# 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

# behav: make yourself an ethoscope, by Quentin, Luis et al

<< Exploded drawing of an archetypal ethoscope. The machine is composed of ... >>

<< The ethoscope could be customised for a range of different scenarios >>

<< Another possible use of ethoscopes is the adaptation of the platform to detect behavior of other animals >>

Studying insect behavior? Make yourself an ethoscope. Oct 19, 2017.

https://m.phys.org/news/2017-10-insect-behavior-ethoscope.html

Quentin Geissmann, Luis Garcia Rodriguez, et al. Ethoscopes: An open platform for high-throughput ethomics. PLOS Biol 15 (10): e2003026. doi: 10.1371/journal.pbio.2003026

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2003026

# gst: it would use chaos to compute efficiently

<< When you’re really harried, you probably feel like your head is brimful of chaos. You’re pretty close. Neuroscientists say your brain operates in a regime termed the “edge of chaos,” and it’s actually a good thing. It’s a state that allows for fast, efficient analog computation of the kind that can solve problems that grow vastly more difficult as they become bigger in size >>

<< A micrograph shows the construction of a Mott memristor composed of an 8-nanometer-thick layer of niobium dioxide between two layers of titanium nitride >>

Samuel K. Moore. Memristor-Driven Analog Compute Engine Would Use Chaos to Compute Efficiently. Oct  9, 2017

https://spectrum.ieee.org/nanoclast/semiconductors/devices/memristordriven-analog-compute-engine-would-use-chaos-to-compute-efficiently

FonT

"When you’re really harried" ... only?

# ai: artificial intelligence AlphaGo becomes its own teacher

AA << introduce an algorithm based solely on reinforcement learning, without human data, guidance or domain knowledge beyond game rules. AlphaGo becomes its own teacher >>

David Silver, Julian Schrittwieser et al. Mastering the game of Go without human knowledge. Nature. 2017; 550: 354–9 doi: 10.1038/nature24270 Oct 18, 2017

http://www.nature.com/nature/journal/v550/n7676/full/nature24270.html

also

# s-ai: handling imperfect information (from scratch), by Libratus. Feb 4, 2017.

http://flashontrack.blogspot.it/2017/02/s-ai-handling-imperfect-information.html

# gst: adhesive performances (sticky approaches): a single type of toe pad (with lots of friction) vs multi functional "drunken stumbles"

AA << shows how different groups of lizards – geckos and anoles – took two completely different evolutionary paths to developing the beneficial trait of sticky toe pads >>

<< anoles seemed to commit to a single type of toe pad, one that generates lots of friction. As a group, they were able to develop sticky toe pads early. Geckos, meanwhile, opted for an evolutionary “drunken stumble,” and seemingly didn’t commit to a single approach, instead evolving toe pads that generate plenty of friction in some species and others that excel at sticking directly to a surface >>

Layne Cameron, Travis Hagey. An evolving sticky situation. Oct 12, 2017

http://msutoday.msu.edu/news/2017/an-evolving-sticky-situation/

https://www.sciencedaily.com/releases/2017/10/171012123031.htm

Travis J. Hagey, Josef C. Uyeda, et al. Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards. Evolution.  2017; 71 (10): 2344–58 doi: 10.1111/evo.13318 Sep 13, 2017

http://onlinelibrary.wiley.com/doi/10.1111/evo.13318/abstract

# gst: cooperating vs self-serving bacteria in transitional (noise) scenarios

AA << study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an environment that randomly switches between states of abundance and scarcity >>

AA << consider two scenarios—one of pure resource competition, and one in which one strain provides a public good—and investigate how environmental randomness (external noise) coupled to demographic (internal) noise determines the population’s fixation properties and size distribution >>

Karl Wienand, Erwin Frey, Mauro Mobilia. Evolution of a Fluctuating Population in a Randomly Switching Environment. Phys. Rev. Lett. 119, 158301 Oct 11, 2017

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.119.158301

AA << showed that a randomly changing environment can create a level playing field between self-serving bacteria and bacteria that work together >>

<< Cooperating bacterial populations are more likely to survive in changing habitats >>

Fluctuating environments can help cooperating bacteria. Oct 12, 2017

https://m.phys.org/news/2017-10-fluctuating-environments-cooperating-bacteria.html

# pharma: waiting for new 'magic strings': psilocybin to treat depression

AA << data fill an important knowledge gap regarding the post-treatment brain effects of psilocybin, and are the first in depressed patients [..] A ‘reset’ therapeutic mechanism is proposed >>

Robin L Carhart-Harris, Leor Roseman, et al. Psilocybin for treatment-resistant depression: fMRI-measured brain mechanisms. Sci Rep  2017; 7 (13187) doi: 10.1038/s41598-017-13282-7

https://www.nature.com/articles/s41598-017-13282-7

<< Patients taking psilocybin to treat depression show reduced symptoms weeks after treatment following a 'reset' of their brain activity >>

Ryan O'Hare. Magic mushrooms may 'reset' the brains of depressed patients. Oct 13, 2017.

http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/newssummary/news_12-10-2017-16-22-36

'Magic mushrooms' may 'reset' the brains of depressed patients, study suggests. Oct 13, 2017

https://www.sciencedaily.com/releases/2017/10/171013091018.htm

to update:

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