# gst: apropos of 'normal' (jazzy?) codes, bacteria encode hidden, free-floating genes outside their genome.

AA << show that bacteria break that rule and can create free-floating and ephemeral genes, raising the possibility that similar genes exist outside of our own genome. >>️

<< What this discovery upends is the notion that the chromosome has the complete set of instructions that cells use to produce proteins, (..) We now know that, at least in bacteria, there can be other instructions not preserved in the genome that are nonetheless essential for cell survival. (..) The DNA molecule is a fully functioning, free-floating, transient gene. >> Samuel Sternberg. 

Bacteria Encode Hidden Genes Outside Their Genome—Do We? Columbia University Irving Medical Center. Aug 8, 2024. 

https://www.cuimc.columbia.edu/news/bacteria-encode-hidden-genes-outside-their-genome-do-we   

Stephen Tang, Valentin Conte, et al. De novo gene synthesis by an antiviral reverse transcriptase. Science. doi: 10.1126/ science.adq0876. Aug 8, 2024. 

https://www.science.org/doi/10.1126/science.adq0876

Also: 

codes https://flashontrack.blogspot.com/search?q=codes

DNA  https://flashontrack.blogspot.com/search?q=dna

RNA  https://flashontrack.blogspot.com/search?q=rna

CRISPR  https://flashontrack.blogspot.com/search?q=crispr

normal, jazz, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, codes, dna, rna, crispr, normal, jazz

# gene: bacteria and archaea CRISPR everywhere in nature

<< Single-celled bacteria and archaea use CRISPR systems to defend themselves against viruses known as bacteriophages. (..) Until now, researchers had identified six types of CRISPR system, designated I–VI. >>

AA << developed an algorithm called FLSHclust, which analyses genetic sequences in public databases. (..) By looking at the predicted function of the clusters, the researchers found around 130,000 genes associated in some way with CRISPR, 188 of which had never been seen before, >>️️

<< It’s a treasure trove for biochemists, >> Lennart Randau.

Sara Reardon. ‘Treasure trove’ of new CRISPR systems holds promise for genome editing. Nature. doi: 10.1038/ d41586-023-03697-w. Nov 23, 2023. 

https://www.nature.com/articles/d41586-023-03697-w

Han Altae-Tran, Soumya Kannan, Feng Zhang, et al. Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering. 

Science, Vol 382, Issue 6673. doi: 10.1126/ science.adi1910. Nov 23, 2023. 

https://www.science.org/doi/10.1126/science.adi1910

Also: 'CRISPR' in https://flashontrack.blogspot.com/search?q=crispr  

Keywords: genome, gene, crispr, crispr system, ai, artificial intelligence

# gst: ab.normal (fuzzy, bizarre) Nature; apparently, ancient bacterial parasites could have used CRISPR to self-defense and 'interference' for Ma ...

<< In recent years, the development of CRISPR technologies and gene-editing scissors in particular have taken the world by storm. Indeed, scientists have learned how to harness these clever natural systems in the biotech and pharmaceutical industries, among other areas. >>

<< New research (..) shows that we are not the first to find a way to exploit the benefits of the CRISPR technique. Apparently, primitive bacterial parasites have been doing so for millions of years. >>

<< Until recently, CRISPR-Cas was believed to be a defense system used by bacteria to protect themselves against invading parasites such as viruses, much like our very own immune system protects us. However, it appears that CRISPR is a tool that can be used for different purposes by diverse biological entities, (..) Here we found evidence that certain plasmids use type IV CRISPR-Cas systems to fight other plasmids competing over the same bacterial host. >> Rafael Pinilla-Redondo.

Humans are not the first to repurpose CRISPR. University of Copenhagen. Mar 24, 2020.

https://phys.org/news/2020-03-humans-repurpose-crispr.html

Rafael Pinilla-Redondo, David Mayo-Muñoz, et al. Type IV CRISPR–Cas systems are highly diverse and involved in competition between plasmids.  Nucleic Acids Research, Vol. 48, Issue 4, Pages 2000–12. doi: 10.1093/nar/gkz1197. Dec 27, 2019.

https://academic.oup.com/nar/article/48/4/2000/5687823

Also

keyword 'CRISPR' (Clustered Regularly Interspaced Short Palindromic Repeat) in PubMed:

 "CRISPR"[all] AND (Review[ptyp]) AND ("last 3 years"[PDat])

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

keyword 'CRISPR' in FonT:

https://flashontrack.blogspot.com/search?q=crispr

keyword 'interferenza' | 'interferente' in Notes (quasi-stochastic poetry):

https://inkpi.blogspot.com/search?q=interferenza

https://inkpi.blogspot.com/search?q=interferente

# epidem: silent invasions, the case of Candida auris.

<< Bacteria are rebelling  >>

<< The germ, a fungus called Candida auris, preys on people with weakened immune systems, and it is quietly spreading across the globe. >>

Matt Richtel,  Andrew Jacobs. DEADLY GERMS, LOST CURES. A Mysterious Infection, Spanning the Globe in a Climate of Secrecy. The rise of Candida auris embodies a serious and growing public health threat: drug-resistant germs. NYT. April 6, 2019.

https://www.nytimes.com/2019/04/06/health/drug-resistant-candida-auris.html

<< The recent rate of emergence of pathogenic fungi that are resistant to the limited number of commonly used antifungal agents is unprecedented. The azoles, for example, are used not only for human and animal health care and crop protection but also in antifouling coatings and timber preservation. The ubiquity and multiple uses of azoles have hastened the independent evolution of resistance in many environments. One consequence is an increasing risk in human health care from naturally occurring opportunistic fungal pathogens that have acquired resistance to this broad class of chemicals. >>

Matthew C. Fisher, Nichola J. Hawkins, et al.  Worldwide emergence of resistance to antifungal drugs challenges human health and food security. Science  May 18, 2018
Vol. 360, Issue 6390, pp. 739-742  doi: 10.1126/science.aap7999

http://science.sciencemag.org/content/360/6390/739

FonT

Per nostra - di noi umani - fortuna oggi si puo' analizzare, studiare ed eventualmente manipolare in modo fine il codice genetico di virus, batteri, etc. grazie alla tecnica CRISPR, tecnica a suo tempo (e per molto tempo) considerata di nessuna importanza da entita' di alta- altissima luminescenza ...

Eric S. Lander. The Heroes of CRISPR.
Cell. 14 January 2016, Vol.164(1): 18–28, doi:10.1016/j.cell.2015.12.041

http://www.sciencedirect.com/science/article/pii/S0092867415017055

Also: "CRISPR"

https://flashontrack.blogspot.com/search?q=crispr

https://www.ncbi.nlm.nih.gov/m/pubmed/?term=crispr

# gst: a chaos-inducing approach against superbugs evolution

<< The CHAOS [Controlled Hindrance of Adaptation of OrganismS] method takes advantage of this effect, pulling multiple genetic levers in order to build up stress on the bacterial cell and eventually trigger a cascading failure, leaving the bug more vulnerable to current treatments. The technique does not alter the bug's DNA itself, only the expression of individual genes, similar to the way a coded message is rendered useless without the proper decryption. >>

<< We now have a way to cut off the evolutionary pathways of some of the nastiest bugs and potentially prevent future bugs from emerging at all, >> Peter Otoupal

Chaos-inducing genetic approach stymies antibiotic-resistant superbugs. University of Colorado at Boulder. Sept 3, 2018.

https://m.phys.org/news/2018-09-chaos-inducing-genetic-approach-stymies-antibiotic-resistant.html 

<< While individual perturbations improved fitness during antibiotic exposure, multiplexed perturbations caused large fitness loss in a significant epistatic fashion. >>

Peter B. Otoupal, William T. Cordell, et al. Multiplexed deactivated CRISPR-Cas9 gene expression perturbations deter bacterial adaptation by inducing negative epistasis. Comm  Biol 1 (129) Sept 3, 2018

https://www.nature.com/articles/s42003-018-0135-2

# gene: inducing pluripotent stem cells from mice skin cells using CRISPR tech.

<< In a scientific first, researchers at the Gladstone Institutes turned skin cells from mice into stem cells by activating a specific gene in the cells using CRISPR technology. The innovative approach offers a potentially simpler technique to produce the valuable cell type and provides important insights into the cellular reprogramming process. >>

Gladstone Institutes. Researchers create first stem cells using CRISPR genome activation. Jan 18, 2018.

https://m.phys.org/news/2018-01-stem-cells-crispr-genome.html

AA << study generated authentic iPSCs [induced pluripotent stem cells] with CRISPR activation through precise epigenetic remodeling of endogenous loci and shed light on how targeted chromatin remodeling triggers pluripotency induction. >>

Peng Liu, Meng Chen, et al. CRISPR-Based Chromatin Remodeling of the Endogenous Oct4 or Sox2 Locus Enables Reprogramming to Pluripotency. Cell Stem Cell. 2018; 22 (2): 252 - 61.e4

http://www.cell.com/cell-stem-cell/fulltext/S1934-5909(17)30501-5

# gene: point code cracking machines (without detectable byproducts)

DNA cracking machine

<< The spontaneous deamination of cytosine is a major source of C•G to T•A transitions, which account for half of known human pathogenic point mutations. The ability to efficiently convert target A•T base pairs to G•C could therefore advance the study and treatment of genetic diseases >>

AA << report adenine base editors (ABEs) that mediate conversion of A•T to G•C in genomic DNA >>

<< ABEs advance genome editing by enabling the direct, programmable introduction of all four transition mutations without double-stranded DNA cleavage >>

Nicole M. Gaudelli, Alexis C. Komor, et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 2017 doi: 10.1038/nature24644 Oct 25, 2017
   
https://www.nature.com/nature/journal/vaap/ncurrent/full/nature24644.html

<< there are virtually no detectable byproducts such as random insertions, deletions, translocations, or other base-to-base conversions >>

Researchers extend power of gene editing by developing a new class of DNA base editors. Oct 25, 2017

https://m.phys.org/news/2017-10-enzyme-rewrites-genome.html

RNA cracking machine

<< RNA Editing for Programmable A to I Replacement (REPAIR), which has no strict sequence constraints, can be used to edit full-length transcripts containing pathogenic mutations >>

David B. T. Cox, Jonathan S. Gootenberg, et al. RNA editing with CRISPR-Cas13. Science. Oct 25, 2017:eaaq0180 doi: 10.1126/science.aaq0180

http://science.sciencemag.org/content/early/2017/10/24/science.aaq0180

Researchers engineer CRISPR to edit single RNA letters in human cells. Oct 25, 2017

https://m.phys.org/news/2017-10-crispr-rna-letters-human-cells.html

Lauran Neergaard. Scientists working toward reversible kind of gene editing. Oct. 25, 2017

https://m.phys.org/news/2017-10-scientists-reversible-kind-gene.html

also:

http://flashontrack.blogspot.it/search?q=crispr

# e-tech: store data with CRISPR–Cas tech.; biologists have now joined the party

<< Internet users have a variety of format options in which to store their movies, and biologists have now joined the party. Researchers have used the microbial immune system CRISPR–Cas to encode a movie into the genome of the bacterium Escherichia coli. >>

<< “Cells have this privileged access to all sorts of information,” he [Seth Shipman] says. “I would like to have these molecular recordings functioning in the developing nervous system and recording information.” >>

Heidi Ledford. Lights, camera, CRISPR: Biologists use gene editing to store movies in DNA. Technique demonstrated in E. coli suggests ways to record key events in a cell's life. July 12, 2017

http://www.nature.com/news/lights-camera-crispr-biologists-use-gene-editing-to-store-movies-in-dna-1.22288

Shipman, S. L., Nivala, J., et al. Nature doi: 10.1038/nature23017 (2017).

https://www.nature.com/articles/nature23017.epdf

Also

2073 - a few hints of our presence. Oct 13, 2006.

http://inkpi.blogspot.it/2006/10/2073-few-hints-of-our-presence.html

# s-gene: a CRISPR-based RNA-targeting approach, the begin ...

<< a  new  CRISPR  system,  (..)  targets  RNA  rather  than  DNA (..), has  the  potential  to  open  a  powerful  avenue  in  cellular  manipulation. Whereas  DNA  editing  makes  permanent  changes  to  the  genome  of  a  cell,  the  CRISPR-based RNA-targeting  approach  may  allow  researchers  to  make  temporary  changes  that  can  be adjusted  up  or  down,  and  with  greater  specificity  and  functionality  than  existing  methods  for RNA  interference >>

Researchers  unlock  new  CRISPR  system  for targeting  RNA. June  2,  2016.

http://m.phys.org/news/2016-06-crispr-rna.html

Omar O. Abudayyeh,  Jonathan  S.  Gootenberg,  et al. C2c2 is a single-component  programmable  RNA-guided  RNA-targeting  CRISPR  effector. Science    02  Jun 2016: DOI:  10.1126/science.aaf5573

http://science.sciencemag.org/content/early/2016/06/01/science.aaf5573

# s-gene: Yoshizumi Ishino, Francisco Mojica (et al) wave: SRSR - CRISPR interference

<< We were stunned, it was like the sun rose in the west rather than the east.>>  Ethan Bier

<< We’re  not about to do anything foolish. >>  Anthony James

Shelly Fanon. Gene Drives Could Wipe Out Insect-Borne Disease — But What’s the Price? Nov 29, 2015.

http://singularityhub.com/2015/11/29/gene-drives-can-eliminate-transmissible-diseases-for-good-but-whats-the-price

Yoshizumi Ishino and Francisco Mojica, in: CRISPR, Clustered regularly-interspaced short palindromic repeats.

https://en.m.wikipedia.org/wiki/CRISPR

Eric S. Lander. The Heroes of CRISPR.
Cell. 14 January 2016, Vol.164(1):18–28, doi:10.1016/j.cell.2015.12.041

http://www.sciencedirect.com/science/article/pii/S0092867415017055

# s-gene-lab: bioethics vs CRISPR tech

<< (..) scientists have long had the ability to remove, repair or insert genetic material in cells. But the process was time consuming and expensive. CRISPR (“clustered regularly interspaced short palinodromic repeats”) streamlines gene editing dramatically. Its simplicity has enabled far more scientists to get involved in such work. In a short time, they have now used CRISPR to edit genes in insects, plants, fish, rodents and monkeys >>

<< In April, Chinese scientists reported that they had attempted to alter a gene in nonviable human embryos. The announcement sparked bioethicists to call for a more cautious approach to gene editing >>

http://www.kurzweilai.net/the-crispr-controversy-faster-cheaper-gene-editing-vs-bioethicists

http://www.acs.org/content/acs/en/pressroom/presspacs/2015/acs-presspac-september-9-2015/game-changing-technology-enables-faster-cheaper-gene-editing.html

http://cen.acs.org/articles/93/i35/Genome-Editing-Writ-Large.html

# s-gene-lab: mammalian genome editing new tech: CRISPR-Cpf1

<< A team including the scientist who first harnessed CRISPR-Cas9 system for mammalian genome editing has now identified a different CRISPR system (CRISPR-Cpf1) with the potential for even simpler and more precise genome engineering >>

http://www.sciencedaily.com/releases/2015/09/150925131512.htm

Zetsche et al. Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System. Cell, September 2015 DOI: 10.1016/j.cell.2015.09.038

http://www.cell.com/abstract/S0092-8674%2815%2901200-3

<< The Zhang lab offers free online tools and resources for researchers through its website >>

 http://www.genome-engineering.org