How exactly does the presence of sublethal levels of antibiotics in the environment lead to selective pressure on E. coli to take up a shiga-toxin gene? Current research I have seen indicates the toxin provides an advantage in persistent carriage in livestock and has nothing to do with surviving antibiotics in animal feeds. I strongly agree with the sentiment that antibiotics in agriculture are severely overused, but I do not think this is a valid example.
Good of you to bring up the Miller-Urey experiments. Those experiments and subsequent ones with different atmospheric conditions have demonstrated how easy it is to create complex organic molecules under fairly common conditions (common in a cosmic sense).
Uracil is not an amino acid, it is a pyrimidine. Very necessary for RNA and life, but not an amino acid.
I was just thinking, if they actually wanted to implement this they would have to worry about G4 complexes. That would rule out long stretches of guanine-cytosine, which is a shame as they have a triple hydrogen bonding and would be much stronger for such applications. They could use adenine and thymine or possibly uracil as the bulk of the wire with infrequent GC pairs as reinforcement... something like 5'-(AAA GCG UUU AAA CGC UUU)n -3'
It is doubtful that anyone will be putting these into living organisms... intercalating dyes tend to be serious mutagens and there is really no way to prevent such agents from diffusing out of the "fiber optic" and into the DNA of adjacent cells (cancer anyone?).
Not necessarily, there are several old-school biochemical techniques which can assay for cellulose (involving all kinds of fun acids!). Preparing a sample for EM is quite involved. Also, a heavy metal is necessary as a contrasting agent making sample preparation a decidedly destructive process.
Personally, if I was going to design an assay for material of biological origin I would use the properties of chirality. All complex biological molecules have a handedness. Organic molecules of abiotic origin are a "racemic mixture" where chirality is random. If plane-polarized light is shined through such a sample, no optical rotation is observed. In contrast, a sample of biological origin which consists of a single chiral species (say, a sample of a left-handed amino acid) will rotate the light. These assays have the advantage of being able to detect many of the most important biomolecules (sugars, nucleotides, amino acids). Such an assay would require a light source, a chromatography system, a detector and two plane-polarizing filters. Considerably more portable than an electron microscope.
Of course the surface of Mars is a severely oxidizing environment, so it is debatable how well such labile bonds as those found in cellulose would survive over millions (billions) of years. A salt pan is probably the best place as any to look, as water tends to destroy such bonds.
I work on Chlamydomonas (single celled eukaryotic algae) biochemistry. These little fellas are tough. Give them a few basic nutrients (phosphates, trace minerals) sunlight and air and they will grow like weeds. They can be autotrophic (using light) or heterotrophic if you give them a carbon source (like those found in sewage and agricultural waste). People have also had great success growing these by bubbling the exhaust from incinerators through liquid cultures (exhaust is rich in CO2 and NOx which Chlamy can use). Chlamy has been extensively studied (the genome of C. reinhardtii has been sequenced) and there is a huge library of mutants already available. I saw a presentation at an algae conference last year by people working on this. Holy grail is getting hydrogen while they are growing, then extract oil. Best of all, they are completely harmless (trust me, if they were in any way dangerous I would be dead by now). Algal biodiesel and butanol from agricultural waste are our best hope. Ethanol from food crops is basically a big give-away to agribusiness companies. While hydrogen is promising, biologically derived liquid hydrocarbons can take advantage of the extensive infrastructure that has been built for petroleum fuels.
Hell yes! I was pretty much ready to give up on the whole space conquest genera after the steaming pile that was Masters of Orion 3. Galactic Civ 2 brought me back. It is an incredibly good game! While the graphics are good, the real joy is the gameplay... you can tell they really spent time making the game *fun*. So what if it doesn't push the polygons? It's a fun game that I can play on a limited system. As a bonus there's no crippling copy protection (so you can load it on a laptop and play it on the road without having to remember the CD) and meaningful updates that genuinely improve the gameplay. Guess what most of my friends are getting for Christmas?
You are correct, all life uses L-amino acids (except glycine which lacks a chiral alpha carbon) and D-sugars. This leads to some fascinating biological implications. There have been experiments where an enzyme is re-created using D-amino acids using chemical synthesis. The enzyme is functional, but it will only work on the chiral opposite of the natural enzymes substrate. What this means is that if you were to travel to a planet populated by D-amino acid based life, you could eat as much as possible and still starve (because all the enzymes in your body are tooled for L-aa sand D-sugars). In fact one of the tests being considered for detecting life on other planets involves taking a potentially biological sample, running it over a chromatography column to isolate a single species (say a particular amino acid) and checking it for chirality using plane-polarized light. Such tests have been done in the past on organic meteorite samples, they showed a 50:50 racemic mixture, leading to the conclusion that organic deposits in meteorites are abiotic in origin.
While I am not exactly sure about the whole "reflective clouds to cool the planet" idea, I do know that clouds of phosphate would be a much better idea than sulfate. Phosphate "smoke" (from burning white phosphorous with oxygen) is highly reflective and is often used as a smoke screen. When sulfate is dissolved in water you end up with sulfuric acid, the causative agent of acid rain. Phosphate in water does not form such a strong acid and is in fact a fertilizer. As the phosphate came out of the atmosphere we would end up with a slight increase in the nutrients in the land and oceans (though diluted over the entire surface of the planet the effect would be minimal).
Lysozyme attacks the beta-1,4 linkages in the peptidoglycan cell wall of eubacteria (this groups includes E. coli) making them vulnerable to osmotic pressure and ultimately lysing the cell (thus the name). This is why lysozyme is produced by your body on many of your mucous membranes (tears, saliva etc.) Cloning a gene for the production of lysozyme into E. coli would be lethal to any transformed cells. A common source of lysozyme is egg whites. Lysozyme is used extensively in microbiology research and commercially in several oral care products. Yeast would be an excellent source of cloned lysozyme as it is a eukaryote and lack peptidoglycan. Of course rice works too.
Nolan Bushnell, the guy who founded Atari signed a 7 year non-competition agreement with Warner when they bought out the company. While he was waiting out the agreement he founded "Pizza Time Theater" which became Chuck E. Cheese.
I am not familiar with the economic/ social conditions in Abitibi, but looking on a map it seems to be quite high in latitude. My experience from growing up in Alaska is that climate has a serious impact on suicide rates as well as alcohol consumption. Something about long winters with little sunlight seems to make people go off the deep end.
Actually S. aueus is part of the normal flora of the human body. You have Staph living in several places on your body (it's common in the nose). It cohabitates with other Staphlococci and usually causes no problems. I seriously doubt hospital workers would enjoy washing their noses our with bleach or any other disinfectant. Hygiene is important (hand washing!) but it is impossible to eliminate all bacteria in a medical setting without autoclaving people.
1. The sun uses hydrogen as fuel. When the helium ignites, the sun will expand outward and cook Earth.
2. We should confirm that there are, in fact, planets orbiting one of the stars in the Alpha Centauri group. Just because a cool strategy game postulates a planet (xenofungus!) does not mean one is there. It would suck for an astronaut to wake up after 100 years of cryosleep to find no planets (but he/she could at least get a multi-sun tan). I suggest we start with Mars.
3. Revenge against the middle east? In the age of terrorism... Oderint, dum metuant.
As for the future of the space program. Per ardua ad astra.
Tetraethyl lead won WWII. It was the most advanced octane booster available at the time and was exclusively available to allied forces. Using leaded gasoline provided allied fighter aircraft with more power and performance. This helped overcome the technological advantage that German and Japanese aircraft had at the wars outset. It could be honestly stated that without tetraethyl lead, the air war over Brittain would have been longer or even unwinnable. As for CFCs... they were invented as a refrigerant (a task they excell at). They became a problem when people started using them as propellants in spray cans. If they had never been misused they would probably still be legal and providing us with energy efficient cooling. Considering that Midgely had no formal training in Chemistry, he should be admired for his self-made nature.
Viruses such as HIV can swap genes, but only if two strains infect the same cell. This is why new influenza often comes to us from China, where swine, bird and human all live in close proximity and exchange viruses. The chief engine of genetic change in viruses is caused by antigen drift via mutation. This is due to the error-prone nature of virus replication. However, drug resistance is found in viruses. AIDS has shown resistance to some of the early retrotranscriptase inhibitors (AZT), not due to gene-swapping, but good old fashioned natural selection.
Except that viruses are not sensitive to antibiotics. Viruses are prevented by vaccine and a few interference drugs (i.e. AZT). Bacteria are sensitive to antibiotics and in that sense it is very very important to take the entire prescription. One of the biggest problems in microbiology is antibiotics being perscribed for viral infections, thus costing the patient money and releasing needless antibiotics into the body (encouraging resistant strains).
Antibiotics have to be one of the most overused and abused tools in the microbiological arsenal. They are needlessly added to animal feed and hand soap thus introducing massive amounts of antibiotics into "the wild". This has the effect of selecting for resistant strains and leads to problems such as the infection experienced by this woman. Considering that S. aureus is an incredibly common memeber of the natural skin flora, I would think that this lady has a weak immune system or suffered a big oozing injury on her foot to allow for the infection to establish itself. Staphlococcus aureus can be a fairly nasty little bug. It produces an exotoxin that acts as a super-antigen making the immune system go crazy. It also effects the vagus nerve causing *extreme* nausea. I once exposed myself to this stuff and enjoyed 18 hours of fever and projectile vomiting as a result. Several biological weapon programs have considered using the stuff as a chemical weapon.
This may sound a little odd, but I feel sorry for Miss Rosen. She is, after all, merely trying to do her job of defending the recording industry and its business model. I think it would be fascinating to sit down with her over lunch and listen to her side of the debate without so much of the hype that seems to accompany this topic. I do not think she would convince me to see the world her way, but it would be an interesting way to spend my lunch hour. Who knows, she might just be a very nice person outside of the Internet music nastiness we are all familiar with.
I am still an undergrad in this field, so I may be wrong here, but wouldn't another reason to start small be the avoidance of the need to simulate chaperone proteins? Considering the complex and poorly understood nature of chaperones (i.e. heat shock proteins), it would seem prudent to choose proteins that fold without them. Until we have a good model of the various chaperones and how they work (perhaps a future folding@home project) I do not see a way we could simulate them in silico.
Slashdot Mirror
How exactly does the presence of sublethal levels of antibiotics in the environment lead to selective pressure on E. coli to take up a shiga-toxin gene? Current research I have seen indicates the toxin provides an advantage in persistent carriage in livestock and has nothing to do with surviving antibiotics in animal feeds.
I strongly agree with the sentiment that antibiotics in agriculture are severely overused, but I do not think this is a valid example.
Good of you to bring up the Miller-Urey experiments. Those experiments and subsequent ones with different atmospheric conditions have demonstrated how easy it is to create complex organic molecules under fairly common conditions (common in a cosmic sense).
Uracil is not an amino acid, it is a pyrimidine. Very necessary for RNA and life, but not an amino acid.
I was just thinking, if they actually wanted to implement this they would have to worry about G4 complexes. That would rule out long stretches of guanine-cytosine, which is a shame as they have a triple hydrogen bonding and would be much stronger for such applications. They could use adenine and thymine or possibly uracil as the bulk of the wire with infrequent GC pairs as reinforcement... something like 5'-(AAA GCG UUU AAA CGC UUU)n -3'
It is doubtful that anyone will be putting these into living organisms... intercalating dyes tend to be serious mutagens and there is really no way to prevent such agents from diffusing out of the "fiber optic" and into the DNA of adjacent cells (cancer anyone?).
I hope they didn't use proto-matter!
Not necessarily, there are several old-school biochemical techniques which can assay for cellulose (involving all kinds of fun acids!). Preparing a sample for EM is quite involved. Also, a heavy metal is necessary as a contrasting agent making sample preparation a decidedly destructive process.
Personally, if I was going to design an assay for material of biological origin I would use the properties of chirality. All complex biological molecules have a handedness. Organic molecules of abiotic origin are a "racemic mixture" where chirality is random. If plane-polarized light is shined through such a sample, no optical rotation is observed. In contrast, a sample of biological origin which consists of a single chiral species (say, a sample of a left-handed amino acid) will rotate the light. These assays have the advantage of being able to detect many of the most important biomolecules (sugars, nucleotides, amino acids). Such an assay would require a light source, a chromatography system, a detector and two plane-polarizing filters. Considerably more portable than an electron microscope.
Of course the surface of Mars is a severely oxidizing environment, so it is debatable how well such labile bonds as those found in cellulose would survive over millions (billions) of years. A salt pan is probably the best place as any to look, as water tends to destroy such bonds.
A gas giant with habitable moons. Only 41 LY away, it can't be as remote as Dantooine.
I work on Chlamydomonas (single celled eukaryotic algae) biochemistry.
These little fellas are tough. Give them a few basic nutrients (phosphates, trace minerals) sunlight and air and they will grow like weeds. They can be autotrophic (using light) or heterotrophic if you give them a carbon source (like those found in sewage and agricultural waste). People have also had great success growing these by bubbling the exhaust from incinerators through liquid cultures (exhaust is rich in CO2 and NOx which Chlamy can use). Chlamy has been extensively studied (the genome of C. reinhardtii has been sequenced) and there is a huge library of mutants already available. I saw a presentation at an algae conference last year by people working on this. Holy grail is getting hydrogen while they are growing, then extract oil.
Best of all, they are completely harmless (trust me, if they were in any way dangerous I would be dead by now).
Algal biodiesel and butanol from agricultural waste are our best hope. Ethanol from food crops is basically a big give-away to agribusiness companies. While hydrogen is promising, biologically derived liquid hydrocarbons can take advantage of the extensive infrastructure that has been built for petroleum fuels.
Hell yes!
I was pretty much ready to give up on the whole space conquest genera after the steaming pile that was Masters of Orion 3. Galactic Civ 2 brought me back. It is an incredibly good game! While the graphics are good, the real joy is the gameplay... you can tell they really spent time making the game *fun*. So what if it doesn't push the polygons? It's a fun game that I can play on a limited system. As a bonus there's no crippling copy protection (so you can load it on a laptop and play it on the road without having to remember the CD) and meaningful updates that genuinely improve the gameplay.
Guess what most of my friends are getting for Christmas?
You are correct, all life uses L-amino acids (except glycine which lacks a chiral alpha carbon) and D-sugars. This leads to some fascinating biological implications.
There have been experiments where an enzyme is re-created using D-amino acids using chemical synthesis. The enzyme is functional, but it will only work on the chiral opposite of the natural enzymes substrate. What this means is that if you were to travel to a planet populated by D-amino acid based life, you could eat as much as possible and still starve (because all the enzymes in your body are tooled for L-aa sand D-sugars).
In fact one of the tests being considered for detecting life on other planets involves taking a potentially biological sample, running it over a chromatography column to isolate a single species (say a particular amino acid) and checking it for chirality using plane-polarized light. Such tests have been done in the past on organic meteorite samples, they showed a 50:50 racemic mixture, leading to the conclusion that organic deposits in meteorites are abiotic in origin.
While I am not exactly sure about the whole "reflective clouds to cool the planet" idea, I do know that clouds of phosphate would be a much better idea than sulfate. Phosphate "smoke" (from burning white phosphorous with oxygen) is highly reflective and is often used as a smoke screen. When sulfate is dissolved in water you end up with sulfuric acid, the causative agent of acid rain. Phosphate in water does not form such a strong acid and is in fact a fertilizer. As the phosphate came out of the atmosphere we would end up with a slight increase in the nutrients in the land and oceans (though diluted over the entire surface of the planet the effect would be minimal).
Heh.
n guage
At first I thought you were refering to the Snow White IDL that Apple used to use.
http://en.wikipedia.org/wiki/Snow_White_design_la
Lysozyme attacks the beta-1,4 linkages in the peptidoglycan cell wall of eubacteria (this groups includes E. coli) making them vulnerable to osmotic pressure and ultimately lysing the cell (thus the name). This is why lysozyme is produced by your body on many of your mucous membranes (tears, saliva etc.) Cloning a gene for the production of lysozyme into E. coli would be lethal to any transformed cells.
A common source of lysozyme is egg whites. Lysozyme is used extensively in microbiology research and commercially in several oral care products.
Yeast would be an excellent source of cloned lysozyme as it is a eukaryote and lack peptidoglycan.
Of course rice works too.
"a tech union would be nothing more than a band of mediocre complainers..."
;-)
Sounds quite a bit like slashdot
Nolan Bushnell, the guy who founded Atari signed a 7 year non-competition agreement with Warner when they bought out the company. While he was waiting out the agreement he founded "Pizza Time Theater" which became Chuck E. Cheese.
I am not familiar with the economic/ social conditions in Abitibi, but looking on a map it seems to be quite high in latitude. My experience from growing up in Alaska is that climate has a serious impact on suicide rates as well as alcohol consumption.
Something about long winters with little sunlight seems to make people go off the deep end.
Actually S. aueus is part of the normal flora of the human body. You have Staph living in several places on your body (it's common in the nose). It cohabitates with other Staphlococci and usually causes no problems. I seriously doubt hospital workers would enjoy washing their noses our with bleach or any other disinfectant.
Hygiene is important (hand washing!) but it is impossible to eliminate all bacteria in a medical setting without autoclaving people.
1. The sun uses hydrogen as fuel. When the helium ignites, the sun will expand outward and cook Earth.
2. We should confirm that there are, in fact, planets orbiting one of the stars in the Alpha Centauri group. Just because a cool strategy game postulates a planet (xenofungus!) does not mean one is there. It would suck for an astronaut to wake up after 100 years of cryosleep to find no planets (but he/she could at least get a multi-sun tan). I suggest we start with Mars.
3. Revenge against the middle east?
In the age of terrorism...
Oderint, dum metuant.
As for the future of the space program.
Per ardua ad astra.
Tetraethyl lead won WWII. It was the most advanced octane booster available at the time and was exclusively available to allied forces. Using leaded gasoline provided allied fighter aircraft with more power and performance. This helped overcome the technological advantage that German and Japanese aircraft had at the wars outset. It could be honestly stated that without tetraethyl lead, the air war over Brittain would have been longer or even unwinnable. As for CFCs... they were invented as a refrigerant (a task they excell at). They became a problem when people started using them as propellants in spray cans. If they had never been misused they would probably still be legal and providing us with energy efficient cooling.
Considering that Midgely had no formal training in Chemistry, he should be admired for his self-made nature.
Triclosan, while it is a disinfectant, has been shown to select for strains that also exhibit antibiotic resistance.
No.
It is called retrotranscriptase. Retrotranscriptase is used by HIV to transcribe RNA into DNA, in reverse direction of what transcriptase does.
Viruses such as HIV can swap genes, but only if two strains infect the same cell. This is why new influenza often comes to us from China, where swine, bird and human all live in close proximity and exchange viruses.
The chief engine of genetic change in viruses is caused by antigen drift via mutation. This is due to the error-prone nature of virus replication.
However, drug resistance is found in viruses. AIDS has shown resistance to some of the early retrotranscriptase inhibitors (AZT), not due to gene-swapping, but good old fashioned natural selection.
Except that viruses are not sensitive to antibiotics. Viruses are prevented by vaccine and a few interference drugs (i.e. AZT).
Bacteria are sensitive to antibiotics and in that sense it is very very important to take the entire prescription.
One of the biggest problems in microbiology is antibiotics being perscribed for viral infections, thus costing the patient money and releasing needless antibiotics into the body (encouraging resistant strains).
Antibiotics have to be one of the most overused and abused tools in the microbiological arsenal. They are needlessly added to animal feed and hand soap thus introducing massive amounts of antibiotics into "the wild". This has the effect of selecting for resistant strains and leads to problems such as the infection experienced by this woman.
Considering that S. aureus is an incredibly common memeber of the natural skin flora, I would think that this lady has a weak immune system or suffered a big oozing injury on her foot to allow for the infection to establish itself.
Staphlococcus aureus can be a fairly nasty little bug. It produces an exotoxin that acts as a super-antigen making the immune system go crazy. It also effects the vagus nerve causing *extreme* nausea. I once exposed myself to this stuff and enjoyed 18 hours of fever and projectile vomiting as a result. Several biological weapon programs have considered using the stuff as a chemical weapon.
This may sound a little odd, but I feel sorry for Miss Rosen. She is, after all, merely trying to do her job of defending the recording industry and its business model. I think it would be fascinating to sit down with her over lunch and listen to her side of the debate without so much of the hype that seems to accompany this topic. I do not think she would convince me to see the world her way, but it would be an interesting way to spend my lunch hour. Who knows, she might just be a very nice person outside of the Internet music nastiness we are all familiar with.
I am still an undergrad in this field, so I may be wrong here, but wouldn't another reason to start small be the avoidance of the need to simulate chaperone proteins? Considering the complex and poorly understood nature of chaperones (i.e. heat shock proteins), it would seem prudent to choose proteins that fold without them. Until we have a good model of the various chaperones and how they work (perhaps a future folding@home project) I do not see a way we could simulate them in silico.