People are having fun with #peptides and #MassSpectrometry. Using 6 different proteases, peptide coverage of human proteins dramatically increased. This allowed observation of translation from alternative spliced transcripts and an estimation of the potential deleterious effect of SNPs in coding sequences.

As expected, inclusion of a stop codon led to a lack of detection of peptides originating from transcripts degraded by #NMD.

Fantastic resource.

https://www.nature.com/articles/s41587-023-01714-x

Discussie over MPG / MKI

Er is een fundamentele discussie over aannames bij MPG/MKI berekeningen nodig: De Nationale Milieudatabase (NMD) meldde afgelopen week dat de warmtepomp zó slecht scoort qua milieuimpact, dat nieuwe gebouwen amper nog zouden voldoen aan de MPG eisen. (link)

De oorzaak

http://www.passievoorsystemen.nl/2023/03/aannames-bij-mpg-mki-berekeningen/

#Duurzaamheid #Economie #Techniek #berekenen #innovatie #MKI #model #modellen #MPG #Nationalemilieudatabase #NMD

Ohh, we do like a New Module Day... Even though there's no space left in the Palette.

What to remove? Time for another session of #ModularTetris!

#NMD

#AfterLaterAudio ENVy

Eurorack: the fun moneysink. Funnysink. 🤣

W00t! It's #NMD (New Modules Day)
Happy Nerding FX-Aid and Doepfer Sequential Switch.

YUM!

Thanks also to Elevator Sound (Bristol) for their customary efficiency and generally friendly vibe!

Ócio leva ao vício: Nos Mínimos Detalhes nº12, Mês dos CRIA! Tagmar, Guia de Regras Resumidas https://ociolevaaovicio.blogspot.com/2022/12/nos-minimos-detalhes-n12-mes-dos-cria.html #drpgbr #JIP #MêsdosCRIA #NMD #resenha #Tagmar #vídeo

Ócio leva ao vício: Nos Mínimos Detalhes nº12, Mês dos CRIA! Tagmar, Guia de Regras Resumidas https://ociolevaaovicio.blogspot.com/2022/12/nos-minimos-detalhes-n12-mes-dos-cria.html #drpgbr #JIP #MêsdosCRIA #NMD #resenha #Tagmar #vídeo

Pre-mRNA splicing patterns cannot be accurately defined from total RNA data, unless degradation pathways are inactive. An example, using NMD inactivation (wondering to what extent nuclear degradation could be also involved ?):

https://pubmed.ncbi.nlm.nih.gov/35264448/

#RNAsplicing #nmd #ribosome

Ócio leva ao vício: Nos Mínimos Detalhes nº10, Mês dos CRIA! Arcana Primária https://ociolevaaovicio.blogspot.com/2022/12/nos-minimos-detalhes-n10-mes-dos-cria.html #ArcanaPrimária #JIP #MêsdosCRIA #NMD #resenha #RVG #vídeo

Ócio leva ao vício: Nos Mínimos Detalhes nº10, Mês dos CRIA! Arcana Primária https://ociolevaaovicio.blogspot.com/2022/12/nos-minimos-detalhes-n10-mes-dos-cria.html #ArcanaPrimária #JIP #MêsdosCRIA #NMD #resenha #RVG #vídeo

Ócio leva ao vício: Nos Mínimos Detalhes nº9, Mês dos CRIA! Camaleão https://ociolevaaovicio.blogspot.com/2022/12/nos-minimos-detalhes-n9-mes-dos-cria.html #JIP #Genérico #Camaleão #MêsdosCRIA #NMD #resenha #vídeo

Doddie Weir has died. A sad day for the #Scotland #rugby community, the wider rugby world and #NMD campaigners

Soffor Weir has died. A sad day for the #Scotland #rugby community, the wider rugby world and #NMD campaigners

Went on #wikipedia to see what information about #NMD can be found there. Many, many things are missing, while ridiculously detailed descriptions of pathology linked with NMD perturbation are present. Changing the page: a new goal for the winter holidays.

https://en.m.wikipedia.org/wiki/Nonsense-mediated_decay

#science #ribosome #RNAdegradation

#NMD is a complex process in which RNAs get degraded more or less efficiently, but only if they were read by a ribosome. The number of factors involved in this conserved pathway and the fact that the degradation occurs co-translationally in large RNPs precluded in vitro reconstitutions and in depth mechanistic studies.

We wrote a review about the complexity of RNA degradation through NMD, current issues with published results and perspectives:

https://pubmed.ncbi.nlm.nih.gov/35266563/

#ribosome #molecular

#NMD is a complex process in which RNAs get degraded more or less efficiently, but only if they were read by a ribosome. The number of factors involved in this conserved pathway and the fact that the degradation occurs co-translationally in large RNPs precluded, for the moment, in vitro reconstitutions and in depth mechanistic studies.

We wrote a review about the complexity of RNA degradation through NMD, current issues with published results and perspectives:

https://pubmed.ncbi.nlm.nih.gov/35266563/

#NMD is an RNA degradation pathway that should be taken into account whenever we look at transcripts reaching the cytoplasm of eukaryotic cells. Especially if those transcripts do not have an obvious coding part. Short, randomly present open reading frames are perfectly capable of troubling ribosomes and trigger #RNAdegradation through NMD (#lncRNAs, I'm looking at you).

#RNA biology

#NMD is an RNA degradation pathway that should be taken into account whenever we look at transcripts reaching the cytoplasm of eukaryotic cells. Especially if those transcripts do not have an obvious coding part. Short, randomly present open reading frames are perfectly capable of troubling ribosomes and trigger #RNAdegradation through NMD (#lncRNAs, I'm looking at you).

@jamespblloyd
Thanks for the links. Maybe there is no simple rule to explain when and how RNAs become #NMD substrates. In the paper, the addition of the repeats (1.6kb) led to NMD destabilization of transcripts in both yeast and mammalian cells.

What is very clever is the tethering of variants of Pab1 or Pabp1 that no longer bind poly(A) to the modified RNA, which led to loss of the NMD status.

Btw - it's great to interact on Mastodon to talk about #RNA!