3rd Chromosome Deciphered

veeoh writes: "Another chapter in the human book of life has been published. Scientists working as part of the Human Genome Project(including some from the Wellcome Trust) have deciphered the complete genetic instructions of a third chromosome, one of the 24 bundles of DNA that carry our genetic material. The BBC has an article about the discovery"

Comments

Comparison to mice chromosomes?

[Harumuka]

With the 3rd human genome chromosome completely mapped out, it's time to move on to other chromosomes such as the 17th. According to A Brief History of The Human Genome Project,

For example the 17th chromosome in mice is homologous in large part to the 11th in human beings and of the 35 mapped loci in both organisms on these chromosomes, all but two are ordered into the same sequence.

I wonder how similar 3rd chromosome of mice is to the 3rd chromosome of the human genome. Any research being done in this field?

Re:Comparison to mice chromosomes?

[barawn]

Actually, it's worse than that - chromosomes don't say "make hair like this" - they say "make this protein", and that's -all- they say. To paraphrase a great quote from Alpha Centuari (the game, yes) "You cannot take the gene for an elephant's trunk and put it onto a giraffe, and get a giraffe with an elephant's trunk, because there IS no gene for an elephant's trunk. What you can do with genes is chemistry, because genes code for chemicals."

That said, you don't know HOW a particular protein will interact in a given host unless you know the rest of the chemistry for that host. Stick human growth hormone in a fish, and it won't grow - thus, if you stuck the gene that codes for HGH into a fish, it won't get bigger either.

Then again, all of this is somewhat moot, because for the most part, they do understand a good deal of the biochemistry of animals (including mice) and it's very similar to that of humans.

Re:Comparison to mice chromosomes?

[barawn]

No problem. Actually, the main difficulty understanding genetics is to get over the problem in my previous post - DNA is not like computer instructions - all DNA does is code for protein, and then the protein interacts in the body and 'does what it is supposed to do' (hopefully). The belief that genetic engineering can end all disease, make perfect humans, etc. is a common mistake, and definitely not true - many human diseases are completely agenetic (take cancer, for instance - everyone would probably eventually develop cancer, given enough time) and more importantly, many of the mechanisms in place in living systems are simply to fix or deal with things that break (again, cancer). To make humans immune to cancer, for instance, you'd have to make a better system than nature designed - good luck. You could, however, cure it, and that's the real benefit of genetic engineering, is that it may help us cure and treat diseases better.

The other point is that I do want to stress that the mouse/human comparison is not quite as useless as a first glance might make it seem. The fact is, if we know how a protein (and therefore a gene) behaves in a mouse, and we alter that gene, and see how that protein behaves, we've got a good guess that it will cause the same behavior in humans. It's not -guaranteed-, but it's better than doing the experiment blindly on humans (animal rights activists aside: from a purely practical standpoint, mice breed faster than humans and have a shorter lifespan, so from a completely amoral standpoint, it's better to do it on mice. It's also harder to control the environment). Wow I could still get flamed for that comment.

Re:Comparison to mice chromosomes?

[Quizme2000]

Actually, it's worse than that - chromosomes don't say "make hair like this" - they say "make this protein",

IMHO, thats where the real fun starts is in protien folding. It's extremely difficult to take apart the molecules and fold them correctly back to a stable state. The best analogy i heard was from the director of the HGP, "Its like the highway system, its expensive to build, time consuming, and doesn't generate revenue directly. But it is the first step in the next generation of genetics reaserch needed for sucess."

Re:Comparison to mice chromosomes?

[Otter]

I wonder how similar 3rd chromosome of mice is to the 3rd chromosome of the human genome. Any research being done in this field?

Imagine if you took the 23 human chromosomes, broke them up into a couple of hundred chunks (I forget the exact number) and randomly reassembled them to make the 20 mouse chromosomes. That's what it looks like. So rodent and human chromosomes don't directly map to one another (that site aside) but there are large chunks containing many genes that can be directly compared.

With the mouse genome being sequenced now, that's one of the big things going on -- regions that are similar between the mouse and human sequences are presumably imnportant enough to be conserved over hundreds of millions of years, and therefore give a clue to the location of important features like genes and regulatory elements. That's one of the major pushes in genomics right now.

24?

[Byteme]

I have 46. I am special.

Re:24?

[bats]

There are 24 chromosomes. There are 46 chromosomes. Stop! You're both right.

The average human has 46 chromosomes. There are 23 pairs of them. Of the 23 pairs, 22 pairs consist of similarly constructed mates only differing in the base pairs (AGTC) -- but the structure of the thing is the same. The other set is the XY pair (which determines sex), which are structurally different, ie different sizes, shapes.

So there are 24 kinds of chromosomes, of which most people have 46. Girls have 23 different kinds (no Y) while guys have all 24.

Re:24?

[Byteme]

Then there is Down, Turner's and Klinefelter's syndromes. Down has an extra 21. Turner's is a monosomy X with sexually underdeveloped females. Klinefelter's syndrome are males with extra X chromos, XXY - XXXY. There is also XXX, XXXX and XXXXX female karyotypes with mild effects as the extra X's are inactivated and converted into Barr bodies.

Re:24?

[mindstrm]

Actually...
Females have 23 pairs.
Guys have 22 pairs, plus 2 chromosomes that are not a 'pair'. (XY instead of XX).

The useless Y chromosome, I'm told, is what makes males inferior.

Re:genetic "instructions"

[mrjive]

News flash

Scientists uncover code for flight simulator in 8th chromosome!

Re:Poor practice

[lavaforge]

I for one am glad that my government is competing with the private sector. This doubling of the research makes sure that it is more reliable when it is finished.

How would you like to get a revolutionary new cancer drug, only to find out that the shotgunning method used by Celera missed a few steps? With the government and Celera both having data, errors can be found and corrected before they cost someone dearly.

Re:Poor practice

[pubjames]

I'm appalled that our government would waste so much money on something that could easily be done in the private sector.
[...]
The government should never be competing with the private sector.

Hhmm...

This type of view is often seen on Slashdot. It seems to be a common view in America. It is much less common over here in Europe. (But then we're a bunch of liberal losers, of course...)

Your government put a man on the Moon. Do you think that would have happened if it was left up to the private sector? Similarly with the Genome project. There is masses of work to be done, expensive work, a lot of which is not going to have any immediate financial payback. (Despite what most people think, the mapping of the genome is just a small part of the task ahead to actually understand the whole thing).

Just as the Moon landing would never have taken place without the government, neither would the complete mapping of the Human Genome, and Mankind would be poorer for it.

As a Slashdot reader you may appreciate another perspective. The Internet came out of US government funded work. The Web came out of the CERN project, which is funded by governments internationally. Many of the most commonly-used formats on the web (JPEG, MPEG, MP3) came from EU funded projects. If it was left up to private corporations, it might have taken another twenty years (or more?) before we had anything resembling the Web we have today.

I know a lot of you Americans hate paying taxes and distrust your government, but don't let that blind you to the fact that governments are often the driving force behind new technologies, not corporations.

What does this say about us?

[Zen Mastuh]

From the article, my emphasis added:

The discovery could shed light on why some people are more likely to develop common diseases such as diabetes, obesity or eczema because of their genes.

It's a sad commentary on "civilized" society that three lifestyle-related diseases are presented in a sentence that places the blame on essentially defective genes. Diabetes, now reaching epidemic proportions in adults and children, is nearly always caused by a poor diet. Obesity is caused by poor diet and lack of exercise. As a former sufferer of eczema, I proved for myself that a lifestyle change could cure it. By converse, my lifestyle caused it.

I'm not finding fault with the researchers or trying to cause a ruckus in general, but don't be surprised if these discoveries lead to a society where no one is aware that these (and other) diseases are a result of lifestyle, and every one is lined up at the doctor's office to shell out large sums of $$$ to have their "defective" genes fixed. Remember also that these diseases strain the bodily systems (or cause "imbalance" in non-allotropic medical parlance), and lead to other diseases, causing a potentially endless cycle ending only in bankruptcy/non-insurability/death...

Re:Poor practice

[frenchs]

Some people will see this as "a waste of money". But I would much rather the government spend money through grants and do some research itself, because they can't hold the patents on this information once they finish it. It's OUR money, so it's OUR information when they find it out.

Chimera (unix, linux, windows) is a molecular modeling program developed by UC San Francisco, but it was funded by a government grant from the NIH, so guess what, you can download it for free provided you don't want to make money using it.

The NIH (government orginization) has actually REQUIRED that people that use their money to come up with a protein sequence should deposit it in a freely accessable database

Also, just a side note. If anyone wants to download the program, just grab some protiens from the protien database and load them up. Some stuff you might find interesting in the way of proteins.

tryptophan

hemoglobin

Alcohol Dehydrogenase

DNA (not a protein, but oh well)

Insulin

more...

Enjoy,
Steve

No, what does this say about YOU.

[Xzzy]

> Diabetes, now reaching epidemic proportions in
> adults and children, is nearly always caused by
> a poor diet.

Dude, feel free to talk about your eczema however you want because you probably know a fair a bit about it but don't EVEN go spouting this crap about diabetics unless you're going to get your facts straight.

There's two types of diabetes. While I'll grant that one of them is triggered by lifestyle (but that's not all there is to it, else EVERY obese person in the world would be diabetic, which obviously isn't the case), the other is strictly hereditery.

It usually hits kids just as they start going into puberty; sixth grade and around in there. It has nothing to do with lifestyle; I spent easily half my time tearing around the neighrbood with friends and I was within a few pounds of "average" weight, yet fate still plucked me out and gave me the disease.
Unless of course you're prepared to claim that having an active childhood causes diabetes..

Diabetes is hereditary. Fact, end of story. If I sound pissed off, it's because I am.

Re:genetic "instructions"

[ocie]

There is a secret message:

ATCGATCGATCGATCGACTGAC...
All Your base-pair are belong to us!
...TCGATCGAGCTAGACGTCGTGC

Re:Progress for whom, exactly?

[pubjames]

Doesn't it bother you the least little bit that organizations--whether private or public--are trying so hard to convince us that mapping our genetic material will ultimately benefit the generations to come if we just trust them enough to do the right thing?

No, it doesn't bother me. You're paranoid. Really.

Perhaps there is reason for this level of paranoia in the US. Is there? What is this terrible thing that your government has done to make you Americans feel like this?

I know people who work on projects like the Human Genome project. I've worked on lots of government (UK and EU) funded projects myself. The intentions behind these projects are good. The people doing them are good people.

I'm not so naive as to think that everything governments do is good, but when it comes to things like the Human Genome project, I don't think we have any reason to be paranoid.

Not the Wellcome Trust Centre for Human Genetics

[JeffL]

The work was actually done at the Wellcome Trust Sanger Institute near the town of Cambridge, not at the Wellcome Trust Centre for Human Genetics, part of the University of Oxford.

The WTCHG is actually a cool place that looks for genes for complex diseases, writes useful software, and are heavily invested in using Linux as a scientific computing platform.

They have an 86 cpu Mosix/Linux cluster, and two 8 CPU, 8GB machines running Linux.

Speaking as a scientist...

[Chico Science]

I think I can shed some light on the subject...

The pathology of diabetes is complex. First, one has two recognize there's two types of diabetes. Type 1, called juvenile or insulin-dependent, diabetes and type 2, or non-insulin-dependent, diabetes.

Type 1 is most definitely genetic. While it doesn't have 100% concordance between identical twins, developmental factors can come into play, there is a genetic predisposition. Several genes have been linked with type I diabetes. The primary pathology of this disease is that it is an autoimmune disease. The immune system of the diabetic attacks the cells of the pancreas, depleting the organ of its ability to produce insulin.

Type 2 is a far more complex disorder. The pathology of this disease is that the pancreas is able to produce insulin, albeit not as much as normal people. The significant issue is insulin resistance. The body starts to ignore the metabolic signals of insulin, which causes a feedback loop that ultimately taxes the pancreas and leads to depletion of the pancreatic insulin function (it peters out over time). Due to its complexity and the generalization that it is a disease of obesity, it was considered more of a behavioral disorder (at least more so than type 1). Research, however, is showing there are genetic predispositions to type 2 diabetes (some of this is not even in the genome of the diabetic, but int the small chromosome of the mitochondria, the energy producing organelle in the cells). Also, studies are finding there also seems to be some autoimmunity involved in type 2 diabetes. Lastly, there appears to be a trigger event, believed to possibly be viral.

So, while type 2 diabetes is indeed exacerbated by obesity, one cannot call it a disease of diet.

--

On the topic of obesity, research is showing that there are more factors involved than 'being lazy and eating crap'. On the whole, 'being lazy and eating crap' is bad for your health and its true that our society is progressively leading less healthier lifestyles... but one should note some people can eat crap and not exercise and be perfectly svelte and healthy. Then there are people like one of my colleagues who is a world-class longcourse triathelete, exercises more than anyone I know, eats an exceptionally healthy diet, and can count the number of times she's been sick in the last decade on one hand.. yet she her body mass index puts her in the obese category.

Increasingly, research is showing that adipose (fat) tissue should be considered an organ of the endocrine system. The complex events of endocrine singaling are what regulate resting metabolic rate, glucose and insulin levels, fat metabolism and deposition, caloric intake, response to diet, etc. It is a very complex system that has a lot of factors, including genetic ones.. as well as ones which may be environmental or behavioral but have very definite and difficult to reverse pathologies.

The value of genetics research, pharmacogenetics and pharmacology should not be shrugged off. Yep, put down the donut is good advice, but let's not ignore complexicity because a simple answer sounds nice.

--

Ciao, C.Sc.