I wish i could describe this.
Because of the many interruptions and aggravations with noises, i deleted a long comment on fb i wrote about atelectasis and i got mad that turned into enough motivation to get on the blog and write it all again.
I slept 6 hours and awoke about 2 hours ago and ever since everything that i'm doing is being accompanied by an orchestra of noises. Only thing is they don't seem random but coordinated and synced to what i'm doing. It's like dozens if not hundreds of people use their daily activities guided by a director with the only purpose of interacting and influencing what i'm doing. I mean they do something that can be called daily routines, maybe only slightly exaggerated (most of cars by examples have modified exhausts and one starts every half hour and roars for 10 minutes), but with pauses and break points that can be slightly adjusted by a director or something. One of the effects is i can hardly concentrate. That is if i even am completely awake.
I was outside, could not find any open mole holes in the immediate vicinity of the building. In fact it smells like clean air. When i got back inside, the same old smell of rotten earthworms.
Atelectasis is a very common complication of general anesthesia. Few people, and even those who went through major surgeries know about.
You do not go to sleep. You are being sedated to the point you loose consciousnesses and get paralyzed.
Loosing all pain and feeling comes with a price. You cannot breath on your own anymore. After the sedative is injected in your IV, a skilled anesthesiologist is ready with a tube in his hand and introduce it in your trachea (windpipe) within seconds of you loosing consciousness and stop breathing. It's called intubation. The same second they start the ventilator which pumps rhythmically oxygen or a mixture into your lungs, mimicking breathing. From that moment on until you are weened of the sedative and wake up, your life from this point of view depends on the anesthesiologist. He has to figure how much sedative you are given, how much oxygen, how fast the ventilator should work taking in account lots of parameters.
Your diaphragm muscle is responsible for about half of the volume of air getting to your lungs (the other half is done by your rib cage). When all those muscles get paralyzed, both of the rib cage and diaphragm, any abdominal pressure due to gas (bloating) caused by the food you last ate before surgery may press on the diaphragm muscle during the breath out phase or when the ventilator let the air out of your lungs and tear that muscle to the point it presses against your lungs and collapses them. I bet this parameter is not monitored by the anesthesiologist in any way, because they can give you pure oxygen and you can breath during those hours with maybe half of your lungs capacity and he gets you out of there alive but then after you have to go for a treatment for that collapsed lung which usually is long and not always 100% successful.
About the awake intubation. How weird this is, in the medical world, you may read the results of this google search. I mean theoretically it can be done, a doctor can insert a tube on your trachea without sedation. But aren't you going to want to throw up right away? With local anesthesia and even with light general sedation i bet not many people can take it for more than a few hours, not even thinking about days. You'd have to be fully sedated (induced comma) to take that for a week as i saw claims in media.
On the other hand. Can't do general anesthesia without an anesthesiologist on the spot. (Michael Jackson, remember). I believe it's a rule (at least common sense is telling me that). So who's gonna tell me that all the people that have been on a ventilator had an anesthesiologist next to them, 24/7?
One more reason not to believe every or anything is written these days like always in the media.
Monday, April 27, 2020
Saturday, April 25, 2020
Naga
Vinca couple
Naga couple
It's a bird. It's a snake.
Catholic Church in Vinga, Romania belongs to Hungarian minority. Could the name Hungary, which in Romanian is Ungaria be linguistically related to Vinga and with Huns or noongars. (Later Maygars, possibly from Magars from north-eastern India and Nepal, birth place of Buddha, Budapest).
Naga godess from Belur, India
Hungarian folk costume
Vinca head
Emu birds, cangoroos done on orange color on a cave fresco in Europe?
Yeah, the title. Nagy means great in Hungarian, naga means dragon in Indonesian etc.. It could come from Noongars. The Pama-Nyungan group of aboriginal languages started suddenly 3000 years BC (or could it be a few thousand years earlier) and the original population disappeared. Could they have mass migrated in Eurasia?
However something else just crossed my mind. I heard about gene editing by means of viruses. Can this happen spontaneously in nature. Like a virus infecting an embryo in earliest stages and cause insertion of genes from a different species?
Superman, spiderman, batman, X-men, things like that? Serbia, Sarpa, Seraphim. Could this be the real significance of the Yin-Yang symbol?
What if Darwin didn't say all the truth and selection is accelerated by mutations by viruses that may carry genes from one species to another. If such mutations occurred in an isolated group of humans which came in contact with the remnants of the old human population maybe after the flood (thawing of the last ice age) and mixed with the remnants of the old humans and repopulating the planet could it had be the reason for dramatically shortening the life span of humans, as described in Bible (Matusalemme) who also became much more cunning and aggressive, while keeping a nucleus of the original mutation with most foreign genes to this day.
Monday, April 20, 2020
Lipid Bilayer and (Corona) Virus Spikes
Had an idea and was trying to take a glimpse into cellular biology today. It all started with this type of media articles.
«Under the microscope [electron], coronaviruses appear to be covered with pointy spires, giving them the appearance of having a crown or "corona" -- hence the name. Beneath the crown is the outer layer of the virus, which is made up of lipids, or what you and I would call fat.»
There's something in there that doesn't really click my intuition.
Cells are said to be made of cytoplasm (a gel made 80% of water and other stuff floating in it) covered by fatty membranes. Please note the same type of membrane is shared by cells, bacteria and viruses.
It doesn't look to me like they have any mechanical resistance at all. I mean, bubbles of water based gel surrounded by a double molecule layer of fat.
If i didn't know about extracellular matrix which is made of collagen i'd say the body tissues can't even stay together.
Collagen is a protein that forms 30% of our bodies. To have an idea of how strong this stuff, is, enough to say tendons which are terminations of muscles through which they are attached to bones are made of collagen. If you make a fist you can see and feel them above the wrists of your hands.
By contrast "The cell membranes of almost all organisms and many viruses are made of a lipid bilayer, as are the nuclear membrane surrounding the cell nucleus, and other membranes surrounding sub-cellular structures. The lipid bi-layer is the barrier that keeps ions, proteins and other molecules where they are needed and prevents them from diffusing into areas where they should not be."
First. We may note in this definition again viruses are separated from living organisms. Then. This lipid barrier separate the chemicals from inside the cells by those from outside. What's keeping it together is electrical bonds between molecules of lipid barrier mentioned above with absolutely no mechanical resistance. If it wasn't for extracellular matrix, those things would probably burst like a soap bubble and fall apart.
And my thought went of course to types of cells that "live" outside a cellular matrix. First thing that came to mind is red blood cells. So i looked and to my surprise i saw they lack a nucleus. "The cytoplasm of erythrocytes is rich in hemoglobin, an iron-containing biomolecule that can bind oxygen and is responsible for the red color of the cells and the blood. ... The cell membrane is composed of proteins and lipids, and this structure provides properties essential for physiological cell function such as deformability and stability" So the natural question comes to mind. Are they alive? and of course that Quora answer didn't clarify anything. And on a further search i could not find an answer to the question if they use oxygen for themselves. Why should they. They don't need to burn oxygen to keep the temperature constant because rest of the body does that from them. I think the're more like molecular assemblies than living cells. Of course they wear out and "die" after a number of cycles of oxygen and carbon dioxide carrying.
Viruses. Their membrane is again made of a lipid bylayer. They of course don't have a nucleus because the're not cells though inside they have RNA which is part of the nucleus of living, reproducing cells.
Though they are not alive and obviously can't reproduce, once they entered a host cell they can "command" that cell to produce copies of themselves which sometimes are not "exact copies" and thus they... mutate. Some of the mutants will do less, some more than their "parents". The most complicated "component" the host cell needs to "fabricate" using the viral RNA instructions is the spike protein. In fact, the company who mapped this protein and can produce them uses viral RNA (linked later in this post).
I would assume they didn't provide the Jsmol model for the molecule, but here, for comparison, the molecule of HIV spike. If you click on "cartoon" on style for display option you will see the ribbon model. To compare size with lipid by-layer choose ball and stick.
We've saw so far seen the HIV virus looks identical (at least in some media representations) with coronaviruses. Part of the answer is... they are very similar. But the coronavirus misses something. The second membrane layer or the "matrix protein" seen in HIV of which the spikes are seemed to be anchored to.
There are other diagrams of coronaviruses on the web. They all suggest the "envelope" of the virus is made mostly of fat that includes some proteins.
Other, more scholarly articles, trying to suggests that the envelope of such viruses is made more of proteins than lipids. Or even lipids and unevenly distributed protein.
"We present evidence that suggests M can adopt two conformations and that membrane curvature is regulated by one M conformer. Elongated M protein is associated with rigidity, clusters of spikes and a relatively narrow range of membrane curvature. In contrast, compact M protein is associated with flexibility and low spike density."
"CoV virions are enveloped and consist of four structural proteins (Figure 1b). The RNA genome is encapsidated by the N proteins into a helical nucleocapsid, surrounded by a lipid envelope. Two major glycoproteins, M protein, which has three transmembrane (TM) domains, and S protein, which has a single TM domain; and minor non-glycosylated E proteins with a single hydrophobic domain, are incorporated into the CoV envelope"
By looking at the section (c) of the image below, i try to imagine what is the role of M (from Membrane) and E (from envelope) proteins in the envelope of the virus. Are they tied together in a structure or just caught loose in the fat (lipid) membrane.
US National Library of Medicine National Institutes of Health
"However, a recent electron microscopy study did not detect a well-ordered rigid lattice structure in individual virions, showing instead loosely ordered M-M protein networks [101], suggesting that the lattice-like matrix structure formed by M-M interactions might be flexible and unstable, and so that the model might need some modifications."
By looking at the animated image of the bylayer above and that of the spike protein and the two diagrams from Wikipedia here comes my question. How the gigantic spikes molecule hold onto the loose layer of thin fat (after neglecting the more obvious question that is how corona viruses which are basically a round bubble of fat with RNA inside and spikes outside hold themselves together inside blood). Can't figure yet the size of this protein but is should be certainly 100 times bigger than the two layers of fat acids figured above. Each straight portion of those "ribbons" below is probably as long as half of the thickness of the membrane.
So imagine that. A nanometric blob of fat with some genetic material inside flowing in the air from a sick person nearby getting into your lungs and attacking your cell. That is if your lungs' cilia and mucus don't eliminated them in your esophagus.
But what type of cells this "viruses" "attack" or "attach to"?
«"We then analyzed a total of nearly 60,000 cells to determine whether they activated the gene for the receptor and potential cofactors, thus in principle allowing them to be infected by the coronavirus," reports Soeren Lukassen, one of the lead authors of the study now being published in The EMBO Journal. "We only found the gene transcripts for ACE2 and for the cofactor TMPRSS2 in very few cells, and only in very small numbers." Lukassen and his four co-lead authors Robert Lorenz Chua, Timo Trefzer, Nicolas C. Kahn and Marc A. Schneider discovered that certain progenitor cells in the bronchi are mainly responsible for producing the coronavirus receptors. These progenitor cells normally develop into respiratory tract cells lined with hair-like projections called cilia that sweep mucus and bacteria out of the lungs. Lukassen and his four co-lead authors Robert Lorenz Chua, Timo Trefzer, Nicolas C. Kahn and Marc A. Schneider discovered that certain progenitor cells in the bronchi are mainly responsible for producing the coronavirus receptors. These progenitor cells normally develop into respiratory tract cells lined with hair-like projections called cilia that sweep mucus and bacteria out of the lungs."»
https://www.sciencedaily.com/releases/2020/04/200407131453.htm
But i bet no "virus" is going to attack you if those types of tissues wouldn't be already damaged. As i said above, most of your body's cells are protected by the strong collagen extracellular matrix through which a fat cover virus cannot possibly get through.
Pollutants, of which smoke is one of the worse factors. Smoke is a very complex compound of air born breathable substances of which the worse by far are heavy metals in ash, which can mutate bacteria creating unknown strain to your immune system, and also damage your respiratory tract lining cells.
In fact, the masks people are wearing to protect themselves from "virus" in fact protect them from the pollutants that may damage their respiratory tracts enough to make them vulnerable for infections because viruses are so small they will pass through most filters, not talking about masks.
As for the vaccine:
"The molecule the team produced – and for which they obtained a structure – represents only the extracellular portion of the spike protein, but is enough to elicit an immune response in patients."
And another question that becomes obvious after all this presentation. Can current HIV medicines be effective against coronavirus, since they are so similar?
"There are many newspaper articles citing effectiveness of anti-HIV drugs: ritonavir, lopinavir, either alone or in combination with oseltamivir, remdesivir, and chloroquine; and among these, ritonavir, remdesivir, and chloroquine showed efficacy at cellular level"
And since i put the two diagrams together to show the similarities with HIV virus, i started asking myself. How come they got flu vaccines which target the spikes ("the stems of the lollipop"), for so long and they don't have one for HIV.
"Doing that would require changing how the vaccine attacks the flu virus, which is shaped like a sphere with lollipops protruding from it. Vaccines so far have targeted the candy at the end of the lollipop, which changes every year."
The answer lies somewhere within the amount of money the drug companies get from insurance companies for a long life time supply of expensive antiviral drugs instead of a one time vaccine.
«Under the microscope [electron], coronaviruses appear to be covered with pointy spires, giving them the appearance of having a crown or "corona" -- hence the name. Beneath the crown is the outer layer of the virus, which is made up of lipids, or what you and I would call fat.»
There's something in there that doesn't really click my intuition.
Cells are said to be made of cytoplasm (a gel made 80% of water and other stuff floating in it) covered by fatty membranes. Please note the same type of membrane is shared by cells, bacteria and viruses.
It doesn't look to me like they have any mechanical resistance at all. I mean, bubbles of water based gel surrounded by a double molecule layer of fat.
If i didn't know about extracellular matrix which is made of collagen i'd say the body tissues can't even stay together.
Collagen is a protein that forms 30% of our bodies. To have an idea of how strong this stuff, is, enough to say tendons which are terminations of muscles through which they are attached to bones are made of collagen. If you make a fist you can see and feel them above the wrists of your hands.
By contrast "The cell membranes of almost all organisms and many viruses are made of a lipid bilayer, as are the nuclear membrane surrounding the cell nucleus, and other membranes surrounding sub-cellular structures. The lipid bi-layer is the barrier that keeps ions, proteins and other molecules where they are needed and prevents them from diffusing into areas where they should not be."
First. We may note in this definition again viruses are separated from living organisms. Then. This lipid barrier separate the chemicals from inside the cells by those from outside. What's keeping it together is electrical bonds between molecules of lipid barrier mentioned above with absolutely no mechanical resistance. If it wasn't for extracellular matrix, those things would probably burst like a soap bubble and fall apart.
And my thought went of course to types of cells that "live" outside a cellular matrix. First thing that came to mind is red blood cells. So i looked and to my surprise i saw they lack a nucleus. "The cytoplasm of erythrocytes is rich in hemoglobin, an iron-containing biomolecule that can bind oxygen and is responsible for the red color of the cells and the blood. ... The cell membrane is composed of proteins and lipids, and this structure provides properties essential for physiological cell function such as deformability and stability" So the natural question comes to mind. Are they alive? and of course that Quora answer didn't clarify anything. And on a further search i could not find an answer to the question if they use oxygen for themselves. Why should they. They don't need to burn oxygen to keep the temperature constant because rest of the body does that from them. I think the're more like molecular assemblies than living cells. Of course they wear out and "die" after a number of cycles of oxygen and carbon dioxide carrying.
Viruses. Their membrane is again made of a lipid bylayer. They of course don't have a nucleus because the're not cells though inside they have RNA which is part of the nucleus of living, reproducing cells.
Though they are not alive and obviously can't reproduce, once they entered a host cell they can "command" that cell to produce copies of themselves which sometimes are not "exact copies" and thus they... mutate. Some of the mutants will do less, some more than their "parents". The most complicated "component" the host cell needs to "fabricate" using the viral RNA instructions is the spike protein. In fact, the company who mapped this protein and can produce them uses viral RNA (linked later in this post).
I would assume they didn't provide the Jsmol model for the molecule, but here, for comparison, the molecule of HIV spike. If you click on "cartoon" on style for display option you will see the ribbon model. To compare size with lipid by-layer choose ball and stick.
We've saw so far seen the HIV virus looks identical (at least in some media representations) with coronaviruses. Part of the answer is... they are very similar. But the coronavirus misses something. The second membrane layer or the "matrix protein" seen in HIV of which the spikes are seemed to be anchored to.
There are other diagrams of coronaviruses on the web. They all suggest the "envelope" of the virus is made mostly of fat that includes some proteins.
Other, more scholarly articles, trying to suggests that the envelope of such viruses is made more of proteins than lipids. Or even lipids and unevenly distributed protein.
"We present evidence that suggests M can adopt two conformations and that membrane curvature is regulated by one M conformer. Elongated M protein is associated with rigidity, clusters of spikes and a relatively narrow range of membrane curvature. In contrast, compact M protein is associated with flexibility and low spike density."
"CoV virions are enveloped and consist of four structural proteins (Figure 1b). The RNA genome is encapsidated by the N proteins into a helical nucleocapsid, surrounded by a lipid envelope. Two major glycoproteins, M protein, which has three transmembrane (TM) domains, and S protein, which has a single TM domain; and minor non-glycosylated E proteins with a single hydrophobic domain, are incorporated into the CoV envelope"
By looking at the section (c) of the image below, i try to imagine what is the role of M (from Membrane) and E (from envelope) proteins in the envelope of the virus. Are they tied together in a structure or just caught loose in the fat (lipid) membrane.
US National Library of Medicine National Institutes of Health
"However, a recent electron microscopy study did not detect a well-ordered rigid lattice structure in individual virions, showing instead loosely ordered M-M protein networks [101], suggesting that the lattice-like matrix structure formed by M-M interactions might be flexible and unstable, and so that the model might need some modifications."
By looking at the animated image of the bylayer above and that of the spike protein and the two diagrams from Wikipedia here comes my question. How the gigantic spikes molecule hold onto the loose layer of thin fat (after neglecting the more obvious question that is how corona viruses which are basically a round bubble of fat with RNA inside and spikes outside hold themselves together inside blood). Can't figure yet the size of this protein but is should be certainly 100 times bigger than the two layers of fat acids figured above. Each straight portion of those "ribbons" below is probably as long as half of the thickness of the membrane.
So imagine that. A nanometric blob of fat with some genetic material inside flowing in the air from a sick person nearby getting into your lungs and attacking your cell. That is if your lungs' cilia and mucus don't eliminated them in your esophagus.
But what type of cells this "viruses" "attack" or "attach to"?
«"We then analyzed a total of nearly 60,000 cells to determine whether they activated the gene for the receptor and potential cofactors, thus in principle allowing them to be infected by the coronavirus," reports Soeren Lukassen, one of the lead authors of the study now being published in The EMBO Journal. "We only found the gene transcripts for ACE2 and for the cofactor TMPRSS2 in very few cells, and only in very small numbers." Lukassen and his four co-lead authors Robert Lorenz Chua, Timo Trefzer, Nicolas C. Kahn and Marc A. Schneider discovered that certain progenitor cells in the bronchi are mainly responsible for producing the coronavirus receptors. These progenitor cells normally develop into respiratory tract cells lined with hair-like projections called cilia that sweep mucus and bacteria out of the lungs. Lukassen and his four co-lead authors Robert Lorenz Chua, Timo Trefzer, Nicolas C. Kahn and Marc A. Schneider discovered that certain progenitor cells in the bronchi are mainly responsible for producing the coronavirus receptors. These progenitor cells normally develop into respiratory tract cells lined with hair-like projections called cilia that sweep mucus and bacteria out of the lungs."»
https://www.sciencedaily.com/releases/2020/04/200407131453.htm
But i bet no "virus" is going to attack you if those types of tissues wouldn't be already damaged. As i said above, most of your body's cells are protected by the strong collagen extracellular matrix through which a fat cover virus cannot possibly get through.
Pollutants, of which smoke is one of the worse factors. Smoke is a very complex compound of air born breathable substances of which the worse by far are heavy metals in ash, which can mutate bacteria creating unknown strain to your immune system, and also damage your respiratory tract lining cells.
In fact, the masks people are wearing to protect themselves from "virus" in fact protect them from the pollutants that may damage their respiratory tracts enough to make them vulnerable for infections because viruses are so small they will pass through most filters, not talking about masks.
As for the vaccine:
"The molecule the team produced – and for which they obtained a structure – represents only the extracellular portion of the spike protein, but is enough to elicit an immune response in patients."
And another question that becomes obvious after all this presentation. Can current HIV medicines be effective against coronavirus, since they are so similar?
"There are many newspaper articles citing effectiveness of anti-HIV drugs: ritonavir, lopinavir, either alone or in combination with oseltamivir, remdesivir, and chloroquine; and among these, ritonavir, remdesivir, and chloroquine showed efficacy at cellular level"
And since i put the two diagrams together to show the similarities with HIV virus, i started asking myself. How come they got flu vaccines which target the spikes ("the stems of the lollipop"), for so long and they don't have one for HIV.
"Doing that would require changing how the vaccine attacks the flu virus, which is shaped like a sphere with lollipops protruding from it. Vaccines so far have targeted the candy at the end of the lollipop, which changes every year."
The answer lies somewhere within the amount of money the drug companies get from insurance companies for a long life time supply of expensive antiviral drugs instead of a one time vaccine.