
In his commentary "Before reproducibility must come preproducibility" published in Nature this week, Philip B. Starck invents a new word to urge researchers to provide detailed instructions on how to repeat experiments. https://doi.org/10.1038/d41586-018-05256-0
This is very much in line with the "registered reports" concept fostered by BMC and other publishers. It should be an essential part of research planning.