# evol: flip of the script when an entity invert code sequences

<< Jekyll and Hyde flip of the script when bacteria invert gene sequences. If a cell can diversify its own genome, this can be advantageous in the face of changing environmental conditions. Bacteria have been found that can alter encoded proteins by using the trick of sequence inversion inside genes. >>️

Chia-Chi Chang, Robert R. Jenq. Jekyll and Hyde flip of the script when bacteria invert gene sequences. Nature 634, 42-43. Sep 25, 2024. 

https://www.nature.com/articles/d41586-024-02807-6

Chia-Chi Chang, Robert R. Jenq. Bacteria invert gene sequences to flip the script. Nature. Vol 634. Oct 3, 2024 (pdf)  https://media.nature.com/original/magazine-assets/d41586-024-02807-6/d41586-024-02807-6.pdf

Chanin RB, West PT, et al. Intragenic DNA inversions expand bacterial coding capacity. Nature. 2024 Oct; 634 (8032): 234-242. doi: 10.1038/s41586-024-07970-4. Sep 25, 2024. 

https://pubmed.ncbi.nlm.nih.gov/39322669/

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

Also: 

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

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

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

Also (quasi-stochastic poetry): 

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

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

CODICE https://inkpi.blogspot.com/search?q=codice

Keywords: evolution, codes, DNA, RNA

# 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: collective patterns generated by capillary surfers.

<< Millimeter-sized “surfers” can self-propel across a vibrating liquid surface, interacting with other surfers to create collective patterns. >>

<< Self-propelled objects can move in mesmerizing patterns. The collective movements of groups of such objects typically occur in one of two flow regimes: the inertial regime—think swirling schools of fish in water—or the viscous regime—think swarming colonies of bacteria in mucus. Some self-propelled objects can travel in both flow regimes, a possibility that is less explored. >>️

AA << have studied the motion of a new system of self-propelled objects that move in this intermediate regime, finding that the objects organize into several distinct and tunable motion patterns. >>️️

<< Pairs of self-propelled surfers observed by the team move in one of seven different patterns (the video shows five). These include the “orbit,” where a pair of surfers rotate around a central point; the “tailgate,” where one surfer closely follows another, head to tail in a linear path; and the “jackknife,” where a pair of perpendicular surfers rotate stern to stern around their collision point. >>

<< When only one surfer was present, these mismatched amplitudes propelled the surfer in the direction of its bow. When there were two surfers close to each other, interactions among the waves caused the surfers to either repel each other so that they moved in opposite directions or to come together so that they collectively traced one of seven distinct patterns. >>️

️

Maggie Hudson. Synchronized Surfing of Self-Propelled Particles. Physics 16, s156. Nov 7, 2023. 

https://physics.aps.org/articles/v16/s156

Ian Ho, Giuseppe Pucci, Anand U. Oza, Daniel M. Harris. Capillary surfers: Wave-driven particles at a vibrating fluid interface. Phys. Rev. Fluids 8, L112001. Nov 7, 2023.

https://link.aps.org/doi/10.1103/PhysRevFluids.8.L112001

Anand U. Oza, Giuseppe Pucci, Ian Ho, Daniel M. Harris. Theoretical modeling of capillary surfer interactions on a vibrating fluid bath. Phys. Rev. Fluids 8, 114001. Nov 7, 2023.

https://link.aps.org/doi/10.1103/PhysRevFluids.8.114001

Also: waves, particle, swarm, in: https://www.inkgmr.net/kwrds.html

Keywords: gst, waves, wave-wave, capillary waves, particles, self-propelled particles, fluid-particle interactions, wave-particle interactions

# gst: emergence of self-organizing zigzag patterns among (magnetic) particles suspended in a liquid

<< When molecules or bacteria organize into a long-range pattern, researchers want to understand how the microscopic interactions lead to the macroscopic order. (AA) observed such self-organization in magnetic particles suspended in a liquid and subjected to an oscillating magnetic field. Through experiments and simulations, the team showed that the resulting zigzag pattern is explained by the fluid flow generated around the oscillating particles, not by any details of the particles or the applied field. Similar zigzag patterns have also been seen in charged colloids subjected to oscillating electric fields, so the explanation may cover a range of particle systems. The researchers also believe that understanding and controlling the effect could lead to useful applications in microfluidics devices. >>️

David Ehrenstein. Self-Organized Zigzags from Fluid Flow. Physics 16, 138. Aug 11, 2023.

https://physics.aps.org/articles/v16/138

Gaspard Junot, Marco De Corato, Pietro Tierno. Large Scale Zigzag Pattern Emerging from Circulating Active Shakers. Phys. Rev. Lett. 131, 068301. Aug 11, 2023. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.131.068301

Also: particle, self-assembly, chiral, behav, in: https://www.inkgmr.net/kwrds.html  

Keywords: gst, behavior, particle, self-assembly, self-organization, chiral, active shakers, squirmers, alternating chirality

# ecol: mycological jazz

<< "Mycological" draws conceptually from fungal networks in forests and their interactions. Inspired by the work of ecologist Suzanne Simard, author Michael Pollan, and mycologist Paul Stamets; Krolak saw many parallels between biological networks and the social network known as jazz, as well as, the acoustic networks created when musicians interact through their instruments. Aesthetically, the work is of the free and avant-garde traditions of jazz. Drawing inspiration from John Coltrane to Sonny Sharrock to Makaya McCraven, Krolak seeks to create a space for various elements to play out and find their own connections. >>

Mycological By Nicholas Krolak. All About Jazz. Jan 8, 2022. 

https://www.allaboutjazz.com/media/track-mycological-by-nicholas-krolak

Also

Apropos of 'mycological jazz', a old  perplexity of mine, who knows why substantial funds were no longer allocated to sci research on viruses, bacteria, fungi (..) and their ecological 'jazzy interactions' ... ? 😏

keyword 'virus' | 'bacteria' | 'fungi' in FonT

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

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

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

Also

Much of intelligence (quasi-stochastic poetry). Notes. Dec 16, 2005.

https://inkpi.blogspot.com/2005/12/1929-much-of-intelligence.html

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: jazz, viruses, bacteria, fungi, interactions, acad, scires, funds

# evol: viruses as a facilitator / driver of horizontal gene transfer among eukaryotes

<< Gene exchange between viruses and their hosts acts as a key facilitator of horizontal gene transfer and is hypothesized to be a major driver of evolutionary change. Our understanding of this process comes primarily from bacteria and phage co-evolution, but the mode and functional importance of gene transfers between eukaryotes and their viruses remain anecdotal. >>

AA << systematically characterized viral–eukaryotic gene exchange across eukaryotic and viral diversity, identifying thousands of transfers and revealing their frequency, taxonomic distribution and projected functions. Eukaryote-derived viral genes, abundant in the Nucleocytoviricota, highlighted common strategies for viral host-manipulation, including metabolic reprogramming, proteolytic degradation and extracellular modification. Furthermore, viral-derived eukaryotic genes implicate genetic exchange in the early evolution and diversification of eukaryotes, particularly through viral-derived glycosyltransferases, which have impacted structures as diverse as algal cell walls, trypanosome mitochondria and animal tissues. These findings illuminate the nature of viral–eukaryotic gene exchange and its impact on the evolution of viruses and their eukaryotic hosts. >>️

Irwin, N.A.T., Pittis, A.A., Richards, T.A. et al. Systematic evaluation of horizontal gene transfer between eukaryotes and viruses. Nat Microbiol. doi: 10.1038/ s41564-021-01026-3. Dec 31, 2021. 

https://www.nature.com/articles/s41564-021-01026-3

<< We knew from individual examples that viral genes have played a role in the evolution of eukaryotes. Even humans have viral genes, which are important for our development and brain function, (..)  We wanted to understand more broadly how HGT (horizontal gene transfer) has affected viruses and eukaryotes from across the tree of life. >> Nicholas Irwin. ️

<< We were interested to find that certain groups of viruses, especially those that infect single-celled eukaryotes, acquire a lot of genes from their hosts, (..)  By studying the function of these genes we were able to make predictions about how these viruses affect their hosts during infection. >> Patrick Keeling.

<< Many of these viral-derived genes appear to have repeatedly affected the structure and form of different organisms, from the cell walls of algae to the tissues of animals, (..) This suggests that host-virus interactions may have played an important role in driving the diversity of life we see today. >> Nicholas Irwin. ️

<< These transfers not only have evolutionary consequences for both virus and host, but could have important health implications, >> Patrick Keeling.️

<< we think that this work serves as an interesting reminder that viruses have also contributed to the evolution of life on Earth, >>️ Nicholas Irwin. 

️

New research shows gene exchange between viruses and hosts drives evolution. University of British Columbia. Jan 5, 2022.

https://phys.org/news/2022-01-gene-exchange-viruses-hosts-evolution.html

Also

Nonlinear effects in shaping human evolution, the role of viruses. Jan 15, 2019. 

https://flashontrack.blogspot.com/2019/01/evol-nonlinear-effects-in-shaping-human.html

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

Keywords: evolution, virus, gene exchange, horizontal gene transfer, HGT

# gst: ️apropos of spontaneous active matter, the active droploids.

<< Active matter comprises self-driven units, such as bacteria and synthetic microswimmers, that can spontaneously form complex patterns and assemble into functional microdevices. These processes are possible thanks to the out-of-equilibrium nature of active-matter systems, fueled by a one-way free-energy flow from the environment into the system. Here, (AA) take the next step in the evolution of active matter by realizing a two-way coupling between active particles and their environment, where active particles act back on the environment giving rise to the formation of superstructures. >>️

<< These structures hinge on mutually coupled structure formation processes of the colloids, which form an engine, and the surrounding solvent, which phase separates in regions of high colloidal density and encapsulates the engine within a droplet shell.  >>

️

Jens Grauer, Falko Schmidt, et al. Active droploids. arXiv:2109.10677v1 [cond-mat.soft]. Sep 22, 2021.

https://arxiv.org/abs/2109.10677

Also

keyword 'drop' | 'droplet' in FonT

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

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

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

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

keywords: gst, drops, droplets, colloids, active matter, active droploids, self-assembly, solitons.

# evol: ancient photosynthesis could be as old as life itself

<< the earliest bacteria had the tools to perform a crucial step in photosynthesis,  (..) The finding also challenges expectations for how life might have evolved on other planets. >>️

<< Photosystem II show patterns of evolution that are usually only attributed to the oldest known enzymes, which were crucial for life itself to evolve >> Tanai Cardona.️

<< enzymes capable of performing the key process in oxygenic photosynthesis -- splitting water into hydrogen and oxygen -- could actually have been present in some of the earliest bacteria. The earliest evidence for life on Earth is over 3.4 billion years old and some studies have suggested that the earliest life could well be older than 4.0 billion years old.  Like the evolution of the eye, the first version of oxygenic photosynthesis may have been very simple and inefficient; as the earliest eyes sensed only light, the earliest photosynthesis may have been very inefficient and slow. (..) that oxygen production was present at all so early on means in other environments, such as on other planets, the transition to complex life could have taken much less time. >>️

Photosynthesis could be as old as life itself. Imperial College London. Mar 24, 2021. 

https://www.sciencedaily.com/releases/2021/03/210324142839.htm

Thomas Olivera, Patricia Sanchez-Baracaldo, et al. Time-resolved comparative molecular evolution of oxygenic photosynthesis.Biochimica et Biophysica Acta (BBA) - Bioenergetics, 2021; 1862 (6): 148400. doi: 10.1016/ j.bbabio.2021.148400. Jun 1,  2021.

https://www.sciencedirect.com/science/article/pii/S0005272821000335

Also

Lewis M. Ward, Patrick M. Shih. Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost  lineages and horizontal gene transfer. PLoS ONE 16(1): e0239248. doi:10.1371/journal.pone.0239248. 

Jan 28, 2021. 

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0239248

# gst: NikS, a small RNA molecule uses a sort of 'bet-hedging' strategy to survive and infect

<< More than half of the world's population carries the bacterium Helicobacter pylori in their stomach mucosa. It often causes no problems throughout life, but sometimes it can cause inflammation, and in some cases, it can even lead to the development of stomach cancer. Helicobacter pylori uses several 'virulence' factors that allow it to survive in the stomach and can lead to the development of disease. (AA) report that multiple of these factors are centrally regulated by a small RNA molecule called NikS.  >>

<< The fact that Helicobacter pylori can colonize such a hostile environment as the stomach so successfully is also due to a special genetic strategy: Like other pathogens, H. pylori uses a strategy known as phase variation to adapt as flexibly as possible to changes in its environment. Phase variation means that the bacteria constantly switch expression of a gene at random through genetic mutations, meaning that some bacteria in a population will always be ready to express the important gene when it becomes important—a sort of 'bet-hedging' strategy. >>

Robert Emmerich. Small RNA as a central player in infections. University of Würzburg. Oct 15, 2020. 

https://phys.org/news/2020-10-small-rna-central-player-infections.html   

Sara K. Eisenbart, Mona Alzheimer, et al. A Repeat-Associated Small RNA Controls the Major Virulence Factors of Helicobacter pylori. Mol Cell. vol 80, issue 2, P210-226.E7. doi: 10.1016/ j.molcel.2020.09.009. Oct 15, 2020. 

https://www.cell.com/molecular-cell/fulltext/S1097-2765(20)30617-1

# 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

# life: Black Death way revisited, the hypothesis, by Parag.

<< Good afternoon to everyone online and in the room. (..) Since yesterday, Denmark, Estonia, Lithuania, Netherlands and Nigeria have all reported their first cases. All these cases have links to Italy. 24 cases have been exported from Italy to 14 countries, and 97 cases have been exported from Iran to 11 countries. >>  

Tedros Adhanom Ghebreyesus.

WHO Director-General's opening remarks at the media briefing on COVID-19. WHO. Feb 28, 2020.

https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---28-february-2020

<< A striking overlap exists between the path of today's viral spread and the path of the Black Death in the 1300s. >>

<< It is, of course, far too soon to make such dire predictions about Covid-19. But a striking overlap exists between the path of today's viral spread and the path that emerged in the 1300s. >>

<< The 14th-century plague is said to have originated in northwestern China, with bacteria contracted from marmots. Hebei Province bore the brunt of China’s plague fatalities, with 5 million of its residents perishing in the 1330s. Making its way westward via Silk Road merchants and caravans, the plague took several years to reach Persia, where it killed the Khan overlord Abu Said as well as half the population. In 1347, it entered Europe via Italy’s port of Genoa. >>

<< Now compare that to what we’re seeing today with Covid-19. This time around, the source of illness may have been pangolins or bats instead of marmots. It started in Wuhan, which just happens to be Hebei's capital. The coronavirus reached Iran in a couple of weeks, and so far has infected hundreds of people, even the country’s deputy health minister. Next to Iran, the next worst outbreak is in Italy, with more than 300 cases and rising quickly- and likely spreading through Europe exactly as the plague did centuries ago. >>

<< It is, perhaps no coincidence that, in the past two decades, China has been the origin of SARS, the swine flu, and now the Covid-19 coronavirus. Nor should we be surprised that Iran and Italy have emerged, once more, as waypoints for pandemic spread. What do Iran and Italy have in common today? They are two major anchors of China’s Belt and Road Initiative- also known as the 21st century’s new Silk Roads. >>

Parag Khanna. IDEAS. Covid-19 Is Traveling Along the New Silk Road. Wired. Feb 28, 2020.

https://www.wired.com/story/covid-19-is-traveling-along-the-new-silk-road/

Also

keyword 'virus' by FonT

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

keyword 'virus' by Notes

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

# behav: 'run and tumble' behavior (among bacteria)

<< Bacteria in groundwater move in surprising ways. They can passively ride flowing groundwater, or they can actively move on their own in what scientists call "run and tumble" behavior.  >>

AA << noted a distinct run (movement in one direction) followed by a tumble (a sudden, random change in direction). By calculating the length and timing of these movements, they could develop a simple Continuous Time Random Walk (CTRW) model to predict how the bacteria would move. When compared to current models for bacterial remediation, the CTRW model was better at predicting bacterial transport in many circumstances. The CTRW model is the first step in developing and testing new reactive transport models that incorporate bacterial transport behavior.  >>

Rishi Parashar. Calculating 'run and tumble' behavior of bacteria in groundwater. Environmental Molecular Sciences Laboratory. Oct 31, 2019. 

https://m.phys.org/news/2019-10-behavior-bacteria-groundwater.html  

Xueke Yang, Rishi Parashar, et al. On Modeling Ensemble Transport of Metal Reducing Motile Bacteria. Scientific Reports volume 9, Article number: 14638. Oct 10, 2019. 

https://www.nature.com/articles/s41598-019-51271-0

# 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: programmed cell death (apoptosis) also in algae

<< bacteria that live on single-cellular algae can cause programmed cell death. "It is the first documentation of true apoptosis via bacterial pathogens in microorganisms like algae," >>  Rebecca Case.

Study shows first evidence bacterial-induced apoptosis in algae. University of Alberta.  Mar 21, 2019.

https://m.phys.org/news/2019-03-evidence-bacterial-induced-apoptosis-algae.html    

Anna R. Bramucci, Rebecca J. Case.
Phaeobacter inhibens induces apoptosis-like programmed cell death in calcifying Emiliania huxleyi. Scientific Reports. Volume 9, Article number: 5215 (2019) March 21.

https://www.nature.com/articles/s41598-018-36847-6  

# gst: the complex world of Bacteria; collective oscillations via discontinuous transitions, chemical quorum sensing and brainlike bursts of electricity to communicate.

<< collective oscillations in cell populations can emerge suddenly with nonzero amplitude via a discontinuous transition. >>

Rosa Martinez-Corral, Jintao Liu, et al. Bistable emergence of oscillations in growing Bacillus subtilis biofilms. PNAS Sep 4, 2018;  115 (36) E8333-E8340.  doi: 10.1073/pnas.1805004115

https://www.pnas.org/content/115/36/E8333 

<< As in all communities, cohabiting bacteria need ways to exchange messages. Biologists have known for decades that bacteria can use chemical cues to coordinate their behavior. >>

AA << are now finding that bacteria in biofilms can also talk to one another electrically. Biofilms appear to use electrically charged particles to organize and synchronize activities across large expanses. This electrical exchange has proved so powerful that biofilms even use it to recruit new bacteria from their surroundings, and to negotiate with neighboring biofilms for their mutual well-being. >>

<< Step by step we find that all the things we think bacteria don’t do, they actually do, [..] It’s displacing us from our pedestal. >> Ned Wingreen.

Gabriel Popkin. Bacteria Use Brainlike Bursts of Electricity to Communicate. With electrical signals, cells can organize themselves into complex societies and negotiate with other colonies. Sep 5, 2017

https://twitter.com/QuantaMagazine/status/1071417372500783104

https://www.quantamagazine.org/bacteria-use-brainlike-bursts-of-electricity-to-communicate-20170905/

Also

Gurol M. Suel publ.

http://labs.biology.ucsd.edu/suel/index.html

FonT

intrigante qui l'idea di una Intelligenza Artificiale che, dalle relativamente comode e veloci osservazioni sull'evoluzione di colonie batteriche sotto differenti condizioni, sia in grado di circoscrivere pattern comportamentali di interesse per la modellizzazione (e previsione)  di comunita' altre ...

# tech: it repels everything with some beneficial exceptions

<< Researchers at McMaster University have solved a vexing problem by engineering surface coatings that can repel everything, such as bacteria, viruses and living cells, but can be modified to permit beneficial exceptions. >>

Researchers design "smart" surfaces to repel everything but targeted beneficial exceptions. McMaster University. Oct 24, 2018

https://phys.org/news/2018-10-smart-surfaces-repel-beneficial-exceptions.html

Tohid Didar. Researchers design "smart" surfaces, creating promise for safer implants and more accurate diagnostic tests. Oct 24, 2018.

https://www.eng.mcmaster.ca/news/researchers-design-smart-surfaces-creating-promise-safer-implants-and-more-accurate-diagnostic

# epidem: they fall from the sky

<< Aerosolization of soil-dust and organic aggregates in sea spray facilitates the long-range transport of bacteria, and likely viruses across the free atmosphere. >>

The << results provide an explanation for enigmatic observations that viruses with very high genetic identity can be found in very distant and different environments. >>

Isabel Reche, Gaetano D’Orta, et al. Deposition rates of viruses and bacteria above the atmospheric boundary layer. The ISME Journal.
doi: 10.1038/s41396-017-0042-4. Jan 29,  2018.

https://www.nature.com/articles/s41396-017-0042-4

University of British Columbia.  Viruses - lots of them - are falling from the sky. Feb 6, 2018.

https://m.phys.org/news/2018-02-viruseslots-themare-falling-sky.html

# 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

# s-ecol: asymmetric cooperation during symbiosis (among Polynucleobacteria)

<< Relationships where two organisms depend on each other, known as symbiosis, evoke images of partnership and cooperation. But a new study in Nature Ecology and Evolution shows that, when it comes to certain microorganisms, symbiotic partners are actually being held "hostage" >>

Hostage situation or harmony? Researchers rethink symbiosis. July 27, 2017

https://m.phys.org/news/2017-07-hostage-situation-harmony-rethink-symbiosis.html

Vittorio Boscaro, Martin Kolisko, et al.  Parallel genome reduction in symbionts descended from closely related free-living bacteria. Nature Ecology & Evolution 1, 1160–1167 (2017) doi: 10.1038/s41559-017-0237-0 Publ. July 21,  2017

https://www.nature.com/articles/s41559-017-0237-0