Websites (and some papers) about morphant and mutant comparisons

I've been watching several websites with discussions of morphant and mutant comparisons. Here are links to the sites. The comments sections have been very supportive of Morpholino technology. I'll update this page as I find more.

The Node
Out with the old, in with the new: reassessing morpholino knockdowns in light of genome editing technology
August 6th, 2014
Stefan Schulte-Merker and Didier Y. R. Stainier
http://thenode.biologists.com/out-with-the-old-in-with-the-new-reassessi...

PubPeer
"Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution"
Feb 23rd, 2015
https://pubpeer.com/publications/AA3A9AB44B044BC25BA5252EAC6023#fb26053

Biotechniques
Mutants vs. Morphants
May 2nd, 2015
Rachael Moeller Gorman
http://www.biotechniques.com/news/Mutants-vs.-Morphants/biotechniques-35...

Retraction Watch
PubPeer Selections: Odd citations, “practice makes perfect,” a Nature update
Feb 27rd, 2015
http://retractionwatch.com/2015/02/27/pubpeer-selections-odd-citations-p...

Faculty of 1000
Discussion of: "Reverse genetic screening reveals poor correlation between morpholino-induced and mutant phenotypes in zebrafish."
http://f1000.com/prime/725287967
Requires subscription

Discussion of:"Genetic compensation induced by deleterious mutations but not gene knockdowns."
http://f1000.com/prime/725631655

Nature
Rossi A, Kontarakis Z, Gerri C, Nolte H, Hölper S, Krüger M, Stainier DYR. Genetic compensation induced by deleterious mutations but not gene knockdowns. Nature. 2015;[Epub ahead of print] doi:10.1038/nature14580
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14580.html

ScienceNews
Hesman Saey T. Mutation-disease link masked in zebrafish. ScienceNews. 2015;July 13
https://www.sciencenews.org/article/mutation-disease-link-masked-zebrafish

On Biology (BioMed Central)
Graham Bell. Reproducibility and morpholinos: different methods, different answers. 2015;July 23
http://blogs.biomedcentral.com/on-biology/2015/07/23/reproducibility-mor...

Zebrafish
Gene Tools publishes a response to Kok et al. 2014.
Morcos PA, Vincent AC, Moulton JD. Gene Editing Versus Morphants. Zebrafish. 2015 Oct;12(5):319. doi: 10.1089/zeb.2015.1114.
http://online.liebertpub.com/doi/pdfplus/10.1089/zeb.2015.1114
Points out excessive 20ng/embryo dosing in zebrafish used as evidence of Morpholino off-target effects

Developmental Cell
Blum M, De Robertis EM, Wallingford JB, Niehrs C. Morpholinos: Antisense and Sensibility. Dev Cell. 2015;35(2):145-9. doi:10.1016/j.devcel.2015.09.017
http://www.sciencedirect.com/science/article/pii/S1534580715006188
"Here, we argue that Kok et al. should not be taken as an argument to ban the first-time use of MOs. Instead, adequately controlled MOs should continue to be accepted as generic loss-of-function approach in the absence of genetic evidence, if progress in developmental biology is not to suffer."

BioMed Central Blog network, Graham Bell, 23 July 2015. Reproducibility and morpholinos: different methods, different answers.
https://blogs.biomedcentral.com/on-biology/2015/07/23/reproducibility-mo...
"Finally, returning to the theme of reproducibility in research, both methods might be reliable (repeatable) in the results observed in this case; the trick is to try to be sure about what question you want to ask, and what question a particular method is actually going to help answer."

Proc Natl Acad Sci U S A
Won M, Ro H, Dawid IB. Lnx2 ubiquitin ligase is essential for exocrine cell differentiation in the early zebrafish pancreas. Proc Natl Acad Sci U S A. 2015 Sep 21. pii: 201517033. [Epub ahead of print]
"Recent publications and much informal discussions have raised doubts about the validity of morphant phenotypes. Although this suspicion is undoubtedly well founded in certain instances, we show here that failure of a null mutant to replicate a morphant phenotype may have complex and ultimately insightful reasons. It should be noted that Kok et al. considered the possibility of functional redundancy of paralogs and possible effects of exon skipping in the interpretations. Our example emphasizes the need to consider these and possibly other effects in evaluating mutant versus morphant phenotypes."

PLoS One
Novodvorsky P, Watson O, Gray C, Wilkinson RN, Reeve S, Smythe C, Beniston R, Plant K, Maguire R, M K Rothman A, Elworthy S, van Eeden FJ, Chico TJ. klf2ash317 Mutant Zebrafish Do Not Recapitulate Morpholino-Induced Vascular and Haematopoietic Phenotypes. PLoS One. 2015 Oct 27;10(10):e0141611. doi: 10.1371/journal.pone.0141611. eCollection 2015.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141611
"In summary, our work shows that even in the face of clear evidence of a potentially disruptive mutation induced in a gene of interest, it is currently very difficult to be certain that this leads to loss-of-function, and hence to be confident about the role of the gene in embryonic development."

Trends in Cell Biology
Nathan D. Lawson
Reverse Genetics in Zebrafish: Mutants, Morphants, and Moving Forward
December 2015
http://www.sciencedirect.com/science/article/pii/S0962892415002366
"Gene editing in zebrafish has begun to reveal discordance between mutant phenotypes and those associated with knockdown via morpholino oligonucleotides (MOs). These studies suggest that MOs should not be used as a standalone tool and underscore the need for guidelines that require defined mutants to assess gene function in zebrafish."

PLoS Genet. 2016;12(2):e1005881. doi:10.1371/journal.pgen.1005881
Hu M, Bai Y, Zhang C, Liu F, Cui Z, Chen J, Peng J.
Liver-Enriched Gene 1, a Glycosylated Secretory Protein, Binds to FGFR and Mediates an Anti-stress Pathway to Protect Liver Development in Zebrafish.
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.10...
In replicating Morpohlino results with TALEN-induced mutations, the authors found that the phenotype was more severe with the Morpholino. They sought the reason for the discrepancy and found that compared to wild-type fish, the expression of leg1b was eleveated in leg1a mutants. "These data suggest that the expression of leg1b is mobilized to compensate, at least partially, for the loss of function of Leg1a in the leg1a(zju1) mutant."

EMBO reports (2016) embr.201541532 doi:10.15252/embr.201541532
Zhao Z, Lee RTH, Pusapati GV, Iyu A, Rohatgi R, Ingham PW.
An essential role for Grk2 in Hedgehog signalling downstream of Smoothened.
http://embor.embopress.org/content/early/2016/04/04/embr.201541532
"Our findings indicate a more critical requirement for Grk2 activity than has hitherto been appreciated. The mild morphant phenotype in zebrafish embryos together with the moderate reduction in Shh responsiveness of cells elicited by Grk2 siRNA led to the conclusion that GRK2 acts only to potentiate the response of cells to Hh. However, our analysis of both grk2 embryos and mutant cells reveals that the response to Hh is effectively abolished in the absence of Grk2. Notably, neither zygotic grk2 nor MZgrk2 zebrafish embryos show the developmental retardation reported to occur in Grk2 morphants, suggesting this to be an off‐target effect of the morpholino. This underlines the need for caution in interpreting effects associated with morpholino antisense oligonucleotide injection and the importance of analysing stable transmissible null mutations when characterising gene function. "

Mol Cell Biol. 2016 Sep 6. pii: MCB.00281-16. [Epub ahead of print]
Moore JC, Mulligan TS, Torres Yordán N, Castranova D, Pham VN, Tang Q, Lobbardi R, Anselmo A, Liwski RS, Berman JN, Sadreyev RI, Weinstein BM, Langenau DM.
T cell immune deficiency in zap70 mutant zebrafish.
http://mcb.asm.org/content/early/2016/08/30/MCB.00281-16.abstract
"Here, we describe a zap70 loss-of-function mutation in zebrafish (zap70y442) that was created using TALENs. In contrast to what has been reported in morphant zebrafish, zap70y442 homozygous mutant zebrafish displayed normal development of blood and lymphatic vasculature. Hematopoietic cell development was also largely unaffected in mutant larvae. However, mutant fish had reduced lck:GFP+ thymic T cells by 5 days post-fertilization that persisted into adult stages."

Essay (2016) by Dani Wijesinghe: "Knockdowns versus knockouts: why the phenotypic difference?"
https://medium.com/@daniwijesinghe/knockdowns-versus-knockouts-why-the-p...
(added Dec 2018)