Phage , the virus that cures

[William Gaatjes]

I recently saw this documentary about bacteriophages.

Phage- The virus that cures
The link is dead.
For to see the video, press this link :

Page 14 - Phage , the virus that cures

Page 14 - Seeking answers? Join the AnandTech community: where nearly half-a-million members share solutions and discuss the latest tech.

forums.anandtech.com

Bacteriophages

Horizontal gene transfers

You ask perhaps why i posted this message, well i ask for opinions.

Long ago i bought a scientific american magazine (i think it was). There was some information about the possibility of horizontal gene transfers.

My Opinion is that through vertical gene transfers (aka offspring through sexual reproduction) and evolution a complex lifeform can loose genes. But with horizontal gene transfers a complex lifeform can gain genetic code. And not just a few basepairs but an entire sequence.

EDIT START : I think that it is entirely possible that this gene swapping can also occur between bacteria and viruses and cells of complex lifeforms. Most of the time our error detection/ error correction together with self destruction methods (cell apoptosis) and our immune system combat any change in dna code but radiation( or even cosmic radiation) and toxic materials can cause mailfunction to these error detection/correction systems and our immune system.

Cell apoptosis


EDIT END


Would this statement hold ?

 

[Gibsons]

Originally posted by: William Gaatjes
I recently saw this documentary about bacteriophages.

Phage- The virus that cures

Bacteriophages

Horizontal gene transfers

You ask perhaps why i posted this message, well i ask for opinions.

Long ago i bought a scientific american magazine (i think it was). There was some information about the possibility of horizontal gene transfers.

My Opinion is that through vertical gene transfers (aka offspring through sexual reproduction) and evolution a complex lifeform can loose genes. But with horizontal gene transfers a complex lifeform can gain genetic code. And not just a few basepairs but an entire sequence.

EDIT START : I think that it is entirely possible that this gene swapping can also occur between bacteria and viruses and cells of complex lifeforms. Most of the time our error detection/ error correction together with self destruction methods (cell apoptosis) and our immune system combat any change in dna code but radiation( or even cosmic radiation) and toxic materials can cause mailfunction to these error detection/correction systems and our immune system.

Cell apoptosis


EDIT END


Would this statement hold ?

Which statement?

The immune system can detect changes in the DNA indirectly, but it's far from foolproof. Also, if the change occurs in germline DNA, the immune system of the developing person will see these changes as "self" and not react to them. There are lots and lots of viral sequences in human DNA.

 

[William Gaatjes]

Originally posted by: Gibsons

Which statement?

The immune system can detect changes in the DNA indirectly, but it's far from foolproof. Also, if the change occurs in germline DNA, the immune system of the developing person will see these changes as "self" and not react to them. There are lots and lots of viral sequences in human DNA.

Also, if the change occurs in germline DNA, the immune system of the developing person will see these changes as "self" and not react to them.

I agree. But to make things clear the error detection /correction inside the cell itself is responsible for reparing the dna. And if it fails the cell will execute apoptosis. This will then be seen by the immunesystem and the by macrophage engulfed cell is taken to the lymphatic system to begin it's journey in i think our bowls to be secreted.


This statement :

My Opinion is that through vertical gene transfers (aka offspring through sexual reproduction) and evolution a complex lifeform can loose genes. But with horizontal gene transfers a complex lifeform can gain genetic code. And not just a few basepairs but an entire sequence.

 

[Gibsons]

Originally posted by: William Gaatjes

Originally posted by: Gibsons

Which statement?

The immune system can detect changes in the DNA indirectly, but it's far from foolproof. Also, if the change occurs in germline DNA, the immune system of the developing person will see these changes as "self" and not react to them. There are lots and lots of viral sequences in human DNA.

Also, if the change occurs in germline DNA, the immune system of the developing person will see these changes as "self" and not react to them.

I agree. But to make things clear the error detection /correction inside the cell itself is responsible for reparing the dna. And if it fails the cell will execute apoptosis. This will then be seen by the immunesystem and the by macrophage engulfed cell is taken to the lymphatic system to begin it's journey in i think our bowls to be secreted.


This statement :

My Opinion is that through vertical gene transfers (aka offspring through sexual reproduction) and evolution a complex lifeform can loose genes. But with horizontal gene transfers a complex lifeform can gain genetic code. And not just a few basepairs but an entire sequence.

Oh okay. I think both statements are correct.

Syncytin is a pretty well documented case for gaining a sequence.

 

[William Gaatjes]

Originally posted by: Gibsons

Oh okay. I think both statements are correct.


Syncytin is a pretty well documented case for gaining a sequence.

Yay for me

I read the link you wrote. I had to look up the explanation of all the words in that article.
Correct me if i am wrong please :

In our dna their is a gene coding for a protein that is used to build the envelope (or skin) of the virus. And that the same gene is used in to form the envelope of cells that provide nutrients and protect the blastocyst ? These cells are called trophoblasts ?Later these cells form the placenta ?

If true, Wow. Might be common but very interesting indeed. Is this a human only feature of have all animals using a placenta exhibit this ?


EDIT :

HERV-W , It seems this virus is present in many cancer tissues ?

Herv-W

 

[eggrolls]

Our genome encodes for the proteins embedded in the membrane and the enzymes for phospholipid synthesis.

Viruses with envelopes get their lipid envelopes from either the cellular cytoplasmic membrane or some membrane-bound organelle such as the endoplasmic reticulum or Golgi. They basically "steal" our cell membranes and embed virally-encoded proteins in them.

Some viruses don't have lipid envelopes, so their outermost layer is the capsid protein, which is virally encoded.

 

[William Gaatjes]

Originally posted by: eggrolls
Our genome encodes for the proteins embedded in the membrane and the enzymes for phospholipid synthesis.

Viruses with envelopes get their lipid envelopes from either the cellular cytoplasmic membrane or some membrane-bound organelle such as the endoplasmic reticulum or Golgi. They basically "steal" our cell membranes and embed virally-encoded proteins in them.

Some viruses don't have lipid envelopes, so their outermost layer is the capsid protein, which is virally encoded.

So it is a chicken or the egg question. I wonder if we can ever find out what the oldest virus is. I know there is some research being done on bones and maybe tissues from extincted animals.

Although i think that with this virus it perhaps borrowed the cell membrane but gave us some genetic code in return ?

Something else :
It is proposed that part of life on earth originated from space and another part came from the earth it self.

I have some links here with theories and findings about life and how tough it can be.

Bacteria leaving earth

SAO/NASA ADS Astronomy Abstract Service

The questions of how did life arise and is there life on other planets are some of the most profound questions that humanity asks Although there has been controversial signs of past bacterial life in meteorites which originated on Mars and there are current claims of bacterial life high in the atmosphere the issues of origin by chemical process or contamination make these types of results arguable and they will likely remain that way until a comprehensive theory is developed to explain why the claims might be true This paper proposes a complete theory for the spread of bacterial life throughout the galaxy by combining current knowledge from the fields of bacteriology stellar evolution and space weather Here we show the possibility that the forces of uplift on a charged bacteria particle are sufficient bring at least some lighter types of bacteria high into the ionosphere and subsequently move the charged spore onto magnetic field lines The bacteria spore is then driven down the magnetotail where during a solar storm a structure known as a plasmoid is propelled radially outward into space at velocities exceeding solar system escape velocity From that point the plasmoids are capable of reaching Mars the outer planets and even others systems eventually depositing the bacterial spores either via comets or direct interaction with the receiving planet The solid observational evidence for the strength of the electric fields and the speeds that the plasmoids leave the magnetotail during geomagnetic storms provide a firm.

Bacteria living in the stratosphere

(CNN) -- An international team of scientists has recovered microorganisms in the upper reaches of the atmosphere that could have originated from outer space, a participant in the study said Friday.
The living bacteria, plucked from an altitude of 10 miles (16 km) or higher by a scientific balloon, could have been deposited in terrestrial airspace by a passing comet, according to the researchers.
The microorganisms are unlike any known on Earth, but the astrobiologists "want to keep the details under wraps until they are absolutely convinced that these are extraterrestrial," said study participant Chandra Wickramasinghe, a noted scientist at Cardiff University in Wales.
Could life on Earth have arrived on meteors and comets?
NASA's Ames Research Center posted a cautious reaction to the report on its Astrobiology Web site. NASA said the finding is likely to meet considerable skepticism in the scientific community.
"Aerobiologists might argue that 10 miles is not too high for Earth life to reside, a possibility that Wickramasinghe appears to accept," the statement said.
However, NASA said, a compelling case can be made for the transport of microorganisms through space aboard comets and meteors.
"A recent discovery indicates that microbes can remain dormant for millions of years -- enough time to travel from planet to planet," NASA said.
Disputing critics who suggest that the balloon was contaminated on the ground, Wickramasinghe said the experiment took place with strict controls. He does acknowledge the possibility that terrestrial bacteria could be kicked up into the stratosphere. Living fungal spores have been discovered at altitudes of 7 miles (11 km). But observations from this and a related study suggest the presence of living bacteria far too high in the atmosphere to have originated from the surface of the planet, according to Wickramasinghe. "What is present in the upper atmosphere, critics will say it came from the ground. That is a serious possibility at 15 kilometers, but at 40 or 85 kilometers, you can forget about it," he said Friday.
Wickramasinghe and colleague Sir Fred Hoyle published a report on the Web Friday about evidence that they say strengthens the hypothesis that unusual microbes float through the upper reaches of the atmosphere. Looking at spectral data from the 1999 Leonid meteorite shower, they detected a bacterial "fingerprint" as the tiny space rocks streaked across the sky at a height of 51 miles (83 km).
"The bacteria heated at temperatures high enough to radiate and shine in this (spectral) signature," Wickramasinghe said. Along with Hoyle, Wickramasinghe pioneered "panspermia," the theory that outer space seeded Earth with its first life forms about 4 billion years ago. Wickramasinghe holds that primitive life could still be arriving from space. "If we find microbes at great heights that are not contaminants from the ground, we have to wonder where they came from. One hundred tons of comet and meteor organic debris is deposited in the atmosphere every day."
Javant Narlikar of India lead the atmospheric bacteria sample study, which the Indian Space Research Organization coordinated. The location of the microbe is what most impressed Wickramasinghe, not the composition. It seems like a novel strain of a common bacteria genus on Earth, he said.

UV resisitant bacteria found, working together to shield themselves from UV radation.

Yinjie Yang, Shiho Itahashi, Shin-ichi Yokobori and Akihiko Yamagishi

(Received: May 15, 2008)
(Accepted: September 18, 2008)

Abstract: Five bacterial strains have been isolated from dust samples collected from the upper troposphere and lower stratosphere during several aircraft flights. Most of them displayed much higher resistance to ultraviolet radiation (254 nm) than surface airborne isolates. The role of UV radiation combined with other conditions to determine survivability of bacterial species in the upper atmosphere is discussed. Two strains from the upper atmosphere (ST0316 and TR0125) exhibited extreme UV resistance and tend to form cell clumps or aggregates. Forming cell aggregation might be a strategy to enhance their survivability in the harsh conditions such as high dosage of UV at high altitude.

Bacteria might be in more control then we think, Some researches suggest it is bacteria that help form clouds as well. And a hibernating bacteria was found to be claimed to be 250 million years old reanimated when given nutrients.

spacefaring bacteria

In 2002, several scientists claimed that bacteria high in Earth's atmosphere came from space.
Last year, scientists said that bacteria in the upper atmosphere may actually make rain. Specifically, they said that bacteria can freeze at fairly warm temperatures, so that the "biological ice nuclei" form condensation nuclei which triggers rain. Indeed, some scientists have speculated that bacteria cause rain as a means of transportation, so that they will "rain out" from the upper atmosphere to the surface of a planet. Now, scientists have discovered a "hibernating" bacteria in a salt mine in Utah which they believe has been in suspended animation for 250 million years. There is evidence that this ability to hibernate for long periods of time is also useful for travel through space by the bacteria:
Bacteria have the ability to go into a kind of semi-permanent hibernation, but survival for this long was unheard of. After lying dormant in the salt crystal for 250 million years, the scientists added fresh nutrients and a new salt solution, and the ancient bacteria "re-animated."
Dr. Russell Vreeland, one of the biologists who found the bacteria, pointed out that bacteria can survive the forces [of] acceleration via rubble thrown into space via a meteor impact. If it is possible for a bacteria to survive being [thrown] off the planet and to stay alive within a salt chunk for 250 million years, then in a sort of "reverse-exogenesis" it may be possible that earth's own microbes are already out there.
Indeed, there is a more down-to-earth analogy to the idea of spacefaring bacteria: the humble coconut. Coconuts can float across long distances of water in the ocean, and when they land on a hospitable island, start growing.

ice clouds

A team of UC San Diego-led atmospheric chemistry researchers moved closer to what is considered the 'holy grail' of climate change science when it made the first-ever direct detection of biological particles within ice clouds.

The team, led by Kerri Pratt, a Ph.D. student of atmospheric chemistry Professor Kim Prather, who also holds appointments at Scripps Institution of Oceanography as well as the Department of Chemistry and Biochemistry at UCSD, sampled water droplet and ice crystal residues at high speeds from an aircraft flying through clouds in the skies over Wyoming in fall 2007. Analysis of the ice crystals revealed that they were made up almost entirely of either dust or biological particles such as bacteria, fungal spores and plant material. While it has long been known that microorganisms or parts of them get airborne and travel great distances, this study is the first to yield in-situ data on their participation in cloud ice processes.
Results of the Ice in Clouds Experiment - Layer Clouds (ICE-L), funded by the National Science Foundation (NSF) and the National Centre for Atmospheric Research (NCAR), appear 17 May in the advance online edition of the journal Nature Geoscience.
'If we understand the sources of particles that nucleate clouds and their relative abundance, then we can determine the impact of these different sources on climate,' said Pratt.
The effects of tiny airborne particles called aerosols on cloud formation have been some of the most difficult aspects of weather and climate for scientists to understand. In the climate change science field, which derives many of its projections from computer simulations of climate phenomena, the actions of aerosols on clouds represent what scientists consider the greatest uncertainty in modelling predictions for the future.
'By sampling clouds in real time from an aircraft, these investigators were able to get information about ice particles in clouds at an unprecedented level of detail,' said Anne-Marine Schmoltner of the NSF's Division of Atmospheric Sciences. 'By determining the chemical composition of the very cores of individual ice particles, they discovered that both mineral dust, and, surprisingly, biological particles play a major role in the formation of clouds.'
Aerosols, ranging from dust, soot, sea salt to organic materials, some of which travel thousands of miles, form the skeletons of clouds. Around these nuclei, water and ice in the atmosphere condense and grow leading to precipitation. Scientists are trying to understand how they form as clouds play a critical role by both cooling the atmosphere and affect regional precipitation processes.
ICE-L was the first aircraft-based deployment of the aircraft aerosol time-of-flight mass spectrometer (A-ATOFMS) nicknamed 'Shirley,' which was recently developed at UCSD with funding from NSF. The ICE-L team mounted the mass spectrometer and an ice chamber run by Colorado State University researcher Paul DeMott onto a C-130 aircraft operated by NCAR and made a series of flights through a type of cloud known as a wave cloud. The researchers performed in-situ measurements of cloud ice crystal residues and found that half were mineral dust and about a third contained nitrogen, phosphorus and carbon - the signature elements of biological matter.
The second-by-second analysis speed allowed the researchers to make distinctions between residues of water droplets and ice nuclei in real-time. Ice nuclei are rarer than droplet nuclei and are more likely to create precipitation.
The A-ATOFMS also allowed the unambiguous measurement of biological particles in the cloud ice, which scientists previously concluded serve as ice nuclei based on simulations in laboratory experiments and precipitation measurements. Based on modelling and the chemical composition of measured dust, the ICE-L team was able to identify the source of the dust as Asia or Africa. 'This has really been kind of a holy grail measurement for us,' said Prather. 'Understanding which particles form ice nuclei, which occur at extremely low concentrations and are inherently difficult to measure, means you can further understand processes that result in precipitation. Any new piece of information you can get is critical.'
The findings suggest that the biological particles that get swept up in dust storms help to induce the formation of cloud ice and that their region of origin makes a difference. Prather said initial evidence is increasingly suggesting that dust transported from Asia could be influencing precipitation in North America, for example. Researchers hope to use the ICE-L data to design future studies timed to events when such particles may be playing a bigger role in triggering rain- or snowfall.
Paper co-authors include Anthony Prenni from Colorado State University, Jeffrey French and Zhien Wang of the University of Wyoming, Douglas Westphal of the Naval Research Laboratory in Monterey, Calif., Andrew Heymsfield of the National Centre for Atmospheric Research and Cynthia Twohy of Oregon State University.

Bacteria controlling the airflow in a labexperiment

ScienceDaily (July 16, 2009) — Bacteria know that they are too small to make an impact individually. So they wait, they multiply, and then they engage in behaviors that are only successful when all cells participate in unison. There are hundreds of behaviors that bacteria carry out in such communities. Now researchers at Rockefeller University have discovered one that has never been observed or described before in a living system.

In research published in the May 12 issue of Physical Review Letters, Albert J. Libchaber, head of the Laboratory of Experimental Condensed Matter Physics, and his colleagues, including first author Carine Douarche, a postdoctoral associate in the lab, show that when oxygen penetrates a sample of oxygen-deprived Escherichia coli bacteria, they do something that no living community had been seen to do before: The bacteria accumulate and form a solitary propagating wave that moves with constant velocity and without changing shape. But while the front is moving, each bacterium in it isn’t moving at all. “It’s like a soliton,” says Douarche. “A self-reinforcing solitary wave.”
Unlike the undulating pattern of an ocean wave, which flattens or topples over as it approaches the shore, a soliton is a solitary, self-sustaining wave that behaves like a particle. For example, when two solitons collide, they merge into one and then separate into two with the same shape and velocity as before the collision. The first soliton was observed in 1834 at a canal in Scotland by John Scott Russell, a scientist who was so fascinated with what he saw that he followed it on horseback for miles and then set up a 30-foot water tank in his yard where he successfully simulated it, sparking considerable controversy. The work began when Libchaber, Douarche and their colleagues placed E. coli bacteria in a sealed square chamber and measured the oxygen concentration and the density of bacteria every two hours until the bacteria consumed all the oxygen. (Bacteria, unlike humans, don’t die when starved for oxygen, but switch to a nonmotile state from which they can be revived.) The researchers then cracked the seals of the chamber, allowing oxygen to flow in.
The result: The motionless bacteria, which had spread out uniformly, began to move; first those around the perimeter, nearest to the seals, and then those further away. A few hours later, the bacteria began to spatially segregate into two domains of moving and nonmoving bacteria and pile up into a ring at the border of low-oxygen and no-oxygen. There they formed a solitary wave that propagated slowly but steadily toward the center of the chamber without changing its shape.
The effect, which lasted for more than 15 hours and covered a considerable distance (for bacteria), could not be explained by the expression of new proteins or by the addition of energy in the system. Instead, the creation of the front depends on the dispersion of the active bacteria and on the time it takes for oxygen-starved bacteria to completely stop moving, 15 minutes. The former allows the bacteria to propagate at a constant velocity, while the latter keeps the front from changing shape.
However, a propagating front of bacteria wasn’t all that was created. “To me, the biggest surprise was that the bacteria control the flow of oxygen in the regime,” says Libchaber. “There’s a propagating front of bacteria, but there is a propagating front of oxygen, too. And the bacteria, by absorbing the oxygen, control it very precisely.”
Oxygen, Libchaber explains, is one of the fastest-diffusing molecules, moving from regions of high concentration to low concentration such that the greater the distance it needs to travel, the faster it will diffuse there. But that is not what they observed. Rather, oxygen penetrated the chamber very slowly in a linear manner. Equal time, equal distance. “This pattern is not due to biology,” says Libchaber. “It has to do with the laws of physics. And it is organized in such an elegant way that the only thing it tells us is that we have a lot to learn from bacteria.”

I wonder if all these bacteria have phages as well...


And one more scary parasite to finish the behaviour control part.

Toxoplasma gondii


EDIT: Bad links

 

[Gibsons]

Originally posted by: William Gaatjes

Originally posted by: Gibsons

Oh okay. I think both statements are correct.


Syncytin is a pretty well documented case for gaining a sequence.

Yay for me

I read the link you wrote. I had to look up the explanation of all the words in that article.
Correct me if i am wrong please :

In our dna their is a gene coding for a protein that is used to build the envelope (or skin) of the virus. And that the same gene is used in to form the envelope of cells that provide nutrients and protect the blastocyst ? These cells are called trophoblasts ?Later these cells form the placenta ?

If true, Wow. Might be common but very interesting indeed. Is this a human only feature of have all animals using a placenta exhibit this ?


EDIT :

HERV-W , It seems this virus is present in many cancer tissues ?

Herv-W

eggrolls covered most of the viral assembly stuff - enveloped viruses (usually but not always) use a bit of host membrane as their envelope.

As for syncytin in particular, it seems to be necessary for cell fusion at some developmental stages. This makes some sense, as enveloped viruses usually (maybe always) encode a gene that induces membrane fusion (fusion of the viral envelope with host cell or endosomal membrane).

Difficult for me to sort out just what animals have syncytin and which ones don't. There's more than one, and it's derived from a pretty large family of endogenous retroviruses, so there are homologs, orthologs etc. to worry about. I'd guess all placentals do, but just a guess. Too lazy to blast it right now.

The big picture of what's going on with all the endogenous retroviruses is largely unknown. Roughly 8% of the human genome is apparently derived from viral sequences (can't find the ref, it's in my notes). A lot of these seem to be inactive/degraded/degenerate... But some are not. Some of these do get transcribed in cancer, but I don't think anyone's figured out cause and effect. That doesn't mean that actual infectious virus is produced in those cancers, but it is possible.

For something interesting and scary, read about the Phoenix virus.

 

[William Gaatjes]

Originally posted by: Gibsons

Originally posted by: William Gaatjes

Originally posted by: Gibsons

Oh okay. I think both statements are correct.


Syncytin is a pretty well documented case for gaining a sequence.

Yay for me

I read the link you wrote. I had to look up the explanation of all the words in that article.
Correct me if i am wrong please :

In our dna their is a gene coding for a protein that is used to build the envelope (or skin) of the virus. And that the same gene is used in to form the envelope of cells that provide nutrients and protect the blastocyst ? These cells are called trophoblasts ?Later these cells form the placenta ?

If true, Wow. Might be common but very interesting indeed. Is this a human only feature of have all animals using a placenta exhibit this ?


EDIT :

HERV-W , It seems this virus is present in many cancer tissues ?

Herv-W

eggrolls covered most of the viral assembly stuff - enveloped viruses (usually but not always) use a bit of host membrane as their envelope.

As for syncytin in particular, it seems to be necessary for cell fusion at some developmental stages. This makes some sense, as enveloped viruses usually (maybe always) encode a gene that induces membrane fusion (fusion of the viral envelope with host cell or endosomal membrane).

Difficult for me to sort out just what animals have syncytin and which ones don't. There's more than one, and it's derived from a pretty large family of endogenous retroviruses, so there are homologs, orthologs etc. to worry about. I'd guess all placentals do, but just a guess. Too lazy to blast it right now.

The big picture of what's going on with all the endogenous retroviruses is largely unknown. Roughly 8% of the human genome is apparently derived from viral sequences (can't find the ref, it's in my notes). A lot of these seem to be inactive/degraded/degenerate... But some are not. Some of these do get transcribed in cancer, but I don't think anyone's figured out cause and effect. That doesn't mean that actual infectious virus is produced in those cancers, but it is possible.

For something interesting and scary, read about the Phoenix virus.

Amazing...

That virus is scary indeed. But what worries me is there are no enforced guidelines.
I am sure that the people who work with extinct viruses or lethal ones like polio or the 1918 flu virus do not need enforced guidelines , they know how dangerous the material is they work with. What do you think about this ? Are the precautions taken really that strict ?

My personal opinion is that almost all cancers must be virus related. I think that toxic materials that cause cancer, are not the primary cause, but a catalyst to jump start the process.

What was mentioned in the article was interesting :

Relics of the retrovirus are scattered throughout our genome but have long since lost their infectivity due to mutation. By comparing 10 or so of these dysfunctional relics, Heidmann and his colleagues puzzled out the components of the original virus that must have infected our ancestors eons ago. Using DNA cloning techniques, they then reconstructed a version that can infect human cells. Heidmann says this virus, which he calls Phoenix, is completely harmless. But he thinks it could play a role in cancer research because high levels of similar retroviral particles have been found in many different types of tumors, leading oncologists to suspect that they may help cancers grow.

Here are some more links about viruses and cancer. Might come in handy, however i would not be surprised you already know about them...

Cervical cancer

JC virus

Virus inside brain tumors.


EDIT : typing errors and link :

cache, main memory and mass storage

The researchers report two striking findings. First, the human genome is organized into two separate compartments, keeping active genes separate and accessible while sequestering unused DNA in a denser storage compartment. Chromosomes snake in and out of the two compartments repeatedly as their DNA alternates between active, gene-rich and inactive, gene-poor stretches.

active, gene-rich and inactive, gene-poor stretches

Now does that not sound like cache, main memory and mass storage ?

 

[Gibsons]

Originally posted by: William Gaatjes

Originally posted by: Gibsons

Originally posted by: William Gaatjes

Originally posted by: Gibsons

Oh okay. I think both statements are correct.


Syncytin is a pretty well documented case for gaining a sequence.

Yay for me

I read the link you wrote. I had to look up the explanation of all the words in that article.
Correct me if i am wrong please :

In our dna their is a gene coding for a protein that is used to build the envelope (or skin) of the virus. And that the same gene is used in to form the envelope of cells that provide nutrients and protect the blastocyst ? These cells are called trophoblasts ?Later these cells form the placenta ?

If true, Wow. Might be common but very interesting indeed. Is this a human only feature of have all animals using a placenta exhibit this ?


EDIT :

HERV-W , It seems this virus is present in many cancer tissues ?

Herv-W

eggrolls covered most of the viral assembly stuff - enveloped viruses (usually but not always) use a bit of host membrane as their envelope.

As for syncytin in particular, it seems to be necessary for cell fusion at some developmental stages. This makes some sense, as enveloped viruses usually (maybe always) encode a gene that induces membrane fusion (fusion of the viral envelope with host cell or endosomal membrane).

Difficult for me to sort out just what animals have syncytin and which ones don't. There's more than one, and it's derived from a pretty large family of endogenous retroviruses, so there are homologs, orthologs etc. to worry about. I'd guess all placentals do, but just a guess. Too lazy to blast it right now.

The big picture of what's going on with all the endogenous retroviruses is largely unknown. Roughly 8% of the human genome is apparently derived from viral sequences (can't find the ref, it's in my notes). A lot of these seem to be inactive/degraded/degenerate... But some are not. Some of these do get transcribed in cancer, but I don't think anyone's figured out cause and effect. That doesn't mean that actual infectious virus is produced in those cancers, but it is possible.

For something interesting and scary, read about the Phoenix virus.

Amazing...

That virus is scary indeed. But what worries me is there are no enforced guidelines.
I am sure that the people who work with extinct viruses or lethal ones like polio or the 1918 flu virus do not need enforced guidelines , they know how dangerous the material is they work with. What do you think about this ? Are the precautions taken really that strict ?

My personal opinion is that almost all cancers must be virus related. I think that toxic materials that cause cancer, are not the primary cause, but a catalyst to jump start the process.

Pretty much a certainty that all cancers are not virus related.

Of course some are, and there are probably a few that are that we don't know about. But the data for some cancers is way too clean, imo, for their to still be a hidden virus lurking around playing a role.

Also there are restrictions and regulations on handling infectious material in every country that I'm aware of.

 

[William Gaatjes]

<My personal opinion is that almost all cancers must be virus related. I think that toxic materials that cause cancer, are not the primary cause, but a catalyst to jump start the process.





Pretty much a certainty that all cancers are not virus related.

Of course some are, and there are probably a few that are that we don't know about. But the data for some cancers is way too clean, imo, for their to still be a hidden virus lurking around playing a role.

Also there are restrictions and regulations on handling infectious material in every country that I'm aware of.

I agree on that
Some cancers are virus related some are not.

I have been thinking more about toxic materials...
I do not know all the details when and how specific genes are expressed,
Can it be that certain toxic materials (causing cancer) cause parts of one gene and parts of the next gene to be expressed ? That codons are no longer seen as end or start codons but as part of a an expression ? Perhaps toxic materials cause havoc on a higher level. Perhaps these toxins influence proteins that certain genes are expressed to much , causing an chemical unbalance ?

 

[Gibsons]

The vast majority of carcinogens are mutagens. They cause changes in the DNA sequence of a cell. Some genes cause or regulate cellular growth, and changes in those genes (the right kind of changes) can lead to cancer. There are a few other things that can contribute, but that's the basic idea.

For a start, look here and here.

 

[William Gaatjes]

Some information about talking bacteria by Bonnie Bassler :

talking bacteria

 

[Chriscross3234]

It's kind of a coincidence that I came across this thread. Tomorrow I meet with my research professor/mentor to discuss the details of my undergraduate research project that involves phage display technology. I guess I'll update when I know exactly what I'm going to do.

 

[jagec]

Amazing...

That virus is scary indeed. But what worries me is there are no enforced guidelines.
I am sure that the people who work with extinct viruses or lethal ones like polio or the 1918 flu virus do not need enforced guidelines , they know how dangerous the material is they work with. What do you think about this ? Are the precautions taken really that strict ?

My personal opinion is that almost all cancers must be virus related. I think that toxic materials that cause cancer, are not the primary cause, but a catalyst to jump start the process.

It is foolish to put your faith in "regulations". As most smart people know, rules created by the ignorant leave huge gaps for the better-informed, and rules created by the well-informed require self-enforcement since the details are simply not understood by anyone else. The fact of the matter is that if a well-trained scientist working in a lab wanted to sneak out some dangerous material, it would simply be a matter of pipetting it into a tube and putting it in their pocket, and then walking right out of the lab. One tube with a clear liquid in it looks much the same as another.
Now, as far as brewing industrial batches of the stuff is concerned, that would be a little bit harder. But still achievable for someone determined.

It's only scary if you don't think about the fact that it would be easier and more effective to just buy a bunch of fertilizer and diesel fuel if you wanted to become a mass-murderer. Modern society has placed a great deal of potential power into each and every one of our hands. People rightly fear power, but it's not going away.

 

[Gibsons]

It is foolish to put your faith in "regulations". As most smart people know, rules created by the ignorant leave huge gaps for the better-informed, and rules created by the well-informed require self-enforcement since the details are simply not understood by anyone else. The fact of the matter is that if a well-trained scientist working in a lab wanted to sneak out some dangerous material, it would simply be a matter of pipetting it into a tube and putting it in their pocket, and then walking right out of the lab. One tube with a clear liquid in it looks much the same as another.
Now, as far as brewing industrial batches of the stuff is concerned, that would be a little bit harder. But still achievable for someone determined.

It's only scary if you don't think about the fact that it would be easier and more effective to just buy a bunch of fertilizer and diesel fuel if you wanted to become a mass-murderer. Modern society has placed a great deal of potential power into each and every one of our hands. People rightly fear power, but it's not going away.

luv XKCD

yes, regulations and rules are only useful if they are enforced and enforceable. One of the scary scenarios is someone setting up a lab in a warehouse somewhere. They just have to know what they're doing, be a bit clever, and have some money. Assuming they don't make some fairly obvious mistakes, I don't see how anyone could catch them until they've done their damage. That's probably what happened with the anthrax attacks.

 

[William Gaatjes]

luv XKCD

yes, regulations and rules are only useful if they are enforced and enforceable. One of the scary scenarios is someone setting up a lab in a warehouse somewhere. They just have to know what they're doing, be a bit clever, and have some money. Assuming they don't make some fairly obvious mistakes, I don't see how anyone could catch them until they've done their damage. That's probably what happened with the anthrax attacks.

Indeed.

The problem occurs the most when the materials used are so called "of the shelf" materials.
You need a big database to cross-reference what people buy. And that is privacy related.

To come back to my former posts :

I found this virus to be intriguing. : SV40.

http://en.wikipedia.org/wiki/SV40.

I quote:

Theorized role in human disease

The hypothesis that SV40 might cause cancer in humans has been a particularly controversial area of research.[3] Several different methods have been used to detect SV40 in a variety of human cancers, although how reliable these detection methods are, and whether SV40 has any role in causing these tumors, remains unclear.[4] As a result of these uncertainties, academic opinion remains divided, with some arguing that this hypothesis is not supported by the data,[5] and others arguing that some cancers may involve SV40.[6][7] However, the United States National Cancer Institute announced in 2004 that although SV40 does cause cancer in some animal models, "substantial epidemiological evidence has accumulated to indicate that SV40 likely does not cause cancer in humans".[8] This announcement is based on two recent studies.[9][10]
[edit]
p53 Damage and carcinogenicity

SV40 is believed to suppress the transcriptional properties of the tumor-suppressing p53 in humans through the SV40 Large T-antigen and SV40 Small T-antigen. p53 is responsible for initiating regulated cell death ("apoptosis"), or cell cycle arrest when a cell is damaged. A mutated p53 gene may contribute to uncontrolled cellular proliferation, leading to a tumor.

SV40 may act as a cocarcinogen with crocidolite to cause mesothelioma [11] (review [12])

When SV40 infects nonpermissive cells such as 3T3 mouse cells the dsDNA of SV40 becomes covalently integrated. In nonpermissive cells only the early gene expression occurs and this leads to transformation, or oncogenesis. The nonpremissive host needs the Large T antigen and the small t antigen in order to function. The small t antigen interacts with and integrates with the cellular phosphatase pp2A. This causes the cell to lose the ability to initiate transcription.

Melanocytes from fetuses seem to be affected by the sv40 virus and may hold an explanation to some melanocyte related cancers. That the chance occurs when the person affected is still in the womb can explain a lot.

Since not too long ago i learned that the human genome is not big enough to hold our basic blueprint. That not for every step of the process of development and maintenance and for just learning there is a seperate gene. The way we are "build" is by simultaneously switching different but multiple genes on and off.

It really seems if many of the virus related cancerous diseases are the result of multiple virus infections or a combination of a virus and carcinogen. That our error detection / error correction works great until that system is compromised as well in a cell. Other cancers may even be a combination of carcinogens

The p53 gene is in effect not the repair agent but the part that stops the cell division from completetion if an error is detected and must be corrected. If the p53 fails, the error correction can not occur and daughter cells with faulty DNA emerge. P53 stalls the cell division process until the dna damage is corrected.

EDIT: forgot to mention that the p53 also can activate cell apoptosis.

Amazing when it comes to smoking : Benzopyrene interference causes dna damage. But something must have altered the DNA sequence of p53 already. Because the p53 only halts the division, nothing else. That is , if i can assume that what i have read is correct. This is not really surprising because we inhale air and air is saturated with many particles from organic to inorganic. The air we breath is also filled with bacteria and viruses.





This may seem as pretty standard, but for me it is just an interest and i find it amazing to see how life works.


On a Side note, has anybody else encountered that the password system failed on them ?
I had to reset the password to be able to log in again.
And when i wanted to change my password, i never got to that specific page.
I guess there are a few bugs to be worked out. Although i would expect that some tests where done on a test environment prior before the roll out. Perhaps the problem occurred after a certain maximum number of users was encountered.

I understood that the dailytech forum and the anandtech forum are powered by the same system. My old password still works on dailytech even after the change to a new password for the anandtech forum. It seems the forum is a work in progress. When editting, i can not preview anymore.
I do find the old version of the forum a bit more relaxing. There are way to many buttons and double functions.

 

[William Gaatjes]

It is foolish to put your faith in "regulations". As most smart people know, rules created by the ignorant leave huge gaps for the better-informed, and rules created by the well-informed require self-enforcement since the details are simply not understood by anyone else. The fact of the matter is that if a well-trained scientist working in a lab wanted to sneak out some dangerous material, it would simply be a matter of pipetting it into a tube and putting it in their pocket, and then walking right out of the lab. One tube with a clear liquid in it looks much the same as another.
Now, as far as brewing industrial batches of the stuff is concerned, that would be a little bit harder. But still achievable for someone determined.

It's only scary if you don't think about the fact that it would be easier and more effective to just buy a bunch of fertilizer and diesel fuel if you wanted to become a mass-murderer. Modern society has placed a great deal of potential power into each and every one of our hands. People rightly fear power, but it's not going away.

Indeed. Very true. That is why i am convinced that the only way the human race will survive is through knowledge and compassion. The knowledge is needed to know that you can do something wrong no matter what your hands will carry. The compassion is needed to know that you can hurt other living beings. Besides that, knowledge just comes in handy when you are encountering problems.
And compassion makes you feel good.

Just making people smarter will not make them better persons. I once have seen a documentary about one of the engineers of the H-bomb. He was at the end of his life but did not stop him hoping to see the H-bomb used. You would think that someone with the intelligence to build such a device would also be very human. I was wrong about that and saddened too. But at the same time it does explain human history, the present and unfortunately the future.

 

[Gibsons]

Indeed.
Amazing when it comes to smoking : Benzopyrene interference causes dna damage. But something must have altered the DNA sequence of p53 already. Because the p53 only halts the division, nothing else. That is , if i can assume that what i have read is correct. This is not really surprising because we inhale air and air is saturated with many particles from organic to inorganic. The air we breath is also filled with bacteria and viruses.

p53 does a lot of things. I can't see why benzopyrene can't cause mutations in p53, there's pretty strong evidence it does. http://www.ncbi.nlm.nih.gov/pubmed/...med_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2

 

[William Gaatjes]

p53 does a lot of things. I can't see why benzopyrene can't cause mutations in p53, there's pretty strong evidence it does. http://www.ncbi.nlm.nih.gov/pubmed/...med_ResultsPanel.Pubmed_RVDocSum&ordinalpos=2

Grrrr.
I am seriously starting too lose my patience with this untested crap called vbulletin style forum. I just had to log in 7 times in a row while i was already logged in just to be able to post this message. Crapware in my opinion based on experience.


To come back to your post, I am wondering if the benzopyrene has a specific preference
to lock onto parts of the dna. This is what i retreived from your link :

It has been previously demonstrated that the diol epoxide metabolites of bay region polycyclic aromatic hydrocarbons present in tobacco smoke, e.g., benzo[a]pyrene diol epoxide (BPDE), preferentially bind to the most frequently mutated guanine nucleotides within p53 codons 157, 158, 248, and 273 [Denissenko, M. F., Pao, A., Tang, M., and Pfeifer, G. P. (1996) Science 274, 430-432].

and :

We found that all four N(2)-BPDE-dG diastereomers were formed preferentially at the methylated CG dinucleotides, including the frequently mutated p53 codons 157, 158, 245, 248, and 273.

If i read it correctly, it means that the benzopyrene binds to already mutated parts of p53.
Please correct me if i am wrong. If i am right the question is, what caused the mutation in the p53 gene ? Could it been benzopyrene ? Have there been tests performed that show that benzopyrene also binds preferentially to a working form of p53 ? Is it known that p53 can have naturally occurring mutations that do not interfere with it's function ? And does benzopyrene preferentially binds to the same spots in all these version of p53 ?

If i am wrong, then benzopyrene caused the mutation to form first and that this mutation made it easier for benzopyrene to bind to that specific part in the p53 gene.
That if it is the case i find strange but interesting.

I do find that interesting questions.
Sincerely awaiting your answer...

Me.

 

[Gibsons]

If i read it correctly, it means that the benzopyrene binds to already mutated parts of p53.

p53 has been studied pretty intensely for a very long time. Lots of people have sequenced lots of p53 genes from many many different cancers and normal tissues. When you compile this data, you see some bases mutated very often in cancer samples (usually leading to specific amino acid changes), some not so much.

The general theory is that all the bases are, roughly, equally prone to mutation (this is never exactly true). So, when you sequence p53 from cancer cells, your data is selected - you're looking at mutations that lead to cancer (with some noise too, of course). If you see a few bases mutated over and over again, and a lot of other bases only rarely mutated, the conclusion is usually that those bases lead to cancer.

Another explanation though, is simply that cancer cells have a high mutation rate and there's some bias in these mutations. i.e. the mutations are an effect of cancer, not a cause.

Other data suggests that the former is correct - the mutations in p53 lead to cancer. When you look at the mutated proteins for instance, the common mutations lead to loss or change of function of the protein. Also, some unfortunate people are born with a mutated p53 and they get cancer early and often.
http://en.wikipedia.org/wiki/Li-Fraumeni_syndrome

What the article I linked is talking about is that they can detect a known mutagen/carcinogen binding to some of the specific sequences. I didn't read the whole paper, but they might be suggesting that benzopyrene has a higher than-you-might-expect propensity to cause the cancer associated mutations. i.e. it's not randomly mutating all bases, it's more prone to mutate the important ones than unimportant ones.

 

[William Gaatjes]

p53 has been studied pretty intensely for a very long time. Lots of people have sequenced lots of p53 genes from many many different cancers and normal tissues. When you compile this data, you see some bases mutated very often in cancer samples (usually leading to specific amino acid changes), some not so much.

The general theory is that all the bases are, roughly, equally prone to mutation (this is never exactly true). So, when you sequence p53 from cancer cells, your data is selected - you're looking at mutations that lead to cancer (with some noise too, of course). If you see a few bases mutated over and over again, and a lot of other bases only rarely mutated, the conclusion is usually that those bases lead to cancer.

I wonder if it is tested what those preferred codons actually do.

Another explanation though, is simply that cancer cells have a high mutation rate and there's some bias in these mutations. i.e. the mutations are an effect of cancer, not a cause.

i think both explanations are relevant. The damage in p53 leads to dna damage which is not is no longer corrected. That means that mutation after mutation can arise without a mechanism to correct it. Especially since it is known what p53 has as function.

Other data suggests that the former is correct - the mutations in p53 lead to cancer. When you look at the mutated proteins for instance, the common mutations lead to loss or change of function of the protein. Also, some unfortunate people are born with a mutated p53 and they get cancer early and often.
http://en.wikipedia.org/wiki/Li-Fraumeni_syndrome

I have no doubt about that, knowing what p53 does : Stalling the cell division for dna repaires or setting off apoptosis when the dna damage can not be repaired.

What the article I linked is talking about is that they can detect a known mutagen/carcinogen binding to some of the specific sequences. I didn't read the whole paper, but they might be suggesting that benzopyrene has a higher than-you-might-expect propensity to cause the cancer associated mutations. i.e. it's not randomly mutating all bases, it's more prone to mutate the important ones than unimportant ones.

I still wonder if it can do that. Perhaps it latches on and causes the p53 gene to be interpreted wrong. Or that when the benzopyrene is latched on, that the reading mechanism accidently together with the benzopyrene changes the dna chemicals. I guess that is all in the realm of binding energy and chemistry /physics.

Not so long ago the name super atom was used for an artificially configuration of atoms that collectively behaved like an atom of another element depending on it's elektron configuration.

http://en.wikipedia.org/wiki/Superatom
http://www.sciencedaily.com/releases/2008/07/080701092153.htm

Perhaps nature uses a manipulation form similair as this one described in the link.



Grrrr. i have to enter my password multiple times again while i am logged in. It is only in this thread it seems.

 

[tcsenter]

Very cool:

http://www.usnews.com/science/artic...engineer-hiv-virus-to-halt-brain-disease.html

 

[William Gaatjes]

Very cool:

http://www.usnews.com/science/artic...engineer-hiv-virus-to-halt-brain-disease.html

Cool indeed.

Gene therapy is very promising. But in my opinion should be limited in use until it is actually known how life works. These are dangerous grounds to play on if you can not see the whole playing field. We are constantly invested by bacteria and viruses and recombining of dna happens often. Maybe i am over cautious.

 

[Gibsons]

I wonder if it is tested what those preferred codons actually do.
big snip

In large part, yes. It's not really the codons that are preferred, it's the amino acids they code for. You can take these mutant p53s and compare their properties to wild type p53 and demonstrate biochemical differences. i.e. wild type binds DNA, mutant doesn't.

As for benzopyrene, after some metabolic processing, it covalently attaches to a base in the double helix. If nothing else, this makes it difficult to impossible for DNA polymerase to copy faithfully. (see pic, notice how the opposing bases don't pair up correctly).
http://en.wikipedia.org/wiki/File:Benzopyrene_DNA_adduct_1JDG.png

Finally, I'd bet a reproductive organ that superatoms have nothing whatsoever to do with any of this.