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venerdì 11 ottobre 2024
# evol: flip of the script when an entity invert code sequences
lunedì 19 agosto 2024
# gst: apropos of 'normal' (jazzy?) codes, bacteria encode hidden, free-floating genes outside their genome.
venerdì 23 febbraio 2024
# gst: soft and stiff modes in colloidal particle networks
martedì 31 ottobre 2023
# gst: how to create a helix from a straight rod, “twist” or “bend” approaches.
martedì 25 aprile 2023
# evol: gentle bonobos vs. aggressive chimps ...
venerdì 7 aprile 2023
# gst: packing in slender structures, the geometry of squeezed elastic beams
lunedì 31 gennaio 2022
# evol: the hypothesis of quasi-stochastic 'jazzy' metamechanics of biological evolution (in Arabidopsis thaliana)
martedì 7 luglio 2020
# gst: 'transcriptional burst frequency' modulation (more or less noise) during gene regulation
lunedì 22 giugno 2020
# bots: tiny machinery, nanobots (molecule-sized bots) from 1k to millions swarming together to perform tasks
sabato 30 maggio 2020
# gst: apropos of unexpected Hopfion tangles
martedì 14 aprile 2020
# gene: stuttering, syncopated (but not junk) codes
mercoledì 27 novembre 2019
# phys: the qu-wave of the natural antibiotic gramicidin
sabato 2 novembre 2019
# evol: apropos of our origin, the KhoeSan trunk of the human tree
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.
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.
<< 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:
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
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