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Visualizzazione dei post in ordine di data per la query dna. Ordina per pertinenza Mostra tutti i post
Visualizzazione dei post in ordine di data per la query dna. Ordina per pertinenza Mostra tutti i post

lunedì 19 agosto 2024

# 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. 

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

Also

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


venerdì 23 febbraio 2024

# gst: soft and stiff modes in colloidal particle networks

<< Floppy microscale spring networks are widely studied in theory and simulations, but no well-controlled experimental system currently exists. >> 

AA << show that square lattices consisting of colloid-supported lipid bilayers functionalized with DNA linkers act as microscale floppy spring networks. (AA) extract their normal modes by inverting the particle displacement correlation matrix, showing the emergence of a spectrum of soft modes with low effective stiffness in addition to stiff modes that derive from linker interactions. >>

<< Evaluation of the softest mode, a uniform shear mode, reveals that shear stiffness decreases with lattice size. >>

 AA << results reveal the importance of entropic steric effects. >>
Julio Melio, Silke E. Henkes, Daniela J. Kraft. Soft and Stiff Normal Modes in Floppy Colloidal Square Lattices. Phys. Rev. Lett. 132, 078202. Feb 14, 2024. 

Also: particle, nano, colloids, network, in https://www.inkgmr.net/kwrds.html

Keywords: gst, particle, nano, colloids, network, colloidal network



martedì 31 ottobre 2023

# gst: how to create a helix from a straight rod, “twist” or “bend” approaches.

<< There are two independent ways of creating a helix from a straight rod: curl the rod into a circle and then twist the rod all along its length to convert the ring into a helix (“twist” method), or deform the rod into a sine wave and then bend it with a sinusoidal distortion that curls at right angles to the first sine wave (“bend” method). Both procedures produce the same shape, but they generate different internal stresses within the rod, and their implementations require different amounts of energy. >>️

AA << say that their experiments could serve as a model for many physical systems that undergo handedness transitions, including the tendrils of plants, the flagella of microorganisms, and the strands of DNA molecules.  >>
David Ehrenstein. Two Experimental Observations of Helix Reversals. Physics 16, s158. Oct 24, 2023.  

Paul M. Ryan, Joshua W. Shaevitz,  Charles W. Wolgemuth. Bend or Twist? What Plectonemes Reveal about the Mysterious Motility of Spiroplasma. Phys. Rev. Lett. 131, 178401. Oct 24, 2023. 

Emilien Dilly, Sebastien Neukirch, Julien Derr, Drazen Zanchi. Traveling Perversion as Constant Torque Actuator. Phys. Rev. Lett. 131, 177201. Oct 24, 2023. 

Also: elastic, swim, in https://www.inkgmr.net/kwrds.html

Keywords: gst, elastic, elastic deformation, swimming



martedì 25 aprile 2023

# evol: gentle bonobos vs. aggressive chimps ...


<< Among the great apes, the chimpanzees and the bonobos are the most genetically related to us as we share about 98.7% of our DNA with them. >>️

<< So where exactly do humans stand? We seem to have incorporated the traits of both species, resulting in a tension between our aggressive and harmonious proclivities. Our tendency for conflict mirrors the competitiveness of chimpanzees, and yet the bonobos teach us that we have it in us to be altruistic and that society can be organised in more peaceful ways. This selflessness underlies the large-scale cooperation that has helped Homo sapiens share ideas, form nations, explore the universe and outlast other early humans such as Homo erectus. >>️

Jose Yong. Bonobos and chimps: what our closest relatives tell us about humans. theconversation.com. April 4, 2023. 


Also: 'evolution', 'chimps', 'behav' in https://www.inkgmr.net/kwrds.html

Keywords: evolution, chimps, bonobos,  chimpanzees, behavior


venerdì 7 aprile 2023

# gst: packing in slender structures, the geometry of squeezed elastic beams


<< The behavior of a collection of squeezed elastic beams is determined by geometry, not by complex forces. >>️

Dan Garisto. How Order Emerges in Bendy Beam Bunches. Physics 16, 54. Apr 3, 2023.

<< A collection of thin structures buckle, bend, and bump into each other when confined. This contact can lead to the formation of patterns: hair will self-organize in curls; DNA strands will layer into cell nuclei; paper, when crumpled, will fold in on itself, forming a maze of interleaved sheets. This pattern formation changes how densely the structures can pack, as well as the mechanical properties of the system. >>️

<< Here (AA) study the emergence of order in a canonical example of packing in slender structures, i.e., a system of parallel confined elastic beams. >>️

They << find that the compressive stiffness and stored bending energy of this metamaterial are directly proportional to the number of beams that are geometrically frustrated at any given point.  >>
Arman Guerra, Anja C. Slim, et al. Self-Ordering of Buckling, Bending, and Bumping Beams. Phys. Rev. Lett. 130, 148201. Apr 3, 2023.

Also

keyword 'self-assembly' in FonT

keyword 'elastic' in FonT

keyword 'elastico' in Notes
(quasi-stochastic poetry)

Keywords: gst, self-assembly, beams, buckling, bending, bumping, elasticity





lunedì 31 gennaio 2022

# 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.


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.


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.


Also

keyword 'evolution'  in FonT


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



keyword 'jazz' in FonT


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


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



martedì 7 luglio 2020

# gst: 'transcriptional burst frequency' modulation (more or less noise) during gene regulation

<< In cells, genes are expressed through transcription, a process where genetic information encoded in DNA is copied into messenger RNA (mRNA). The mRNA is then translated to make protein molecules, the workhorses of cells. This entire process is subject to bursts of natural stochasticity—or randomness—which can impact the outcome of biological processes that proteins carry out. >>

<< This work for the first time identifies the role of randomness in altering the outcome of a developmental process.>> Madhav Mani. 

<< By analyzing experimental perturbations of Drosophila's senseless gene against mathematical models, the team determined the sources of the gene's stochasticity, and found that the randomness appears to be leveraged in order to accurately determine sensory neuron fates. >>

<< Let's say you are quickly flipping a light switch on and off, but you want more brightness out of your bulb. You could either get a brighter bulb that produced more photons per unit time, or you could leave the switch 'on' more than 'off,' (..) What we found is that organisms control the amount of gene expression by regulating how often the gene is permitted to switch on, rather than making more mRNAs when it is on. >> Madhav Mani. 

<< From these studies, we are learning rules for how genes can be made more or less noisy, (..) Sometimes cells want to harness the genetic noise—the level of variation in gene expression—to make randomized decisions. Other times cells want to suppress the noise because it makes cells too variable for the good of the organism. Intrinsic features of a gene can imbue them with more or less noise. >> Richard Carthew. 

Alex Gerage. Toward principles of gene regulation in multicellular systems. Northwestern University. Jul 1, 2020.


Rachael Bakker, Madhav Mani, Richard W Carthew. The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts. eLife. doi: 10.7554/eLife.56076. Jun 22, 2020. 



lunedì 22 giugno 2020

# 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.


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. 


Also

keyword 'bot' in FonT





sabato 30 maggio 2020

# gst: apropos of unexpected Hopfion tangles

<< a certain geometrical structure of knots, which scientists call a Hopfion, manifests itself in unexpected corners of the universe, ranging from particle physics, to biology, to cosmology. >>

<< In a recent theoretical study, (..) (AA) discovered the presence of the Hopfion structure in nano-sized particles of ferroelectrics. >>

<< The Hopfion is a very abstract mathematical concept, (..) but the structure shows up in hydrodynamics, electrodynamics and even in the packing of DNA and RNA molecules in biological systems and viruses. >> Valerii Vinokur

<< When we visualized the polarization, we saw the Hopfion structure emerge, (..) We thought, wow, there is a whole world inside of these nanoparticles. >> Igor Luk'yanchuck.

Savannah Mitchem. Novel insight reveals topological tangle in unexpected corner of the universe. Argonne National Laboratory. May 26, 2020.


Luk’yanchuk I., Tikhonov Y., et al. Hopfions emerge in ferroelectrics
 Nat Commun 11, 2433. doi: 10.1038/ s41467-020-16258-w. May 15, 2020.


martedì 14 aprile 2020

# 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


mercoledì 27 novembre 2019

# phys: the qu-wave of the natural antibiotic gramicidin

<< One of the great counterintuitive puzzles of quantum mechanics is wave-particle duality. This is the phenomenon in which objects behave both like particles and like waves. >>

AA << for the first time, have demonstrated quantum interference in molecules of gramicidin, a natural antibiotic made up of 15 amino acids. Their work paves the way for the study of the quantum properties of  biomolecules and sets the scene for experiments that exploit the quantum nature of enzymes, DNA, and perhaps one day simple life forms such as viruses. >>

A natural biomolecule has been measured acting like a quantum wave for the first time. Mit Tech Rew - Emerging Technology from the arXiv. Nov 9, 2019. 

https://www.technologyreview.com/s/614688/a-natural-biomolecule-has-been-measured-acting-in-a-quantum-wave-for-the-first-time/

Armin Shayeghi, Philipp Rieser, et al. Matter-wave interference of a native polypeptide. arXiv:1910.14538v1 [quant-ph]. Oct 31, 2019.

https://arxiv.org/abs/1910.14538

Also

keyword "quantum" in FonT

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

sabato 2 novembre 2019

# 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    


martedì 24 settembre 2019

# 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   

venerdì 23 agosto 2019

# evol: when the dinosaurs died, lichens thrived ...

AA << results imply that multiple historical events during the transition from Mesozoic to Cenozoic eras, including the K-Pg mass extinction event, impacted the evolutionary dynamics in lichen-forming fungi. >>

Jen-Pan Huang, Ekaphan Kraichak, et al.   Accelerated diversifications in three diverse families of morphologically complex lichen-forming fungi link to major historical events. Scientific Reports.  volume 9, Article number: 8518 (2019).   https://www.nature.com/articles/s41598-019-44881-1  

<< We thought that lichens would be affected negatively, but in the three groups we looked at, they seized the chance and diversified rapidly, (..) Some lichens grow sophisticated 3D structures like plant leaves, and these ones filled the niches of plants that died out. >> Jen-Pang Huang.

When the dinosaurs died, lichens thrived. Mass extinction hurt land plants, but DNA shows that some fungus/plant combo organisms rose up. Field Museum, Academia Sinica, Taipei.  - ScienceDaily. Jun 28, 2019.   https://www.sciencedaily.com/releases/2019/06/190628120432.htm

K-Pg mass extinction event   https://en.m.wikipedia.org/wiki/Cretaceous%E2%80%93Paleogene_extinction_event

martedì 16 aprile 2019

# 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

sabato 6 ottobre 2018

# gst: periodic oscillations of flexible knots

AA << study the dynamics of knotted deformable closed chains sedimenting in a viscous fluid. (..) trefoil and other torus knots often attain a remarkably regular horizontal toroidal structure while sedimenting, with a number of intertwined loops, oscillating periodically around each other. (..) this motion (..) is accompanied by a very slow rotation around the vertical symmetry axis. (..) this oscillating mode of the dynamics can spontaneously form even when starting from a qualitatively different initial configuration. (..) the oscillating modes are usually present as transients or final stages of the evolution, depending on chain aspect ratio and flexibility, and the number of loops. >>

Magdalena Gruziel, Krishnan Thyagarajan, et al. Periodic Motion of Sedimenting Flexible Knots. Phys. Rev. Lett. 121, 127801 Sep 18,  2018. doi: 10.1103/PhysRevLett.121.127801.

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.121.127801

The periodic motion of flexible knots, and the connection to DNA. University of Warsaw. Sep 26, 2018.

https://m.phys.org/news/2018-09-periodic-motion-flexible-dna.html

sabato 8 settembre 2018

# gst: even repulsive interactions generate solitons

<< Solitons are nonspreading wave packets that exist in a wide range of real-world systems, including water waves, sound, DNA, optics, and so on. >>

<< Two or more solitons can bind together to form a soliton molecule with dynamics similar to matter molecules, such as vibration, synthesis, and dissociation. >>

<< Formation processes for three types of soliton molecules were studied: ground-, excited-state, and a new one termed an intermittent-vibration soliton molecule. While it is generally believed that attractive interactions of solitons are responsible for the formation of soliton molecules, the authors found that soliton interactions are not limited to attractive interactions. Counterintuitively, even repulsive interactions can lead to the formation of soliton molecules, >>

John Wallace. Investigation with a femtosecond fiber laser finds new type of soliton ‘molecule’. Aug 01, 2018.

https://www.laserfocusworld.com/articles/print/volume-54/issue-08/newsbreaks/investigation-with-a-femtosecond-fiber-laser-finds-new-type-of-soliton-molecule.html

<< For closely‐separated bound solitons, soliton interactions display wide diversities in repeated measurements, including soliton attraction, repelling, collision, vibration, and annihilation. For well‐separated bound solitons, repulsive interactions dominate the soliton interactions. >>

Junsong Peng, Heping Zeng. Build‐Up of Dissipative Optical Soliton Molecules via Diverse Soliton Interactions. Laser & Photonics Reviews 2018, 12, 1800009.

https://onlinelibrary.wiley.com/doi/pdf/10.1002/lpor.201800009 

Also "soliton" in:

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

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

lunedì 3 settembre 2018

# 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

lunedì 25 giugno 2018

# 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

venerdì 11 maggio 2018

# 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