One of the excellent byproducts of genomic databases containing sequences from a wide range of organisms is that by incorporating genetics, evolution and creativity, you can discover important genes in the haystack that is a genome. This report in Cell from Susan Dutcher's lab at Washington University dramatically illustrates this point.
Really Big Haystacks
They examined cilia, the whiplike structures found on the surface of cells, and basal bodies, the structures that anchor the cilia. At least 250 proteins are involved in building cilia and another 150 are involved in basal bodies. This is a lot of genes to look for, like looking for a needle in a haystack. Dutcher's lab used some smart analysis to find those needles.
Start With Some Algae
Cilia in primitive organisms are very similar to those found on human cells. So, a dataset examining genes that humans and a primitive green algae, Chlamydomonas, should include all the genes involved in forming cilia or basal bodies. When this comparison was done, 4,348 matches were found.
Add A Weed
There are a large number of matches because there are a lot of other genes in common between Chlamydomonas and humans than cilia or basal bodies. So, this research group used in interesting evolutionary fact to help them. When plants moved from the sea to land, they lost their genes for building cilia. So, if any of the 4,348 from the dataset of human AND Chlamydomonas matched genes in the plant, Arabadopsis, they must not be related to the creation of cilia. Turns out there were 3,660 matches.
Chlamydomonas AND Human NOT Arabadopsis
The 688 genes left were still a little too many, so they did some comparisons with other genomic sequences (i.e. fly, mouse) to narrow the list. Amazingly, they had a pretty strong group of candidates for the genes they were looking for. They found 92% of the 62 genes that are already known to be involved in the complex creation of cilia. Several genes that had already been identified as being involved diseases of the cilia were also found in this dataset.
The Needles Find Gold
With the dataset validated, they began looking at some of these gens to see if they were associated with anything that might indicate involvement with ciliary function. For one genetic disease that affects cilia, mutations had been found in 6 genes. There was a seventh believed to be hidden amongst 230 genes in a region on chromosome 2. Two of the genes from Dutcher's dataset were also found in this region. When the DNA from people suffering the genetic disease was examined, it turned out that several had mutations in one of the putative cilia genes.
Looking For More Treasure
So, simply by examining genomic databases, using some knowledge of evolution and some information on genetic disease, this work identified a single gene out of all the ones in the human genome as being involved in a specific genetic disease. When trying to understand the workings of complex cellular machines, such as cilia, normal biochemical means are difficult. It is hard to identify each protein involved, particularly ones in low abundance. Using genomic databases in the way Dutcher's lab has will help us narrow in on the important genes involved. Once those are identified, then we can do the biochemistry. Very nifty.
Ribosomes are the site for the translation of messenger RNA (mRNA) into proteins. They move the long mRNA strand through themselves, allowing transfer RNA (tRNA) to sit down at specific sites. These tRNAs have amino acids attached which, through an enzymatic reaction called peptidyl transfer, form the nascent protein. In fact, the ribosome can be viewed as a very large, complex enzyme - a peptidyl transferase.
Make It Happen Faster
A report in the latest PNAS suggests that it is a very unusual enzyme. A catalyst does not allow a reaction to occur that could never occur. It simply lowers the activation energy so that the reaction can occur more rapidly. Instead of happening once every billion seconds, it can happen once every second. As some have said, rather than traveling over the mountain range, catalysts allow the molecules to go around the mountains. Biological catalysts - enzymes - can lower the activation energy in one of two ways, decreasing enthalpy (the 'heat' of the reaction) or decreasing entropy (the chaotic randomness of the reaction). Almost all of the protein enzymes increase the rate of reaction by lowering enthalpy.
Order From Chaos
The ribosome appears to be different. It has little effect on enthalpy at all. It decreases entropy, creating order in a process that would otherwise be much slower. By carefully aligning tRNAs bearing amino acids with mRNA containing information, it permits the creation of a peptide chain. Not a normal enzyme, but an incredibly important one.
The motion of soft-bodied organisms, such as worms and caterpillars, is not something that gets most people's attention. Stories like this sure do, which was on Daypop's Top 40 for a while. Yuck.
Soft BugsA more scientific approach can be seen in this report from Tufts University. Barry Trimmer is trying to understand and mimic the locomotion of caterpillars. Then he wants to build soft-bodied robots that could navigate through buildings, or the space shuttle or our own bodies. Think of this as a tapeworm for good. Luckily, this will take years before we see anything like this. Luckily.
Having lived in Texas, I know of the danger fire ants pose. The introduction of the South American form in the 30s was a great example of how an agressive invader without natural enemies could wreck ecological damage. Often we respond by trying to introduce a natural enemy, usually with equally disasterous results. In this case, it looks like nature may have found an enemy for these fire ants without our help.
A South American Visitor
Thelohania solenopsae is a small protozoan that normally infects the South American form of the fire ant. It weakens the queen and will eventually destroy the colony. Nice thought but scientists were worried about what would happen to other native ant species if this protozoan was introduced here.
It Is Already Here
In 1998, this organism WAS found in an ant colony in Florida (Don't bother trying to read the article. Elsevier wants an outrageous $30 to read a paper that is 6 years old! Here is a free look at the abstract). The question then became, was this also an introduced organism or was it already here in the US but now found in a new host?
Is It Really Different Or Just A Cousin?
DNA tests indicate that the North American version differs from the South American. And this report indicates that it can now be found in fire ant colonies in 120 of 157 counties in Texas. So, finding out if this is a natural form that has now found a way to infect fire ants, or whether genetic drift from an introduced form of the South American protozoan occurred, is very important. One implies we may have a natural enemy of the fire ant up here. The other implies that other native forms of ants could be at risk. As one of the scientists says, "If you really want to disrupt the ecosystem, disrupt the ants."
Well, it looks like I royally screwed up. Not only did I not upload the files I thought I had earlier in the week but I can not find the local copies I usually make. Too much traveling. Not enough backup. Maybe I just dreamed that I had written something. Somewhat like Fermat's Last theorem, I had some wonderful words but perhaps the computer could not contain them. I've had a hard day. I'll get it back on track tomorrow. I hope!
Sorry for the lack of posts the last week. I actually wrote several and thought I had saved them for posting. Seems I screwed up. And, like an idiot, I did not do my normal checkup on the site to make sure it had been updated with the new posts. Seems I am burning my candle at both ends AND the middle.
So, I think I have backups of some of the posts. I am paranoid enough to always keep local copies. I'll try to get them up soon. Its past my bedtime now.
PMVS describes a condition seen in a small number of women. It stands for premenstrual voice syndrome. During certain times of the month, the vocal chords of some woman undego apparently hormonal driven changes. There was a loss in suppleness of the vocal chords, resulting in "less vocal stability and an inability to sing high notes."
Le Jazz No Longer Hot
Although they do not present any evidence that this would have an effect on vocal chord surgery, they do suggest that the syndrome should be taken into effect. I wonder if this knowledge would have had any effect on the surgery Julie Andrews had in 1997 that resulted in the loss of her singing voice. I can not find any articles that provide real details of the surgery (other than botched) but I wonder if performing the surgery at a different time would have made a difference?
Gold nanoparticles. Sounds like some sort of marketer's dream. Mix the lure of gold with the hype of nanoscience. But it is really true. This sort of technology could really revolutionize diagnostics, etc. if they can be brought to market.
Very Fast. Very Sensitive.
I wrote about this earlier. New work from the researchers at Northwestern extends this technology. They now think they can create a system that can detect DNA sequences with greater sensitivity than PCR. Thus, the ability to detect as few as 10 molecules of DNA in minutes.
In A Doctor's Office
In many cases, identifying a particular organism as the culprit in an illness can take quite a bit of time. For some bacteria, it takes almost as long to identify them as the course of the disease. Many times, doctors start courses of treatment without really knowing what is the real cause. Using technology such as this to get the answer in minutes could forever change the practice of medicine. Something this sensitive is extremely powerful.
Sorry for the longish breaks. As anyone who has ever tried to raise money for a new company knows, it is very time-consuming. We have wonderful technology with an experienced management team but no one just hands over big sums of money. We on the phone talking with venture capitalists, on the road presenting to them, following up on the presentations. While things are really picking up from last year, it is still pretty much a buyer's market for almost anything that is not already in Phase II clinical trials.
So, I have less time for writing. My son's soccer still comes before that. But I do find it relaxing to read the literature and write about what I see. So I will try harder to find the time. At least a lot of hotels have high speed internet connections. That makes some things easier.
Making large libraries of short peptides, say 10 amino acids long, has been difficult. Well, making them is not really that hard but getting a library that can be used for drug development is tough. That is because these peptides are not very stable once put into a living system. They are rapidly degraded.
New Uses For Old Chemistry
But recent work has described a method that might get around this. Researchers at Johns Hopkins have applied some chemistry that has been around since the 1970s. Using some very efficient, fairly simple reactions, they can protect parts of the amino acids that will prevent them from being degraded. But, how to put these amino acids together in order to make a polypeptide?
Cell-Free Biochemistry
They start with a process called in vitro translation. A cell-free extract can take mRNA and translate it into a polypeptide. This is because the extract contains all the machinery to do this. The important aspect for the present work is the presence of charged tRNAs. Charged tRNAs act as adaptor molecules, having one end that interacts with the mRNA on a ribosome, and another end that is attached to one of the 20 amino acids found in every polypeptide. The ribosome holds the mRNA and brings in the appropriate charged tRNA, carrying its specific amino acid. This amino acid is added to the end of a nascent polypeptide chain and the cycle starts all over.
Chemistry In A Dish
What the current research does is to modify a mixture of all 20 charged tRNAs. altering the amino acid on each so that it will be protected from degradation. They then add this mixture to a in vitro translation system, along with some mRNAs. The mRNAs are then translated using the modified charged tRNAs. This creates a polypeptide that is now also modified at specific positions, rendering it very stable.
Needle In A Haystack
Pretty neat and a nice way to create a large library of peptides that can be used to screen for a specific activity. There are a few problems. As described, the resulting set of polypeptides is a large mixture of many different polypeptides. As they say, there can be 1013 different polypeptides in the mix. Somewhere along the way, a specific peptide that has a specific activity must be isolated. From the description in the press release, it is not obvious how they propose to do this.
Not Much There
Also, the amount of each different polypeptide in the mixture is quite small. There might only be 10-100 copies of each specific polypeptide in the mix. Many biological systems are not that sensitive and require a lot more polypeptide to see an effect. Scaling up to create many more copies is possible but is not trivial.
Fun For Chemists
But, this is a nifty new way to create a huge library of compounds to screen in biological assays. Pharmaceutical chemists love new ways to create compound libraries of high complexity. This approach can certainly do this and holds out some promise if applied to some specific assays. Then, they just have to figure out what to do next. Producing therapeutic doses of a 10 amino acid polypeptide is not trivial. But, being chemists, I am sure they will figure out novel ways to mimic the peptide in ways that make production much easier.
People can and have made lots of jokes about Viagra but here is a nice story about a very important use for the drug, saving infants with chronic pulmonary hypertension, which is normally fatal. The thing is, Viagra would probably never have been developed solely to treat these infants. The market is too small to justify the huge expense for drug development. But once those costs are borne by something big, like ED, there is a trickle down approach that extends the use to other illnesses. I hope Viagra can keep these children alive long enough for their body to heal itself.
Well, this study sure took all the fun out of eating an Egg McMuffin and hash browns. Seems that this 900 calorie meal sends all sort of inflammatory signals into the bloodstream, signals that are not seen if the same number of calories come from fruits and fiber.
All well and good but the rest of the report is filled with a large number qualifiers (ifs, mays and perhaps). It is also a small study. An interesting observation. And I certainly think that lots of pro-inflammatory signals could be harmful to certain people. But I would hesitate to extrapolate this without a lot more work and a better understanding of just what is happening, how prevalent is it, what foods is it tied to, whether it is seen after any fast or only at breakfast?
Living Code has a new look. We have moved to a Movable Type system, which allows comments, trackbacks, categories and a lot more. I'll be adding more of these as time goes on. Should be fun.
Most lab mice live no more than 2 years. Some live longer by being fed a very low calorie diet. But researchers in Michigan have a mouse that is over 4 years old. This is the equivalent of a human who is 136 years old. These scientists are trying to understand what are some of the genetic underpinnings of extreme life span. Understanding both the environmental and the genetic processes that determine long life will be extremely important. Let's just hope it does more than just lead to older mice.
I liked the fact that they had to keep the smaller, male mouse in a cage with a larger female in order to keep him warm. What a homey touch.
Here is a nice use of modern techniques to create plants that can degrade pollutants, such as toluene. These new plants can live in regions that kill normal plants. They release less toluene to the air and apparently degrade the molecule without deleterious effects.
And It Is Natural
The researchers did this without using any techniques that should upset people. They used bacteria, called endophytes, that normally inhabit the root system of specific plant types. These bacteria were mixed with other bacteria that are able to degrade toluene but do not grow well on the host plant. Through a natural process called bacterial conjugation, some of the genes that permit degradation were transferred to the endophytic bacteria. The researchers then selected for those endophytes that could now degrade toluene.
Bacterial Sex
Now, conjugation happens all the time in Nature. It is one way that antibiotic resistance spreads so rapidly. The key here is that the scientists then applied selective pressure to isolate endophytes that could degrade toluene. They took these new forms of the endophytic bacteria and applied then to the host plant. As can be seen by the photo, levels of toluene that would normally fatal to the plant had no effect.
Other Natural Applications
This approach uses nothing that could not occur in Nature. The key is that it applies direct selective pressure to isolate the appropriate bacteria, rather than relying on purely natural approaches. Normal natural selection could accomplish the same thing but might take a long time to do so. There are bacteria that can degrade almost anything. Finding ways to naturally move these genes to appropriate bacteria should not cause any problems for those afraid of genetically engineered plants. Once the toluene is gone, there is no selective pressure for the bacteria and they should lose these genes, reverting to the old form. Pretty ingenious.