[InfiniteMind (OP)]

As I do not have much knowledge in biology and viruses I have come to this section.
1) Please give me some detailed information on working of a virus. Also I would like to know if viruses can be designed to alter the genetic code of an living organism. The question that arises in my mind is that, can a virus be formed so that it carries a specific genetic information and infect the target cell and thus altering its genetic code?
2) Is it necessary that a DNA thread holds the genetic information? I mean can there be any other system or structure that does the same function as of DNA?
3) Can humans function on any other gas than Oxygen?
I am more into physics and math and I have null knowledge in biology....Your answers will be appreciated. Thank you.

[CliffordK]

There are different types of viruses:

• Double Stranded DNA
• Single Stranded DNA
• Double Stranded RNA
• Single Stranded RNA (Positive Sense)
• Single Stranded RNA (Negative Sense)
• Reverse Transcriptase

They all must have either DNA or RNA to carry the genetic material. 

Prions are a special type of "infectious" material in which a normal protein takes on an abnormal configuration, and is able to catalyze the abnormal folding of the proteins.  Thus, they can be transmitted without DNA/RNA.

A hot area of research is to design custom viruses to insert specific genes into their target cells for gene therapy.  Generally not specifically targeting the gametes, although there apparently is some viral DNA in our genome.

Double Stranded DNA, or Reverse Transcriptase viruses are often chosen so that they form DNA in the target cells.  Viruses are often organ specific, which can be utilized to target specific organs in the patient.

Humans do require oxygen to oxidize carbon.  However, certain muscles can function for brief periods anaerobically, or without oxygen.

The majority of the oxygen you breathe in is also exhaled.  CO₂ buildup is one of the issues.  There are diving "rebreathers" that scrub the CO₂, and allow one to rebreathe the oxygen, thus significantly reducing the amount of oxygen needed to be carried. 

There apparently have been experiments with mice breathing highly oxygenated aqueous solutions.

[InfiniteMind (OP)]

assume that there were no oxygen on earth and in that case was it possible for life to still develop on earth? also can i argue that O₂ is not the most efficient gas for life to exist?

Humans do require oxygen to oxidize carbon.  However, certain muscles can function for brief periods anaerobically, or without oxygen.

The majority of the oxygen you breathe in is also exhaled.  CO₂ buildup is one of the issues.  There are diving "rebreathers" that scrub the CO₂, and allow one to rebreathe the oxygen, thus significantly reducing the amount of oxygen needed to be carried. 

[RD]

assume that there were no oxygen on earth and in that case was it possible for life to still develop on earth? ...

The first life on Earth was anaerobic, to which oxygen was toxic ...  http://en.wikipedia.org/wiki/Oxygen_Crisis

[CliffordK]

No oxygen in what sense?

No free oxygen?

The early Earth's atmosphere would have been oxygen poor, likely a mix of CO₂ and Nitrogen. 

Plants released the oxygen that we now have available in our atmosphere.

Some anerobic bacteria and yeasts can take long-chain hydrocarbons and convert them to short chain hydrocarbons, and derive energy.  Potentially one could have life that would live on primarily on different hydrogen and carbon compounds without oxygen.  Although, oxygen is a component of water (H₂O), and some critical compounds in Earth life such as ATP.

Animals tend to depend on the high energy content of hydrocarbons + free oxygen.  Even aquatic animals get oxygen from the water.  However, the green sea slug (elysia chlorotica) may in fact be able to survive without free oxygen.

[evan_au]

1) I would like to know if viruses can be designed to alter the genetic code of an living organism.

Yes, retroviruses can insert extra pieces of DNA into the host cell.
The virus would then normally multiply within the cell and kill it. However, researchers are trying to produce disabled viruses that can safely carry extra pieces of DNA into a cell without killing the cell.

2) Is it necessary that a DNA thread holds the genetic information? I mean can there be any other system or structure that does the same function as of DNA?

Bacteria are able to store and transmit genetic information in the form of plasmids, which are a loop of genetic material, in addition to the cell's genetic material.
But plasmids still use the familiar DNA to store the genetic information for transcription into proteins.

3) Can humans function on any other gas than Oxygen?

Humans have a very much smaller gut than some other species which rely on vegetation. Biologists think that this is possible because humans consume high-energy food like fruit, nuts, cooked meat and vegetables - and extract energy by reacting them with oxygen (through a number of intermediate steps).

Gases that are common at Earth's temperatures include:

• Hydrogen & Helium: These gases are very light, and rare in the atmosphere. But some bacteria can get energy from processing H⁺ ions
  
• Nitrogen: The dominant gas in the atmosphere, but it is very stable. Turning Nitrogen into bio-available fertiliser is a major energy consumer.
  
• Compounds of the above elements plus the likes of Carbon and Sulphur:
  
  • Carbon dioxide and water are too stable
    
  • Compounds of Nitrogen & hydrogen (Ammonia) and Carbon/Hydrogen (eg methane) are broken down by UV & biological processes.
    
  • Bacteria can get some energy by metabolising metal sulphides

Humans would have trouble surviving on other gases - carbon dioxide, water & nitrogen are too stable, and chlorine/fluorine are too unstable.

[InfiniteMind (OP)]

first of all thank you for your help. i really appreciate it...

Yes, retroviruses can insert extra pieces of DNA into the host cell.
The virus would then normally multiply within the cell and kill it. However, researchers are trying to produce disabled viruses that can safely carry extra pieces of DNA into a cell without killing the cell.

Now the thing is, I have hemophilia. Its a blood clotting disorder. The F9 gene responsible for formation of coagulation factor IX is mutated. Is it possible, that through a virus, I can deliver a correct gene to my liver?

[InfiniteMind (OP)]

Nitrogen: The dominant gas in the atmosphere, but it is very stable. Turning Nitrogen into bio-available fertiliser is a major energy consumer.

Humans would have trouble surviving on other gases - carbon dioxide, water & nitrogen are too stable, and chlorine/fluorine are too unstable.

how does the human body know which gas is unstable? I mean N₂ bond enthalpy is around 940kj mol^-1...and oxygen is about 500...how does the living organism know which gas is better.... If it were quantity of gas we could argue that  nitrogen would be the gas we intake but apparently oxygen is the the gas we function on. So, how do living organism know that oxygen is easier to react with?

[evan_au]

Is it possible, that through a virus, I can deliver a correct gene to my liver?

Genetic Engineering is theoretically possible, with a variety of results demonstrated in plants and animals, plus some promising early results for some human diseases.

It is a challenge to reach a sufficient fraction of cells to make a difference to quality of life, and there are fears about side-effects such as cancer. So at present you would have to describe it as controversial, but promising.

And, as always in medicine, don't hold your breath waiting for it to become available to the public.

For now, transfusion of factor IX seems to be a fairly effective therapy, with supplies derived from blood donations, but genetically-modified yeast may also become a feasible source.

[InfiniteMind (OP)]

For now, transfusion of factor IX [nofollow] seems to be a fairly effective therapy, with supplies derived from blood donations, but genetically-modified yeast may also become a feasible source.

yes I know, I am currently on the same therapy. But, it is pretty expensive 2500$ for a single infusion. From where I come (India) only few people can afford it. A more permanent solution would be much better for poor people. That's why I raised this topic. I am planning to do some research on making viruses but these things are not encouraged much in India.

so my idea is to use a virus to cure hemophilia. Is it possible to execute such an idea?
everyone who can help is welcome. Please I really need this..

[InfiniteMind (OP)]

Here is why I mentioned the following points in my first post:

2) Can only DNA be used to store genetic info?: I asked this because I am wondering if one can replace the DNA system with some other, much simpler, mechanism. I know this sounds extreme but, can one create such a biological mechanism that can program an organism? If one can, why not use it to alter the liver of a hemophiliac? If no DNA no disease! Anyway this theory is a bit extreme.

3) Do humans function on any gas other than oxygen?: I asked this question because I want to know if factor IX can be made nasal. The idea is that, we replace the mechanism of hemoglobin with a molecule that can carry coagulation factor IX as well. This way, by breathing that gas, the coagulation factor is infused in the blood stream. That way it would become much easier for a person to treat themselves during bleeding episodes.

I Know that both these theories are way too extreme. that is why I have put forth my questions in this section, in hope of getting an expert opinion. Your reply will be appreciated. Thank you.

[CliffordK]

Both Factor VIII & Factor IX are proteins. 

If you ate them, the majority of the protein would be digested, and you wouldn't benefit significantly.

As far as inhaling, you can inhale a large number of gases without significant adverse effects.  For example, you can inhale the inert gases, Helium, Neon, Argon, etc, and they will not harm the body, except for asphyxiation.  Nitrous oxide (and a great many other gases) can act as an anesthetic , as well as altering one's mental state.

Steroids, and many asthma medications are often administered with inhalers, but they are smaller molecules than your clotting factors.

In the USA, both Hemophilia Factor VIII & IX are available as recombinant proteins, and thus do not require blood products. 

There was some research about inhaled insulin.  Presumably a similar approach could be used with Factor VIII or IX.  There is also research about IM, and other non-IV injection methods for the factors.  Using purified products means less needs to be administered than using blood or blood plasma, and would also make it easier and safer for home administration.

Look up on the web:
BeneFix® Coagulation Factor IX

I'm not sure how it is purchased, but perhaps your pharmacy could purchase it direct from the manufacturer. 

I'm not sure how medical insurance works in India.  The USA is now wrestling with an insurance transformation that is designed to provide better coverage for patients with chronic conditions

[CliffordK]

As far as virus gene therapy.  It certainly has to begin with animal research.

It is quite possible that gene regulation would be poor for genes delivered with a viral vector.
What are the effects of having too much Factor VIII or IX? 

The info on Benefix is interesting.  Apparently they chose ovary cells as they normally secrete hormones, but apparently can be modified to secrete the Factor IX proteins. 

It may not be good to implant a hamster ovary, but perhaps one could create an implantable organ designed to slowly make and secrete the Factor.  Possibly modifying tissue ex-vivo, then re-implanting it. 

How old are you?  Could you get into a biology PhD. program with gene therapy research in India?

[InfiniteMind (OP)]

.
What are the effects of having too much Factor VIII or IX? 

There are no undesirable effects of having too much of Factor VIII or IX. It is in fact beneficial as it lasts for a long time.

[InfiniteMind (OP)]

How old are you?  Could you get into a biology PhD. program with gene therapy research in India?

I am actually very young... I am almost 17. This new year I will get into my first year of engineering. And besides I am actually studying subjects related to physics.

[RD]

... What are the effects of having too much Factor VIII ...

Hypercoagulability ...

Excess Factor VIII: A Common Cause of Hypercoagulability

http://www.medscape.com/viewarticle/502267

[InfiniteMind (OP)]

... What are the effects of having too much Factor VIII ...

Hypercoagulability ...

Excess Factor VIII: A Common Cause of Hypercoagulability

http://www.medscape.com/viewarticle/502267 [nofollow]

normally 10000- 12000 units of factor is enough. I take about 3500 units and it lasts for about a week. So, thrombophilia doesn't occur in such cases. Normally people have about 200-300% of clotting factor in their body. Infusion of coagulation factor VIII or IX just increases it from -1 to 50-60%. In such case hyper coagulation doesn't occur.

[evan_au]

There is certainly an economic and research dilemma in truly curing hemophilia (or indeed, any disease).

Research costs lots of money (well over a billion dollars, by the time a drug is approved for use in most countries), and has a very high failure rate (well over 90% of drugs that looked promising in the lab run into some insurmountable obstacle in human clinical trials).

Pharmaceutical companies need some assurance that they will make back this money (plus a reasonable profit) before they embark on development of a drug. This is achieved by awarding patents on drugs, which allows the manufacturer to recoup the development costs at a faster rate before the patent expires and it becomes a "generic" drug, effectively distributed at close to manufacturing cost.

Charging $2500 per week for a chronic condition is an economically attractive proposition, even if very few people can afford it; a genetically engineered source that halved the cost and doubled the number of people who could afford it still represents a sizeable market value. A national health system that paid for those who needed the treatment would increase the market even further.

However, a true cure (such as the genetically engineered virus you suggest) would cost a similar amount to bring to market, but would be a single injection (or short series of injections). Even at $2500 per injection, a cure cannot pay back the development costs as fast as a temporary treatment which costs $2500 per week for a lifetime.

There are genuine concerns about the long-term safety of genetic treatments. To minimise these risks, some of the proposed genetic treatments only have short-term effects, which must be repeated regularly. For example, some treatments for cystic fibrosis require a weekly inhalation treatment (the lungs are the primary target in this disease).

It is suggested that these economic & research considerations has led to a reduction in research into new antibiotics (since bacteria will rapidly develop resistance), and a greater emphasis on temporary treatments for chronic conditions.

Clearly, a for-profit company would rather invest on something which produces a regular income stream, rather than a one-off payment. Research into true cures is most likely to come from philanthropists like Bill Gates, PhD students who work almost for free, charitable associations of disease sufferers who really want a cure, or a national health system that sees that a true cure will be more economical for the nation as a whole than a temporary treatment.

In the meantime, modern genetic screening techniques offer a significant opportunity for pharmaceutical companies to recover some money that has already been wasted on "failed" drugs. The adverse effects that are noted in clinical trials often affect a small fraction of the population - perhaps only 10%.

By doing genetic screening of people who suffer adverse effects, it is theoretically possible to identify individuals who should not take the drug, and bring the drug to market at a fraction of the normal cost - since some of the clinical trials have already been done. This is certainly a different approach than is common today, where there is a strong economic incentive for people who drop out of a clinical trial to be "swept under the carpet".

[evan_au]

PS: I get the impression that some of the side-effects of drugs have to do with individual differences between the activity of enzymes which break down the drug molecule.

• Those who don't have an active enzyme to break down the drug find that it builds up in their system, until it becomes toxic. These people may still find that the drug is useful, but at much lower dosage.
  
• Those who have an overactive enzyme breaking down the drug will find that it never reaches a therapeutic dose in their system, so they see no improvement. These people may still find that the drug is useful, but at much higher dosage.

Many of these enzymes reside in the liver, and some in the gut. A person's repertoire of these enzymes could be fairly cheaply tested with "gene chip" technology.

[yellowcat]

Gene therapy for haemophilia has worked in dogs:
http://www.bbc.co.uk/news/health-24993155