# gst: apropos of weak bonds, hydrophobic cohesion to stabilize the double helix of DNA

<< The main stabilizer of the DNA double helix is not the base-pair hydrogen bonds but coin-pile stacking of base pairs, whose hydrophobic cohesion, requiring abundant water, indirectly makes the DNA interior dry so that hydrogen bonds can exert full recognition power. (..) (AA) speculate that hydrophobic catalysis is a general phenomenon in DNA enzymes. >>

<< The forces that stabilize the DNA double helix are a prerequisite for the secure storage of genetic information but their modest strength is also necessary for the efficient processes of replication, transcription, recombination, and repair systems-wherein thermal fluctuations, or "breathing," play an important role >>

Bobo Feng, Robert P. Sosa, et al. Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects. PNAS.  116 (35) 17169-17174; Aug 27, 2019.  doi: 10.1073/ pnas.1909122116.    https://www.pnas.org/content/116/35/17169

DNA is held together by hydrophobic forces. Chalmers University of Technology. Sep 23, 2019.     https://m.phys.org/news/2019-09-dna-held-hydrophobic.html   

# gene: stuttering, syncopated (but not junk) codes

<< All organisms have DNA, the genetic material that provides a blueprint for life. The long double-helix-shaped DNA molecules in the body's cells are first translated into RNA molecules and then translated into proteins that ensure the functioning of the cell and the entire organism. But there are large parts of the DNA that are not used for making proteins. This is called 'junk DNA', because its function remained unclear for a long time. However, a certain type of junk DNA that is found in mosquitoes and which repeats itself dozens of times, known as 'satellite DNA', has now been shown to play an essential role in the early development of mosquito embryos. >>

Stuttering DNA orchestrates the start of the mosquito's life. Radboud University Medical Center. Apr 9, 2020.

https://www.sciencedaily.com/releases/2020/04/200409100332.htm 

AA << results reveal a mechanism by which satellite repeats regulate global gene expression in trans via piRNA-mediated gene silencing that is essential for embryonic development. >>

Rebecca Halbach, Pascal Miesen, et al. A satellite repeat-derived piRNA controls embryonic development of Aedes. Nature 580, 274–277. doi: 10.1038/s41586-020-2159-2. 

Apr 1, 2020.

https://www.nature.com/articles/s41586-020-2159-2

Also

keyword 'piRNA' in ncbi pubmed

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

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

# 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

# evol: the origins of life on earth could be arisen from the same set of DNA and RNA precursor molecules

<< the first living things on Earth may have used both RNA (ribonucleic acid) and DNA (deoxyribonucleic acid), as all cell-based life forms do now. In contrast, the prevailing scientific view—the "RNA World" hypothesis—is that early life forms were based purely on RNA, and only later evolved to make and use DNA. >>

<< These new findings suggest that it may not be reasonable for chemists to be so heavily guided by the RNA World hypothesis in investigating the origins of life on Earth, >>

Ramanarayanan Krishnamurthy. Building blocks of DNA and RNA could have appeared together before life began on Earth. The Scripps Research Institute. April 1, 2019.

https://m.phys.org/news/2019-04-blocks-dna-rna-life-began.html  

Jianfeng Xu, Nicholas J. Green, et al. Prebiotic phosphorylation of 2-thiouridine provides either nucleotides or DNA building blocks via photoreduction. Nature Chemistry. doi: 10.1038/s41557-019-0225-x April 1, 2019.

https://www.nature.com/articles/s41557-019-0225-x

# s-gene: epigenetics: much more (m6dA)

<< Epigenetics (epi - the Greek prefix meaning ‘on top of’) is the study of how genes are switched on or off. It is thought to be one explanation for how our environment and behaviour, such as our diet or smoking habit, can affect our DNA and how these changes may even be passed down to our children and grandchildren >>

http://www.cam.ac.uk/research/news/epigenetic-discovery-suggests-dna-modifications-more-diverse-than-previously-thought

<< Methylation of cytosine deoxynucleotides generates 5-methylcytosine (m5dC), a well-established epigenetic mark. However, in higher eukaryotes much less is known about modifications affecting other deoxynucleotides. Here, we report the detection of N6-methyldeoxyadenosine (m6dA) in vertebrate DNA, specifically in Xenopus laevis but also in other species including mouse and human. Our methylome analysis reveals that m6dA is widely distributed across the eukaryotic genome and is present in different cell types but is commonly depleted from gene exons. Thus, direct DNA modifications might be more widespread than previously thought >>

Magdalena J Koziol, Charles R Bradshaw, et al. Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications. Nature Structural & Molecular Biology, 2015; DOI: 10.1038/nsmb.3145

http://www.nature.com/nsmb/journal/vaop/ncurrent/full/nsmb.3145.html

# s-tech: DNA as a nano transistor

<< As electronics get smaller they are becoming more difficult and expensive to manufacture, but DNA-based devices could be designed from the bottom-up using directed self-assembly techniques such as ‘DNA origami’ >>

http://www.kurzweilai.net/will-this-dna-molecular-switch-replace-conventional-transistors

Juan Manuel Artés, Yuanhui Li,  et al. Conformational gating of DNA conductance. Nature Communications, 2015; 6: 8870 DOI: 10.1038/ncomms9870

http://www.nature.com/ncomms/2015/151209/ncomms9870/full/ncomms9870.html

# e-tech: all kind of info storable in DNA

AA have << (..) detailed one of the first complete systems to encode, store and retrieve digital data using DNA molecules, which can store information millions of times more compactly than current archival technologies. >>

<< “Life has produced this fantastic molecule called DNA that efficiently stores all kinds of information about your genes and how a living system works — it’s very, very compact and very durable,” said co-author Luis Ceze, UW associate professor of computer science and engineering.“We’re essentially repurposing it to store digital data — pictures, videos, documents— in a manageable way for hundreds or thousands of years.” >>

Jennifer Langston. UW team stores digital images in DNA and retrieves them perfectly. April 7, 2016.

http://www.washington.edu/news/2016/04/07/uw-team-stores-digital-images-in-dna-and-retrieves-them-perfectly/

# s-chem: self-assembling 'origami' nanoscale architectures by DNA staple strands

<< DNA origami is a technique that uses hundreds of short DNA oligonucleotides, called staple strands, to fold a long single-stranded DNA, which is called a scaffold strand, into various designer nanoscale architectures >>

Hong F, Zhang F, et al. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem Rev. 2017 Jun 12. doi: 10.1021/acs.chemrev.6b00825.

https://www.ncbi.nlm.nih.gov/pubmed/28605177

# s-gene: extensive, quantitative perturbation approach to trace "the poetry" of gene regulatory networks

<<  DNA  content  of  our  genomes  resembles  a  complex  biological  language,  composed  of  coding  regions and  regulatory  regions.  Although  protein-coding  regions  in  DNA  could  be  compared  to  a  traffic  signal  –  utilizing  a  simple  stop  or  go  message  –  the regulatory  regions  in  DNA  are  more  like  poetry. “The  regulatory  sites  in  DNA  operate  like  a  light  switch  to  turn  a  gene  on  and  off.  In  animals,  it’s  extremely  complex,”  said  David  Arnosti (..) “There  might  be  hundreds  of  protein  factors  in  the  cell  that  bind  to  the gene  and  impact  activity.  And  there  might  be  hundreds  of  binding  places.” He  compares  the  “language”  used  in  these  regulatory  sites  to  poetry. “It  may  be  Emily  Dickinson,  or  Shakespeare  or  Allen  Ginsberg;  but  all  are  using  ‘words’  to  evoke  thoughts  and  emotions,  to  control  the  message” >>

Val  Osowski, Layne  Cameron. DO GENES EXPRESS THEMSELVES THROUGH POETRY? A  new study  from  Michigan  State  University  makes  inroads  in  learning  to  “read”  the  genome,  a  key  goal  of  modern  biology. Published:  May  9,  2016

http://msutoday.msu.edu/news/2016/do-genes-express-themselves-through-poetry/

To  understand  transcription  factor  interactions  on  enhancers  << (..) an  extensive,  quantitative  perturbation  analysis targeting  the  dorsal-ventral  patterning  gene  regulatory  network  (GRN)  controlled  by  Drosophila NF-κB  homolog  Dorsal [was used to test] the effects  of  cooperativity,  repression,  and factor  potency >>

Rupinder  Sayal,  Jacqueline  M  Dresch, et al. Quantitative  perturbation-based  analysis  of  gene expression  predicts  enhancer  activity  in  early Drosophila  embryo. eLife  2016;5:e08445. Published  May  6,  2016

http://dx.doi.org/10.7554/eLife.08445

# 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

# gst: the dance of complex knots (in DNA), from mobile to jammed states

AA << show for the first time experimentally that knots can go from a mobile to a jammed state by varying an applied strain rate, and that this jamming is reversible >>

Alexander R. Klotz, Beatrice W. Soh, and Patrick S. Doyle. Motion of Knots in DNA Stretched by Elongational Fields.  Phys. Rev. Lett. 120, 188003. May 3, 2018.

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.120.188003

Anne Trafton. Chemical engineers discover how to control knots that form in DNA molecules. Massachusetts Institute of Technology. May 3, 2018.

https://m.phys.org/news/2018-05-chemical-dna-molecules.html

# evol: the hypothesis of quasi-stochastic 'jazzy' metamechanics of biological evolution (in Arabidopsis thaliana)

<< Mutations occur when DNA is damaged and left unrepaired, creating a new variation. The scientists wanted to know if mutation was purely random or something deeper. What they found was unexpected. >>️

<< We always thought of mutation as basically random across the genome, (..) It turns out that mutation is very non-random and it's non-random in a way that benefits the plant. It's a totally new way of thinking about mutation. >> Grey Monroe. ️

Study challenges evolutionary theory that DNA mutations are random. UC Davis. Jan 12, 2022.

https://phys.org/news/2022-01-evolutionary-theory-dna-mutations-random.html

Monroe JG, Srikant T, et al. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature. doi: 10.1038/ s41586-021-04269-6. Jan 12, 2022.

https://www.nature.com/articles/s41586-021-04269-6

FonT 

for a long time I have developed the suspicion that the small plant cared for by grandmother on the windowsill could be a not trivial image of (r)evolution ... 

The three ways of the plastoquinone inside the photosystem II complex. May 23, 2017.

https://flashontrack.blogspot.com/2017/05/s-phyto-three-ways-of-plastoquinone.html

Also

keyword 'evolution'  in FonT

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

keyword 'evolution' | 'evoluzione'  in Notes (quasi-stochastic poetry)

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

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

keyword 'jazz' in FonT

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

keyword 'jazz' in Notes (quasi-stochastic poetry):

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

keywords: evol, dna, mutations, randomness, quasi-stochasticity, jazz

# s-acad: no "junk", but only fresh thinking

<< Science  rests  on  data,  of  that  there  can  be  no  doubt.  But  ... >>

<< (..) so  the  next  best  thing  is  precision  medicine,  where  we look  at  how  genetically  similar  people  react  and  then  assume  that  a  given  person  will  respond in  a  similar  way. >>

Peter  Coveney, Edward  R  Dougherty. Big  data  has  not  revolutionised  medicine  we  need  big  theory  alongside  it. 19  April  2016,  16:02  CEST

https://theconversation.com/big-data-has-not-revolutionised-medicine-we-need-big-theory-alongside-it-55356

FonT: ironicamente, chi a suo tempo ha coniato (o usato piu' o meno acriticamente) il termine "junk DNA" forse non ha preso in considerazione il fatto che quella parte di codice, benche' di serialita' (sequenzialita') quasistocastica, avrebbe potuto contenere la parte piu' importante del "sistema operativo" della vita, vale a dire  il kernel dove risiedono le istruzioni di differenziazione, di regolazione, di riparazione sul codice ... e forse anche le banche dati storiche e mnesiche ...  istruzioni e banche dati di "assoluta  precisione", per dire ...

" junk DNA" cfr http://www.ncbi.nlm.nih.gov/pubmed/?term=%22junk+dna%22

# rmx-s-gst: inner dances: to get a sense ...

<< To get a sense for supercoiled DNA,  imagine twisting a piece of string. Let the string go, and it unwinds. Twist it enough, and it folds back on itself. The degree of twist puts stress on the string, which governs the shape it takes >>

http://www.scientificamerican.com/article/how-strange-twists-in-dna-orchestrate-life/

Rossitza N. Irobalieva, Jonathan M. Fogg, et al. Structural diversity of supercoiled DNA. Nature Communications 6, Article number: 8440 doi:10.1038/ncomms9440

http://www.nature.com/ncomms/2015/151012/ncomms9440/full/ncomms9440.html

# s-age: dietary restriction to extend lifespan

<< Dietary  restriction  is  known  to  extend  lifespan  in  many  species.  It  has  now  been  shown  to  reduce  DNA damage  and  extend  lifespan  in  mice  modelling  human  DNA-repair  disorders. >>

J.  Oshima,  G. M.  Martin. Ageing:  Dietary  protection  for  genes. Nature   537,   316–317  (15  September  2016)   doi:10.1038/nature19427 Published  online   24  August  2016.

http://www.nature.com/nature/journal/v537/n7620/full/nature19427.html

W.  P.  Vermeij  M.  E.  T.  Dolle'. Restricted  diet  delays  accelerated  ageing  and genomic  stress  in  DNA-repair-deficient  mice. Nature Volume: 537, Pages: 427–431 Date published: 15 September 2016 DOI: doi:10.1038/nature19329

http://www.nature.com/nature/journal/v537/n7620/full/nature19329.html

FonT: nella costellazione di "ricette" anti- invecchiamento la restrizione alimentare, intesa non come "dieta" ma come "stile di vita", e' l'approccio che nel corso degli ultimi decenni ha avuto (e ha tuttora nella letteratura scientifica internazionale) conferme sperimentali significative; uno stile che sa  associare (giornalmente) controllo alimentare bilanciato e attivita' fisica "dolce" (secondo una generica pratica zen, ad es.) sembra  l'approccio meno rischioso e il piu' efficace tra quelli proposti.

# bots: tiny machinery, nanobots (molecule-sized bots) from 1k to millions swarming together to perform tasks

<< Multi-disciplinary research has led to the innovative fabrication of molecule-sized robots. Scientists are now advancing their efforts to make these robots interact and work together in the millions. >>

AA << have made molecular robots with three key components: microtubules, single-stranded DNA, and a light-sensing chemical compound. The microtubules act as the molecular robot's motor, converting chemical energy into mechanical work. The DNA strands act as the information processor due to its incredible ability to store data and perform multiple functions simultaneously. The chemical compound, azobenzene derivative, is able to sense light, acting as the molecular robot's on/off switch. (..) (They) have successfully controlled the shape of those swarms by tuning the length and rigidity of the microtubules. Relatively stiff robots swarm in uni-directional, linear bundles, while more flexible ones form rotating, ring-shaped swarms.>>

<< A continuing challenge, though, is making separate groups of robots swarm at the same time, but in different patterns. This is needed to perform multiple tasks simultaneously. >>

Scientists working to make molecule-sized robots swarm together to perform tasks. National Institute for Materials Science. Jun 18, 2020.

https://phys.org/news/2020-06-scientists-molecule-sized-robots-swarm-tasks.html   

Arif Md. Rashedul Kabir, Daisuke Inoue,  Akira Kakugo. Molecular swarm robots: recent progress and future challenges.  Science and Technology of Advanced Materials. 21:1, 323-332. doi: 10.1080/ 14686996.2020.1761761. Jun 16, 2020. 

https://www.tandfonline.com/doi/full/10.1080/14686996.2020.1761761 

Also

keyword 'bot' in FonT

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

keyword 'self-assembly' in FonT

https://flashontrack.blogspot.com/search?q=self-assembly

# s-gst-evol: tiny tweaks to modulate hairy bittercress (Cardamine hirsuta)

<< Millions of years ago, some plants in the mustard family made the switch from simple leaves to complex leaves through two tiny tweaks to a single gene. One tweak to a small enhancer sequence gave the gene a new domain of expression in the leaf. Paradoxically, the other tweak sub-optimised its function in this new domain. But together, these changes gave rise to fit plants with complex leaves. >>

P. Huijser. A small piece of DNA with a large effect on leaf shape. Nov. 17, 2016

http://m.phys.org/news/2016-11-small-piece-dna-large-effect.html

Francesco Vuolo, Remco A. Mentink et al. Coupled enhancer and coding sequence evolution of a homeobox gene shaped leaf diversity. Genes & Development (2016). Nov.16, 2016, doi: 10.1101/gad.290684.116

http://m.genesdev.cshlp.org/content/early/2016/11/16/gad.290684.116

# evol: apropos of our origin, the KhoeSan trunk of the human tree

<< Where was the evolutionary birthplace of modern humans? The East African Great Rift Valley has long been the favoured contender – until today. (AA) new research has used DNA to trace humanity’s earliest footsteps to a prehistoric wetland called Makgadikgadi-Okavango, south of the Great Zambezi River. >>

<< KhoeSan have the most diverse mitogenomes of anyone on Earth, which suggests their DNA most closely resembles that of our shared common ancestors. If we all sit on branches of the human family tree, then KhoeSan are the tree's trunk. >>

Vanessa Hayes. Humanity’s birthplace: why everyone alive today can call northern Botswana home. University of Sydney. Oct 28, 2019.

https://theconversation.com/humanitys-birthplace-why-everyone-alive-today-can-call-northern-botswana-home-125814

Eva K. F. Chan, Axel Timmermann, et al.  Human origins in a southern African palaeo-wetland and first migrations. Nature (2019) doi:10.1038/s41586-019-1714-1. Oct 28, 2019.

https://www.nature.com/articles/s41586-019-1714-1    

# 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

# gene: the genetic stochastic kernel inside A. asiatica

AA << report the first example of dual coding: Ascoidea asiatica stochastically encodes CUG as both serine and leucine in approximately equal proportions >>

Stefanie Muhlhausen, Hans Dieter Schmitt, et al.  Endogenous Stochastic Decoding of the CUG Codon by Competing Ser- and Leu- tRNAs in Ascoidea asiatica. Current Biology 28, 1–12 Jul 9, 2018 doi.org/10.1016/j.cub.2018.04.085

https://www.cell.com/current-biology/fulltext/S0960-9822(18)30557-8

Microbe breaks 'universal' DNA rule by using two different translations. University of Bath. Jun 14, 2018

https://m.phys.org/news/2018-06-microbe-universal-dna.html