QualityControl4Genes - Revision history

Rachel: /* Update June 2024 */

2024-06-27T21:41:16Z

Update June 2024

Rachel: /* Update March 2024 */

2024-06-27T21:40:04Z

Update March 2024

Rachel at 21:39, 27 June 2024

2024-06-27T21:39:08Z

Rachel: /* Update March 2024 */

2024-06-27T21:35:04Z

Update March 2024

Rachel at 07:54, 1 April 2024

2024-04-01T07:54:15Z

Rachel at 14:12, 29 March 2024

2024-03-29T14:12:08Z

Rachel at 14:09, 29 March 2024

2024-03-29T14:09:37Z

Rachel: /* Update March 2024 */

2024-03-29T13:51:31Z

Update March 2024

Rachel at 13:49, 29 March 2024

2024-03-29T13:49:19Z

Rachel at 13:24, 29 March 2024

2024-03-29T13:24:24Z

@@ Line 87: / Line 87: @@
 SIMPLE PRESENTATION and PREPRINT to come.
-How we can do all the experiments necessary, from RNA analyses to imaging (of subnuclear architecture and pore complexes and out to some potential outer nuclear membrane cavity and ultimately the polyribosomes) in combination with green-tagged markers, will be a great challenge.
+How we can do all the experiments necessary, from RNA analyses to imaging (of subnuclear architecture and pore complexes and out to some potential outer nuclear membrane cavity and ultimately the polyribosomes) in combination with green-tagged markers? It will be a great challenge.
-Maybe other collaborations could be possible - hoping that many labs will be interested...
+Maybe other collaborations could be possible - hoping that many labs might be interested in these, also as tools...

@@ Line 72: / Line 72: @@
 More experiments to come and writing of an article!  Here is a recent image from the last trip up to Basel... [[File:Smg4KIhead19mar24.png|thumb|A nematode head shows red signal expressed from the gene in its ordinary genetic locus, thanks to synthetic biology tools and help in the Mango lab at the Biozentrum in Switzerlerland. / ''Une tête de nématode montre un indicateur rouge exprimé à partir du gène dans son locus génétique normal, grâce aux outils de biologie synthétique et à l'aide du laboratoire Mango du Biozentrum en Suisse.'']] Hoping to learn much more in combination with other GFP tagged components of the pathway and nuclear (nuclear pore?) markers.
-'''Update June 2024'''
+=== '''Update June 2024''' ===
 Another small deletion is made, and we will see...
 Here are two gonadal pictures (epifluor again) of Smg-4::mCherry KI delta1 in the ''smg''-sensitive ''unc-54'' background,
-[[File:KU11x63Gpostgonadrg.png|left|thumb|Smg-4::mCherry KI delta1 in the ''smg''-sensitive ''unc-54'' background showing bright cells that could include coelomocytes...]]
+[[File:KU11x63Gpostgonadrg.png|left|thumb|Smg-4::mCherry KI delta1 in the ''smg''-sensitive ''unc-54'' background, showing bright cells that could include coelomocytes...]]
 If you would like to learn more too, or have ideas - do not hesitate to write! =)

@@ Line 84: / Line 84: @@
 =)
-[[File:KU11x63Gpostgonad.png|left|thumb|the nomarski optics image shows early embryos and an oocyte in the midst of being fertilised...]]
+[[File:KU11x63Gpostgonad.png|left|thumb|Q nomarski optics image shows early embryos and a not yet fertilised oocyte ...]]
-<nowiki>*</nowiki><small>another gene mutant, [https://www.nature.com/articles/nmeth.1463 SID-1], could still be tried for the RNAi feeding experiment given the results seen here, and the human UPF3-X function in the brain.</small>
+Maybe other collaborations could be possible - hoping that many labs will be interested...
 Some References from the excerpt above:

@@ Line 70: / Line 70: @@
 speckles of the Smg-4 shuttling protein in a larval brain!
 [[File:FirstKnockInR15b.png|thumb|mCherry signals in the brain of in the Smg-4:KnockIn strain]]
-More experiments to come and writing of an article!  Here is a recent image from the last trip up to Basel... [[File:Smg4KIhead19mar24.png|thumb|A nematode head shows red signal expressed from the gene in its ordinary genetic locus, thanks to synthetic biology tools and help in the Mango lab at the Biozentrum in Switzerlerland. / ''Une tête de nématode montre un indicateur rouge exprimé à partir du gène dans son locus génétique normal, grâce aux outils de biologie synthétique et à l'aide du laboratoire Mango du Biozentrum en Suisse.'']] Hoping to learn much more in combination with other GFP tagged components of the pathway and nuclear (nuclear pore?) markers.  If you would like to learn more too, or have ideas - do not hesitate to write! =)
+More experiments to come and writing of an article!  Here is a recent image from the last trip up to Basel... [[File:Smg4KIhead19mar24.png|thumb|A nematode head shows red signal expressed from the gene in its ordinary genetic locus, thanks to synthetic biology tools and help in the Mango lab at the Biozentrum in Switzerlerland. / ''Une tête de nématode montre un indicateur rouge exprimé à partir du gène dans son locus génétique normal, grâce aux outils de biologie synthétique et à l'aide du laboratoire Mango du Biozentrum en Suisse.'']] Hoping to learn much more in combination with other GFP tagged components of the pathway and nuclear (nuclear pore?) markers.
 Please contact rachel (at) hackuarium (dot) ch...
 =)

@@ Line 17: / Line 17: @@
 Here is the [https://drive.google.com/file/d/1Vw_f71P4g2F9_E1V4VNZ4x0B5i1MvB78/view?usp=share_link original paper about the cloned worm gene] (Aronoff et al, 2001), ''smg-4'', which defines a family of conserved genes.
-In humans, there are two copies of this gene on different chromosomes, with the X-linked one tied to Intellectual Disabilities, and [https://www.cmmc-uni-koeln.de/de/research/research-areas-projects/research-area-c/niels-gehring-c-07 more interesting features] in knockdown and attempts to knock this QC mechanism out in cells...
+In humans, there are two copies of this gene on different chromosomes, with the X-linked one tied to Intellectual Disabilities, and [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9108619/ more interesting features] in knockdown and attempts to knock this QC mechanism out in cells...
 Additional feedback loops can affect activity or even expression levels, for appropriate function.

@@ Line 50: / Line 50: @@
 (To note: 'rescue' makes the worms paralysed in this genetic context. It is just due to the fact that a myosin heavy chain gene is the target... We project a simpler explanation of it all, soon...)
-The study began with rescue attempts using DNA fragments made by PCR, and attempts to KnockDown the gene with RNA interference (RNAi).  Although the amplified transgenes worked a charm, products derived from mutant strains did not rescue, and had the sequences predicted, of course.  For work published so long ago, we decided that finally the new tools of synthetic biology would being used.  =)
+The study began with rescue attempts using DNA fragments made by PCR, and attempts to KnockDown the gene with RNA interference (RNAi).  Although the amplified transgenes worked a charm, products derived from mutant strains did not rescue, and had the sequences predicted, of course.
-Crispr based KnockOuts and a Knock-In have already been generated. However, in fact, the RNAi feeding, even in a super-sensitive mutant strain, ''rrf-3'', did not give any effect.***
+Crispr based KnockOuts and a Knock-In have already been generated. However, in fact, the RNAi feeding, even in a super-sensitive mutant strain, ''rrf-3'', did not give any effect.*
 We also confirmed the deletion sequence of a mutant made with psoralen-uv, and this is interesting as it keeps the key domain, but the what is left of the gene only partially rescues (egg laying, but not muscle function).
@@ Line 77: / Line 77: @@
-<nowiki>**</nowiki><nowiki>*</nowiki><small>another gene mutant, [https://www.nature.com/articles/nmeth.1463 SID-1], could still be tried for the RNAi feeding experiment given the results seen here, and the human UPF3-X function in the brain.</small>
 Nonetheless, with the KO a simple loss of function, and this KnockIn still to confirm for rescue of the unc-54(r293) allele, we can't help thinking how much we have to learn, still.  How we can do all the experiments necessary, from RNA analyses to imaging (of subnuclear architecture and pore complexes and out to some potential outer nuclear membre cavity and ultimately the polyribosomes) in combination with green-tagged markers, will be a great challenge.

@@ Line 11: / Line 11: @@
 As Nietzsche said - you have made your way from worm to man, but much within you is still worm...
-This key pathway has the responsibility of removing mRNAs that might express dominant negative or toxic fragments of otherwise good genes.  Errors are normal, and all the stages of gene expression - from transcription, to splicing, to translatin to protein or activating other functions - can be subject to mistakes. Prevention is what mRNA surveillance is about.  However, these genes also have developmental roles and natural targets which they regulate. More than 10% of the RNAs made in eukaryotes are affected by this system, and further gene expression regulation is possible even out in sub-cellular compartments, like dendrites...
+This key pathway has the responsibility of removing mRNAs that might express dominant negative or toxic fragments of otherwise good genes.  Errors are normal, and all the stages of gene expression - from transcription, to splicing, to translating to protein or activating other functions - can be subject to mistakes. Prevention is what mRNA surveillance is about.  However, these genes also have developmental roles and natural targets which they regulate. More than 10% of the RNAs made in higher eukaryotes are affected by this system, and further gene expression regulation is possible even out in sub-cellular compartments, like dendrites...
-There is even recent [https://www.cell.com/trends/neurosciences/pdf/S0166-2236(23)00161-3.pdf Trends in Neurosci] about it all...
+There is even recent article in [https://www.cell.com/trends/neurosciences/pdf/S0166-2236(23)00161-3.pdf Trends in Neurosci] about it all...
 Here is the [https://drive.google.com/file/d/1Vw_f71P4g2F9_E1V4VNZ4x0B5i1MvB78/view?usp=share_link original paper about the cloned worm gene] (Aronoff et al, 2001), ''smg-4'', which defines a family of conserved genes.

@@ Line 7: / Line 7: @@
 Interested to learn more?
-Here is the [https://pubmed.ncbi.nlm.nih.gov/38437914/ link to the recent paper one of the the human orthologues] of this nématode gene, ''smg-4,'' and how it, hUPF3p-X is regulated by microRNAs and active in the brain. Regulation of genes in thymus and brain via the interplay of [https://www.sciencedirect.com/science/article/pii/S1097276511003303 microRNA action on RNA surveillance factors affecting target gene expression] was [https://www.sciencedirect.com/science/article/pii/S1097276511003248 already shown by 2011].
+Here is the [https://pubmed.ncbi.nlm.nih.gov/38437914/ link to the recent paper about one of the the human orthologues] of this nématode gene, ''smg-4,'' and how it, hUPF3p-X is regulated by microRNAs and active in the brain. Regulation of genes in thymus and brain via the interplay of [https://www.sciencedirect.com/science/article/pii/S1097276511003303 microRNA action on RNA surveillance factors affecting target gene expression] was [https://www.sciencedirect.com/science/article/pii/S1097276511003248 already shown by 2011].
 As Nietzsche said - you have made your way from worm to man, but much within you is still worm...