Quorum sensing (Introduction)

by David Turell @, Saturday, November 09, 2013, 17:33 (4032 days ago)

I've presented this before I think: Bacterial colonies use chemicals to communicate and to adapt group behavior. It is all at the molecular level, and I conclude DNA manages it since sRNA (small) are used:-http://www.newscientist.com/article/dn17390-why-microbes-are-smarter-than-you-thought.html-
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3730234/

Quorum sensing

by David Turell @, Sunday, November 10, 2013, 02:59 (4032 days ago) @ David Turell

Listen to this lecture:-http://www.bbc.com/future/story/20120614-how-bacteria-talk-Great lecturer

Quorum sensing

by David Turell @, Wednesday, January 21, 2015, 16:27 (3594 days ago) @ David Turell

Bacterial communication by chemical molecules:-"To date, the best known communication between bacteria occurs via the N-acyl homoserine lactone (AHL): The enzyme Luxl produces signals that are recognised by the LuxR receptor, at which point the bacteria develop certain properties and modulate their behaviour towards one another. Since a certain number of bacteria must be available for this to occur, this process is known as "quorum sensing."-"However, Heermann's and Bode's working groups investigate bacteria that possess a LuxR receptor, but not the enzyme Luxl. In the current study, the microbiologists have investigated the bacteria Photorhabdus asymbiotica, which is a deadly pathogen in insects, which also infects humans and can cause skin infections. These bacteria communicate via the signal molecule dialkylresorcinol, which recognised the associated LuxR receptor. "The influence on the pathogenic properties of the bacteria is at its strongest in this 'quorum sensing' system. P. asymbiotica requires dialkylresorcinol and in this way coordinates the communication with the conspecifics for the successful infection of the larvae," says Helge Bode, whose group in 2013 also described the biosynthesis of this new signal molecule."-http://www.sciencedaily.com/releases/2015/01/150121083640.htm

Quorum sensing; more research

by David Turell @, Tuesday, April 07, 2015, 18:42 (3518 days ago) @ David Turell

All done by molecular reactions:-http://phys.org/news/2015-04-mechanisms-social-networking-bacteria.html-"As he explains, "Individual bacteria within a population communicate with members of the group through a process called quorum sensing, where chemical signals and extracellular peptides serve as the language for bacterial communication." It is not just "social" networking, he adds. Bacterial communities use quorum sensing to control a variety of biomedically relevant biological processes.-"In a new paper in a recent early online edition of Molecular Microbiology, he and co-authors Kristina Boguslawski and Patrick Hill describe how they deciphered this bacterial communication to reveal new mechanisms of regulating gene expression in the model bacterium Bacillus subtilis.-"'Research in my lab is devoted to deciphering these different bacterial languages, understanding how bacteria perceive these signals, and determining how bacteria use this information to regulate biological processes at the molecular level," says Griffith. "In this paper, we have expanded the range of biological processes known to be controlled by a plasmid-encoded quorum response pair known as Rap60-Phr60.-"Using biochemical approaches, the authors found that Rap60 regulates the activity of two important transcription factors by "mechanisms never before observed for Rap proteins," says Griffith. "This work changes the way we think about these important regulatory proteins. The implications likely extend beyond Bacillus biology as they represent potential novel targets for the development of antibiotic and therapeutics in pathogenic bacteria.'"

Quorum sensing; more research

by dhw, Wednesday, April 08, 2015, 12:56 (3518 days ago) @ David Turell

DAVID: All done by molecular reactions:-http://phys.org/news/2015-04-mechanisms-social-networking-bacteria.html-QUOTE: "As he explains, "Individual bacteria within a population communicate with members of the group through a process called quorum sensing, where chemical signals and extracellular peptides serve as the language for bacterial communication." It is not just "social" networking, he adds. Bacterial communities use quorum sensing to control a variety of biomedically relevant biological processes.
"'Research in my lab is devoted to deciphering these different bacterial languages, understanding how bacteria perceive these signals, and determining how bacteria use this information to regulate biological processes at the molecular level," says Griffith. -Presumably your introductory remark “all done by molecular reactions” is meant to indicate that there is no cognition involved and everything is done automatically. As I see it, this article (and the clause you have emphasized) explains how bacteria use their own languages to communicate in order to decide the best way to use the information. The molecular activity is known, but how it is directed is not known. “Bacteria use quorum sensing to control...” does not mean “Bacteria are controlled by...” Here is another paragraph which vividly describes procedures that seem anything but automatic.-QUOTE: “Each species of bacteria has its own unique language, the authors say. In addition, there are "universal signals, analogous to Morse code, used for communication between different species of bacteria," says Griffith. "In microbial communities, bacteria within a similar group communicate with one another, while other groups are eavesdropping or even disrupting the others' communication. It is biological espionage. Bacteria that can communicate with one another and work together as a group will be more successful in competing for resources than individuals.”-Decisions are clearly being made all the time, and what the researchers have discovered is how bacteria communicate, not how they take those decisions. Perhaps you think that a description of how humans vibrate their vocal chords, waggle their tongues, open and close their lips etc. explains how and why they choose their words.

Quorum sensing; more research

by David Turell @, Thursday, April 09, 2015, 02:15 (3517 days ago) @ dhw

dhw: As I see it, this article (and the clause you have emphasized) explains how bacteria use their own languages to communicate in order to decide the best way to use the information. The molecular activity is known, but how it is directed is not known. “Bacteria use quorum sensing to control...” does not mean “Bacteria are controlled by...” -I understand that. The obvious answer is the instructions in their DNA guides them into how to handle each stimulus. -> dhw: QUOTE: “Each species of bacteria has its own unique language, the authors say. In addition, there are "universal signals, analogous to Morse code, used for communication between different species of bacteria," says Griffith. "In microbial communities, bacteria within a similar group communicate with one another, while other groups are eavesdropping or even disrupting the others' communication. It is biological espionage. Bacteria that can communicate with one another and work together as a group will be more successful in competing for resources than individuals.”-All perfectly true.
> 
> dhw: Decisions are clearly being made all the time, and what the researchers have discovered is how bacteria communicate, not how they take those decisions.-Simple: a bacteria receives a signal molecule, A, and a stimulus strength, B. A & B elicit a response of either D, E, or F depending upon the quality of A & B. My kidney cells do this all the time to decide how much sodium to remove from my blood. The single celled bacteria is no different. And my kidney cells cooperate all the time, just as your favorite cooperating bacteria do. Your kidney cells are just like mine. Aren't you thankful they are automatic, so you don't have to think about them?-Same old issue: bacteria can look like they are decision-making by simply following the on-board rules. They have to eat and poop just like we do, and they don't think about it any more than we do.

Quorum sensing; fights viral infections

by David Turell @, Sunday, November 20, 2016, 00:30 (2926 days ago) @ David Turell

Bacteria in large communities use quorum sensing and gene modification to protect themselves against infection by viruses:

http://phys.org/news/2016-11-bacteria-ramp-immune-response-viral.html

"Bacteria can boost their own immune systems by "talking" to each other, surprising new research from New Zealand's University of Otago shows.

"People have long understood the advantages of living in communities and bacteria are no different, often residing in close quarters to share resources. However, there are also potential drawbacks to community life as high-density bacterial populations are more vulnerable to the spread of viruses - just like people in a crowded bus or a daycare centre," he says.

"The breakthrough came when the researchers discovered that the ability of bacteria to gauge the number of cells in their communities enabled the bacteria to boost the power of their CRISPR-Cas immune systems to prevent viral outbreaks.

"Associate Professor Fineran says the bacteria sense the population density by "talking" to each other using a form of chemical communication known as quorum sensing.

"'The higher the population density, the stronger the communication between cells becomes, which results in greater coordination of immune defenses," he says.
Adrian Patterson, a PhD student and first author on the paper, says the study shows that bacterial cells preemptively elevate their immunity when they are most at risk of a virus spreading through the population.

"'They both increase their ability to generate new immune memories and strengthen existing immunity by up to 500-fold," Mr Patterson says.

"The role of CRISPR-Cas in providing bacteria with viral immunity was only discovered in the past decade.

"The systems create genetic memories of specific past viral infections by taking little snippets of the viruses' DNA and storing them in memory banks to aid in recognising and destroying future infections.

"One of the least understood aspects of the CRISPR-Cas field is how bacteria control the activity of these systems. Too much activity can result in an autoimmune-like disease, killing the host cell, but too little activity might allow viruses to wipe out entire bacterial communities. The team's research shows that by openly communicating with each other, bacteria strike the right balance between these two outcomes."

Comment: Quorum sensing occurs as bacteria gather in numbers and sense chemicals from each other. In this case the CRISPR-Cas mechanisms modifies the DNA to accept info about previous viral attacks. This is exactly as Shapiro would predict they do, modifying DNA to respond to stimuli.

Quorum sensing; fights viral infections

by dhw, Sunday, November 20, 2016, 12:12 (2925 days ago) @ David Turell

QUOTE: “The team's research shows that by openly communicating with each other, bacteria strike the right balance between these two outcomes."

David’s comment: Quorum sensing occurs as bacteria gather in numbers and sense chemicals from each other. In this case the CRISPR-Cas mechanisms modifies the DNA to accept info about previous viral attacks. This is exactly as Shapiro would predict they do, modifying DNA to respond to stimuli.

Yes, indeed. And Shapiro believes bacteria are intelligent beings. All physical processes, including our own, involve the use of chemicals. With larger organisms, you accept that when decisions are made, the use of chemicals is directed by an intelligent mind. But you insist that an intelligent mind demands a brain, except that you believe in an afterlife, which means that an intelligent mind does not demand a brain:

Jesse Bering (Under “Afterlife: sceptical thought”): My bet remains that immortal souls — yours, mine, and Ian Stevenson’s — are but the elusive shadows dancing on the walls of our physical brains.

David’s comment: A skeptic just like Blackmore. Not hallucinations.

I should add that last week I had the doubtful pleasure of attending a talk on consciousness by Blackmore, and her muddled thinking left me sceptical of sceptics!

Quorum sensing; fights viral infections

by David Turell @, Sunday, November 20, 2016, 15:15 (2925 days ago) @ dhw

QUOTE: “The team's research shows that by openly communicating with each other, bacteria strike the right balance between these two outcomes."

David’s comment: Quorum sensing occurs as bacteria gather in numbers and sense chemicals from each other. In this case the CRISPR-Cas mechanisms modifies the DNA to accept info about previous viral attacks. This is exactly as Shapiro would predict they do, modifying DNA to respond to stimuli.

dhw: Yes, indeed. And Shapiro believes bacteria are intelligent beings. All physical processes, including our own, involve the use of chemicals. With larger organisms, you accept that when decisions are made, the use of chemicals is directed by an intelligent mind. But you insist that an intelligent mind demands a brain, except that you believe in an afterlife, which means that an intelligent mind does not demand a brain:

Jesse Bering (Under “Afterlife: sceptical thought”): My bet remains that immortal souls — yours, mine, and Ian Stevenson’s — are but the elusive shadows dancing on the walls of our physical brains.

Dualism solves all! As for Shapiro he says bacteria are sentient, which means they receive stimuli and properly respond to them by modifying their own DNA, nothing more.

Quorum sensing; fights viral infections

by dhw, Monday, November 21, 2016, 12:46 (2924 days ago) @ David Turell

QUOTE: “The team's research shows that by openly communicating with each other, bacteria strike the right balance between these two outcomes."
David’s comment: Quorum sensing occurs as bacteria gather in numbers and sense chemicals from each other. In this case the CRISPR-Cas mechanisms modifies the DNA to accept info about previous viral attacks. This is exactly as Shapiro would predict they do, modifying DNA to respond to stimuli.

dhw: Yes, indeed. And Shapiro believes bacteria are intelligent beings. [...}

DAVID: {...} As for Shapiro he says bacteria are sentient, which means they receive stimuli and properly respond to them by modifying their own DNA, nothing more.

As quoted on 10 November (my bold):

Exeter meeting: "...we have a great deal to learn about chemistry, physics and evolution from our small, but very intelligent, prokaryotic relatives."

Shapiro: 'Evolution: A view from the 21st century' (p. 143): “Living cells and organisms are cognitive (sentient) entities that act and interact purposefully to ensure survival, growth and proliferation. They possess corresponding sensory, communication, information-processing, and decision-making capabilities.”

I know you don’t believe in cellular intelligence, but please stop pretending that when Shapiro says cells are very intelligent, he means they are not intelligent.

Quorum sensing; fights viral infections

by David Turell @, Monday, November 21, 2016, 15:00 (2924 days ago) @ dhw

dhw: As quoted on 10 November (my bold):

Exeter meeting: "...we have a great deal to learn about chemistry, physics and evolution from our small, but very intelligent, prokaryotic relatives."

Shapiro: 'Evolution: A view from the 21st century' (p. 143): “Living cells and organisms are cognitive (sentient) entities that act and interact purposefully to ensure survival, growth and proliferation. They possess corresponding sensory, communication, information-processing, and decision-making capabilities.”

I know you don’t believe in cellular intelligence, but please stop pretending that when Shapiro says cells are very intelligent, he means they are not intelligent.

All of Shapiro's statements are true, but they describe automatic activity. Bacteria are intelligently designed. We are back to our individual viewpoints.

Quorum sensing: how it works in bacteria and viruses

by David Turell @, Monday, November 07, 2022, 01:32 (748 days ago) @ David Turell

Sensing extruded chemicals:

https://www.the-scientist.com/sponsored-article/brush-up-quorum-sensing-in-bacteria-and...

Individual bacteria use quorum sensing to detect and respond to changes in cell density as a coordinated group. For example, the first reported evidence of quorum sensing was in two marine bacterial species that emit light in response to high cell density, which is responsible for bioluminescence in various marine hosts. Researchers have identified many species of bacteria that interrelate gene regulation with their neighbors to control a variety of processes, including symbiosis, virulence, antibiotic resistance, and biofilm formation.

"Quorum sensing is mediated by bacteria producing, releasing, and detecting extracellular signaling molecules called autoinducers. Typically, when individual bacteria divide, they produce and release autoinducers. When cell density is low, these molecules diffuse in the environment, and bacteria regulate gene expression independently. Autoinducer levels increase as bacteria continue to divide, and when the extracellular concentration of these signaling molecules reaches a certain threshold, individual bacteria detect that the quorum threshold has been reached. As a result, they regulate signaling pathways and gene transcription in response to the surrounding cell population density. When bacteria sense a quorum, they typically make more proteins involved in autoinducer production, which creates a positive feedback loop to maintain coordinated behaviors related to high population density. Induction of the feedback loop is why quorum signaling molecules are commonly called autoinducers.

"Both gram-negative and gram-positive bacteria use quorum sensing. Generally, gram-negative bacteria employ acylated homoserine lactones as autoinducers, which diffuse into the environment passively. In contrast, gram-positive bacteria typically use processed oligopeptides, which must be actively secreted through their cell wall.

"Intraspecies quorum sensing allows a variety of bacteria to communicate and alter their behavior in response to bacteria of the same species. Additionally, interspecies quorum sensing between different bacterial species can lead to both conflict and collaboration. For example, enteric bacteria in the human gut microbiome coordinate behavior with each other and against harmful bacteria. Unfortunately, interspecies quorum sensing is not always to the benefit of humans; some bacteria coordinate with one another to enhance each other’s virulence and form symbiotic relationships to create biofilms that protect pathogens from antibiotics.

"Bacteria regulate virulence genes and other pathogenic factors with quorum sensing. Activating virulence genes at low cell density might alert the host defence response, which prevents invading bacteria from establishing themselves. As such, opportunistic bacteria control virulence genes through quorum sensing to wait until they achieve a sufficient cell density to overpower host defence mechanisms. Once the optimum autoinducer concentration threshold is reached, they synthesize virulence factors to ensure their infection and survival.

***

"While studying quorum sensing’s role in mediating viral infection of bacteria, researchers identified a comparable communication system in temperate bacterial phages—viruses that enter either the lytic or lysogenic pathway when they infect a bacterium. Viruses in the lytic pathway kill and lyse their host bacterial cell, but in the lysogenic cycle, the phage integrates its genetic material into the bacterial genome and keeps its host alive. Researchers discovered that some phages monitor the concentration of arbitrium—the viral equivalent of an autoinducer—to decide when to switch from the lytic to lysogenic pathway. This decision is based on the density of lysed infected bacteria in their environment, which helps viruses avoid depleting all available hosts. Scientists hypothesized that arbitrium signals may also alter the activity of important bacterial genes, and that this quorum sensing-like communication system may be common among phages and possibly some human viral pathogens.

Comment: obviously both bacteria and viruses have receptors for these specific signaling molecules and built-in automatic responses to teh elvels involved..

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