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Author Topic: Structure Of An Entire HIV Genome Decoded  (Read 6077 times)

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Offline Rev. Moon

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Structure Of An Entire HIV Genome Decoded
« on: August 05, 2009, 09:05:57 PM »

I did not know that this had not been completed.  One more thing (yet) that I did not know about this darned virus.   Wonder what this will mean as far as developing new treatments.

http://www.sciencedaily.com/releases/2009/08/090805133015.htm
"I have tried hard--but life is difficult, and I am a very useless person. I can hardly be said to have an independent existence. I was just a screw or a cog in the great machine I called life, and when I dropped out of it I found I was of no use anywhere else."

Offline xman

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #1 on: August 05, 2009, 09:40:45 PM »
another addition to the long list of discoveries. i can't understand why the article claims the discovery will lead to the development of antiviral drugs. we still have antiviral drugs so were is the difference? we don't need treatments. we need a cure.


 
« Last Edit: August 05, 2009, 09:47:08 PM by xman »
sign the petition launched by the aids policy project addressed to the nih aimed to increase the money needed to find the cure:

http://www.aidspolicyproject.org/petition_for_the_nih

we can make a difference and we need to fight. please support them! it doesn't cost you anything. they need it now more than ever!

Offline Rev. Moon

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #2 on: August 05, 2009, 09:57:26 PM »
another addition to the long list of discoveries. i can't understand why the article claims the discovery will lead to the development of antiviral drugs. we still have antiviral drugs so were is the difference? we don't need treatments. we need a cure.


 

I can understand what you mean xman, but the development of new therapies/treatment is always important, especially for those who have perhaps resistance to existing meds.  I am not a big believer in the idea that a "cure" will be found in the near/immediate future (no offense, and not a pessimist here... it can be hoped for,  but I'd rather know that a better understanding of the virus is reached leading to more successful / less harmful treatments).  Just my opinion.
"I have tried hard--but life is difficult, and I am a very useless person. I can hardly be said to have an independent existence. I was just a screw or a cog in the great machine I called life, and when I dropped out of it I found I was of no use anywhere else."

Offline Ann

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #3 on: August 06, 2009, 06:48:47 AM »

another addition to the long list of discoveries. i can't understand why the article claims the discovery will lead to the development of antiviral drugs. we still have antiviral drugs so were is the difference? we don't need treatments. we need a cure.
 

Gee whiz, X, did you even consider that maybe one day one of those treatments you so like to deride just might turn out to be a cure? ::) Honestly!

Ann
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"...health will finally be seen not as a blessing to be wished for, but as a human right to be fought for." Kofi Annan

Nymphomaniac: a woman as obsessed with sex as an average man. Mignon McLaughlin

HIV is certainly character-building. It's made me see all of the shallow things we cling to, like ego and vanity. Of course, I'd rather have a few more T-cells and a little less character. Randy Shilts

Offline georgep77

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #4 on: August 06, 2009, 10:24:00 AM »
another addition to the long list of discoveries. i can't understand why the article claims the discovery will lead to the development of antiviral drugs. we still have antiviral drugs so were is the difference? we don't need treatments. we need a cure.


 
You are just Hopeless X.....  the meds we have today, saving millions of lives, came from those discoveries years ago.....and I understand your point too...I don't think the big pharm is looking for a cure, they want to keep doing money.

   But the cure will come...im pretty sure of that
   there are many smart & kind people involved in the HIV research      :D
Come on Sangamo,  Geovax,  Bionor immuno, ...Make us happy !!!
+ 2008

Offline sensual1973

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #5 on: August 06, 2009, 12:19:24 PM »
well said georgep77,lets be optimsitic in the way we think,thats what atleast keeps me going.
God grant me the serenity to accept the things i can not change.

Offline Miss Philicia

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #6 on: August 06, 2009, 01:07:42 PM »
Being skeptical of a cure is in no way implying that one is a pessimist either in general or about the current rate of improvement in HIV treatment.  Frankly many of you here lack the context to realize what improvements there have been in the past five years, at least in any real meaningful way.
"Iíve slept with enough men to know that Iím not gay"

Offline Inchlingblue

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #7 on: August 06, 2009, 02:34:15 PM »
When I first read this thread I was confused because I was pretty sure that HIV's genome was already known. It turns out that the sequence of the genome was known but not the shape (or as the title of the thread states, the structure). As the article below states, this is important because "genomes donít look anything like the neatly linear, bar code-like pictures returned by basic sequencing techniques." Maybe they can use this research, along with the recent high-resolution imaging of HIV's capsid, to come up with agents that can inhibit capsid assembly, which research suggests may be mutation-proof.

There's a good and brief article in WIRED that elaborates a bit and has a neat view of HIV's genome shape, kind of like an aerial view of an ancient Mayan city (or somethin'):

Mapping HIV Genomeís Shape, Not Just Sequence

August 5, 2009

The cellular equivalent of a rough wiring diagram for HIV gives further evidence that the architecture of its genome, not just its sequence, explains how the deadly virus works.

Researchers at the University of North Carolina used chemical compounds that linked to pieces of HIVís genome to trace its shape and arrangement. Their morphological reverse-engineering was necessary because HIV stymies standard atomic-level microscopes.

Unlike most genomes, the genetic code of HIV is made from single-stranded RNA rather than double-stranded DNA. Its units are small, densely packed and very hard to work with. As a result, though scientists have identified HIVís genes and their order, just one-fifth of its genome has been described in precise spatial detail.

Thatís important because genomes donít look anything like the neatly linear, bar code-like pictures returned by basic sequencing techniques. In reality, genomes are arranged in intricate, three-dimensional loops and whorls. And just as a list of machines isnít very useful without a description of their arrangement on a factory floor, structure matters.

In a commentary accompanying the findings, published Wednesday in Nature, University of Michigan chemist Hashim Al-Hashimi called them an ďaerial view.Ē The map is still not complete or truly high-resolution. Itís also a one-time representation of an ever-shifting target. But even so, itís detailed enough to suggest that the architecture of certain spots in the HIV genomeís middle regions coordinates protein manufacture.

Until now, high-resolution imaging efforts have focused on the genomeís tips. Researchers can now target other regions in greater detail, and perhaps see where a wrench might be thrown into the viral assembly line. ďThe quest for a high-resolution structure of the entire HIV-1 RNA genome has begun in earnest,Ē writes Hashimi.


LINK:

http://www.wired.com/wiredscience/2009/08/hivtopograph/



[attachment deleted by admin]
« Last Edit: August 06, 2009, 03:24:12 PM by Inchlingblue »

Offline Ann

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #8 on: August 06, 2009, 03:08:40 PM »

There's a good and brief article in WIRED that elaborates a bit and has a neat view of HIV's genome shape, kind of like an aerial view of an ancient Mayan city (or somethin'):

http://www.wired.com/wiredscience/2009/08/hivtopograph/


Looks like a crop-circle gone mad to me!
Condoms are a girl's best friend

Condom and Lube Info  



"...health will finally be seen not as a blessing to be wished for, but as a human right to be fought for." Kofi Annan

Nymphomaniac: a woman as obsessed with sex as an average man. Mignon McLaughlin

HIV is certainly character-building. It's made me see all of the shallow things we cling to, like ego and vanity. Of course, I'd rather have a few more T-cells and a little less character. Randy Shilts

Offline georgep77

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #9 on: August 06, 2009, 03:21:20 PM »
Looks like a crop-circle gone mad to me!

Im pretty sure thats an alien crop-circle      :P
Come on Sangamo,  Geovax,  Bionor immuno, ...Make us happy !!!
+ 2008

Offline Inchlingblue

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #10 on: August 06, 2009, 03:49:45 PM »
Yes, a crop circle, but definitely not a nice, normal one, rather, as Ann said (but in British English), a crop circle gone wild!

I came across another article, in Chemical and Engineering News, that sheds more light on the relevance/significance of this research.

The article states: Scientists may have uncovered a new level in the hierarchy of biological information embodied in RNA. Specifically, they have found that the RNA genome of an HIV-1 virus contains many highly structured regions

The importance of highly-structured regions is that this implies these regions are important and necessary in the HIV life cycle and that, disrupting them just may disable the virus. In other words, these are likely to be HIV's weak spots.

The study shows that "the HIV genome is packed full of structures," Weeks says. "Right away, we knew that we needed to prove that these structures were not an accident." In collaboration with virologists Ronald Swanstrom and Christina L. Burch at UNC, the researchers find that these structures occur in many HIV variants and are therefore likely to play critical roles in viral replication.

They don't yet know the function of all these structured regions, but they hypothesize that many help determine the structure of the proteins encoded by those sequences. Weeks suspects that regions that are more highly structured move slowly through the ribosome as it translates the RNA into proteins. "The idea is that the ribosome pauses close to the end of every protein domain to allow that domain to fold up into its correct shape, without interference from the other domains of the protein," he says.


LINK:

http://pubs.acs.org/cen/news/87/i32/8732news2.html

« Last Edit: August 08, 2009, 01:27:15 PM by Inchlingblue »

Offline xman

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #11 on: August 06, 2009, 08:14:40 PM »
but the development of new therapies/treatment is always important, especially for those who have perhaps resistance to existing meds.

yes you're right. the issue is that those resistant to current meds need new treatments now and not in 10 years. the crisis of new treatments was announced some months ago and the current pipeline is an arid desert with only one or two drugs in phase 3 and near fda approving. but most of the infected people will die before this findings are useful tools to combat the virus. please tell those great discoveries to all the patients resistant to the drugs available. the most important issue is always underestimated: time. we can't ask to the infected people to wait because the virus we are carrying doesn't wait.
« Last Edit: August 06, 2009, 08:30:08 PM by xman »
sign the petition launched by the aids policy project addressed to the nih aimed to increase the money needed to find the cure:

http://www.aidspolicyproject.org/petition_for_the_nih

we can make a difference and we need to fight. please support them! it doesn't cost you anything. they need it now more than ever!

Offline xman

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #12 on: August 06, 2009, 08:19:01 PM »
did you even consider that maybe one day one of those treatments you so like to deride just might turn out to be a cure? ::) Honestly!

Ann


yes one day will have a mars colony and the possibility to enjoy a starcruise to the rings of saturn and we will also have nanomachines able to reach our organs and repair them.

with all respect (and i have very much for you, believe me), did you ever consider how many people will die from the virus until that day?
sign the petition launched by the aids policy project addressed to the nih aimed to increase the money needed to find the cure:

http://www.aidspolicyproject.org/petition_for_the_nih

we can make a difference and we need to fight. please support them! it doesn't cost you anything. they need it now more than ever!

Offline xman

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #13 on: August 06, 2009, 08:48:41 PM »
You are just Hopeless X.....  

you're absolutely wrong. i'm not hopeless. i'm concerned because i don't ignore the risks involved with taking the current medicines and the long term effects of the virus on our body even if suppressed. i also fear for those that have resistance to most of the drugs available or those without access to the drugs at all. with the current crisis and funding cuts in the vaccine research and the financial assistance for treatment in california, i don't see much reason for optimism now.
« Last Edit: August 06, 2009, 08:53:55 PM by xman »
sign the petition launched by the aids policy project addressed to the nih aimed to increase the money needed to find the cure:

http://www.aidspolicyproject.org/petition_for_the_nih

we can make a difference and we need to fight. please support them! it doesn't cost you anything. they need it now more than ever!

Offline GNYC09

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #14 on: August 06, 2009, 11:11:29 PM »
xman, I find your responses curious if not disingenuous since you come across as some big champion of those resistant to meds meanwhile you yourself have stated that you are "newly diagnosed" and "Not on meds and healthy. VL 64000, CD4 696 24%".  Do you happen to be resistant to some meds, which you are lucky enough not to be on? 

For somebody that has only known they were HIV+ for a short while, you seem to be pretty sure that "most of the infected people will die before this findings are useful tools".  How do you know this?  I mean, really, why not admit this is just your opinion?

Your last 60+ posts are all negative.  The irony is that it goes against the grain of what many LTS on these boards have been providing based on their long-term experiences: HOPE.  I understand the anger and/or despair you may be feeling-I'm not immune from feeling the same- but I wonder if you've taken the time to absorb some of what some of what these long-term survivors have said: that with the medicines we have today being poz is not a death sentence. 

I am working on my feelings of anger & despair through therapy - you may want to consider doing the same.


Offline J220

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #15 on: August 07, 2009, 02:06:05 AM »
...did you ever consider how many people will die from the virus until that day?

Are you for real??? You actually think those of us living with this disease longer than you are not aware of this??? Talk about a patronizing and arrogant comment. You act like you're the only one in the world infected, and as if you alone know something we don't....get some perspective already.

 

"Hope is my philosophy
Just needs days in which to be
Love of Life means hope for me
Born on a New Day" - John David

Offline elf

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #16 on: August 07, 2009, 01:19:12 PM »
More details they find about HIV, less and less we know about the disease (we lose the general picture). Most vaccines were made back in the end of 19th century when scientists (like Pasteur or Koch) knew nothing, zip, nada about immunology or genetics.  ???

Offline GNYC09

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #17 on: August 07, 2009, 06:14:10 PM »
elf, I'd love to hear your supporting facts.  Here is an interesting timeline of vaccines on wikipedia, which shows the opposite to be true.

Offline Miss Philicia

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #18 on: August 07, 2009, 07:28:05 PM »
pft!  facts.
"Iíve slept with enough men to know that Iím not gay"

Offline GNYC09

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #19 on: August 07, 2009, 07:37:57 PM »
lol!

Offline Rev. Moon

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #20 on: August 07, 2009, 08:12:36 PM »
pft!  facts.

Miss P. you seriously crack me up with just a few words sometimes :P

Being new, I am starting to notice two "schools of thought" within these boards:  those who are realistic and grateful for the advances that have been made in just a few years (while I am new HIVer, my first lover --and life mentor/inspiration-- is a LTS who perhaps wouldn't have lasted over twenty years if it weren't for the miracle of science), and those who under the guise of optimism for a cure throw an eppy every time that a bit of news is posted (within this group we have "sub-sets" that include conspiracy theorists, moaners, and other colourful characters).  I'm sure that they mean well, but in the process they cause other members to ignore this corner within the forums.

PS./ Inchlingblue, thank you for your additional posts.  When I opened this thread I knew that you'd be able to enlighten me a bit more on the subject.
« Last Edit: August 07, 2009, 11:03:33 PM by livebythemoon »
"I have tried hard--but life is difficult, and I am a very useless person. I can hardly be said to have an independent existence. I was just a screw or a cog in the great machine I called life, and when I dropped out of it I found I was of no use anywhere else."

Offline freaky_dream

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #21 on: August 07, 2009, 09:30:53 PM »
More details they find about HIV, less and less we know about the disease (we lose the general picture). Most vaccines were made back in the end of 19th century when scientists (like Pasteur or Koch) knew nothing, zip, nada about immunology or genetics.  ???



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Offline elf

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #22 on: August 08, 2009, 01:17:23 PM »
Ok, now we have all words translated, but we don't know how to put them together to make sense (we need to find a grammar)...

Offline freaky_dream

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #23 on: August 08, 2009, 06:35:56 PM »
Ok, now we have all words translated, but we don't know how to put them together to make sense (we need to find a grammar)...

It's already being done. That's what CHAVI and a couple other consortium's world wide are attempting to do.

Offline Inchlingblue

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #24 on: August 08, 2009, 07:29:19 PM »
I came across another article on this research that has some additional information which is interesting.

And, by the way, the researcher doesn't see an ancient Mayan village nor a crop circle, he thinks HIV's genetic structure looks like......a charm bracelet (I don't see it but...I'll take his word for it). This is what he said:

"Its structure resembles a charm bracelet," said Weeks. "It is a long single strand with all these RNA structures hanging off it."

I thought this bit was interesting:

While the research team has not determined the function of all the RNA "charms," Weeks said one function of the structures appears to be the regulation of how the virus mutates.

"The hallmark of HIV is its rapid mutation," said Weeks. "Our study helps us to better understand how this happens, so we can learn how the virus attacks, replicates, evades and lies in wait
."

LINK:

Mapping of AIDS genome portends better drugs

http://www.canada.com/health/Mapping+AIDS+genome+portends+better+drugs/1865635/story.html
« Last Edit: August 08, 2009, 07:30:56 PM by Inchlingblue »

Offline brazilianman

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #25 on: August 08, 2009, 08:09:25 PM »

the work is being done for remove hiv
now we need a little luck

Offline xman

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #26 on: August 09, 2009, 01:20:11 PM »
AIDS cure still years away - Geneva expert
by Jeremy Allen
Geneva - August 7, 2009 | 09:01
Robin Offord, one of the world's leading experts on HIV, explains the science behind a breakthrough at the University of North Carolina, where scientists have unravelled the structure of the virus that can lead to AIDS. The Geneva University professor also tells Swisster that discovering a way to effectively combat the virus will take years.

http://www.swisster.ch/en/news/science_tech/audio-aids-cure-still-years-away-geneva-expert_118-2229240

Any comments?
« Last Edit: August 09, 2009, 01:31:50 PM by xman »
sign the petition launched by the aids policy project addressed to the nih aimed to increase the money needed to find the cure:

http://www.aidspolicyproject.org/petition_for_the_nih

we can make a difference and we need to fight. please support them! it doesn't cost you anything. they need it now more than ever!

Offline sensual1973

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #27 on: August 09, 2009, 01:57:58 PM »
so much discoveries every now and then about the nature of the virus,yet the same boring sentence i've been hearing almost 10 years ago: "we are years away from a major break through" bla bla bla.
God grant me the serenity to accept the things i can not change.

Offline Inchlingblue

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #28 on: August 09, 2009, 02:59:53 PM »

Any comments?

I think it's a very interesting interview, thanks for posting. Offord calls these new findings "a very important dimension of new knowledge to what we already knew."

I don't think it takes an HIV expert to know that the fruits of this research are years away. How many years? Not even the most knowledgeable expert can answer that. Maybe 2 years? Maybe 5 years? Maybe 10, 20, 30 years?

Personally I enjoy reading and learning about the research, I don't get too caught up in how soon or how far away the fruits of same may be as long as things are still moving forward on the research front.
« Last Edit: August 09, 2009, 08:02:26 PM by Inchlingblue »

Offline Inchlingblue

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Re: Structure Of An Entire HIV Genome Decoded
« Reply #29 on: August 14, 2009, 12:10:39 PM »
I just want to say, for the record, that the picture of the HIV genome structure, above, is only a small part of it, the HIV RNA genome is very large, composed of two strands of nearly 10,000 nucleotides each. This is the caption for the pic above:

Structures found in the HIV RNA genome as identified by UNC researchers. Spheres indicate individual RNA nucleotides. Approximately 2000 nucleotides of the 10,000 nucleotide long HIV genome are shown.

LINK:

http://www.thebody.com/content/news/art53142.html

 


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