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|Paper: PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components||
Another brick pulled from the wall concealing the mechanism of genetic compensation. Nonsense-mediated decay appears again.
Ma Z, Zhu P, Shi H, Guo L, Zhang Q, Chen Y, Chen S, Zhang Z, Peng J, Chen J. PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components. Nature. 2019;[Epub ahead of print] doi:10.1038/s41586-019-1057-y
|Wednesday, April 3, 2019 - 11:38|
|mutant-morphant disagreement in zebrafish - a story||
Here is a story of mutant-morphant disagreement in zebrafish and its effects on one investigator's research. http://thenode.biologists.com/dead-ends-in-research-can-be-new-beginnings/research/
|Tuesday, April 2, 2019 - 11:11|
|Antisense delivery enhancement strategies: meta-analysis||
Comparison of enhancements to antisense delivery (peptides, dendrimers, etc.)
Assisted delivery of antisense therapeutics in animal models of heritable neurodegenerative and neuromuscular disorders: a systematic review and meta-analysis.
van der Bent ML, Paulino da Silva Filho O, van Luijk J, Brock R, Wansink DG.
Sci Rep. 2018 Mar 8;8(1):4181. doi: 10.1038/s41598-018-22316-7.
|Tuesday, March 26, 2019 - 08:54|
|Photo-Morpholinos: no longer a displayed product line||
We are removing Photo-Morpholinos as a displayed product line. Photo-Morpholinos are hard to use - we have made many but they have led to few publications. Any Photo-Morpholino project involves far more interation and development time than a simple Morpholino knockdown; there are many parameters that need to be optimized and several Photo-Morpholino sequences will likely need to be tested. Labs have ordered them without the funding needed to purchase multiple oligos to fine-tune the system sufficiently to get good data; we end up with disgruntled customers.
|Friday, February 15, 2019 - 14:45|
|Letter to Editor: Morpholino-Mediated Gene knockdown in Zebrafish: It's All About Dosage and Validation||
Morpholino-Mediated Gene knockdown in Zebrafish: It's All About Dosage and Validation.
Van Gils M, Vanakker OM.
J Invest Dermatol. 2019 Jan 29. pii: S0022-202X(19)30042-9. doi: 10.1016/j.jid.2019.01.017. [Epub ahead of print] No abstract available.
This is a discussion of specificity and p53-mediated effects in the context of a reply to a commentary on a recent paper.
|Monday, February 4, 2019 - 11:03|
|Review of DMD therapies for restoring dystrophin expression||
Restoring Dystrophin Expression in Duchenne Muscular Dystrophy: Current Status of Therapeutic Approaches.
Shimizu-Motohashi Y, Komaki H, Motohashi N, Takeda S, Yokota T, Aoki Y.
J Pers Med. 2019 Jan 7;9(1). pii: E1. doi: 10.3390/jpm9010001. Review.
|Thursday, January 10, 2019 - 08:26|
|Essay: "Knockdowns versus knockouts: why the phenotypic difference?"||
Here is an essay by Dani Wijesinghe entitled "Knockdowns versus knockouts: why the phenotypic difference?" from 2016.
Her last line: "No matter how blinding it may be to the current genetic reductionist paradigm, to close curtains on one of the few windows through which light is coming is to leave us in the dark."
|Thursday, December 6, 2018 - 11:01|
|Knockdown causing stress response (Lai et al. 2018): my response to a good study||
In the Lai et al. 2018 preprint from Didier Stainier's group, Morpholino knockdown of vegfaa showed no stress gene response. This demonstrates that the stress gene upgregulation seen with knockdown of egfl7 and some other transcripts is not a response to the Morpholino backbone but a response to the loss of the target's expression. The Robu et al.
|Friday, November 30, 2018 - 12:26|
|Phosphorothioates, Morpholinos and cellular changes||
Here is a discussion of protein interactions and other cellular changes caused by phosphorothioate oligos that are not seen with Morpholinos.
Flynn LL, Li R, Aung-Htut MT, Pitout IL, Cooper J, Hubbard A, Griffiths L, Bond C, Wilton SD, Fox AH, Fletcher S. Interaction of modified oligonucleotides with nuclear proteins, formation of novel nuclear structures and sequence-independent effects on RNA processing. bioRxiv. 2018:446773[Preprint] doi:10.1101/446773
|Tuesday, October 23, 2018 - 12:35|
|How I really feel about five-mispair oligos||
I try to send this message with any designs involving five-mispair oligos. A brief version is farther down.
** Argument for using a different specificity control instead of the five-mispair
|Wednesday, September 26, 2018 - 11:46|