Les Invalides

 
This is my fourth visit to Paris but it's the first time I've been to Les Invalides. The tomb of Napoleon Bonaparte is much more impressive than I ever expected.

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Pictures of Paris

 


The church is St. Germain des Prés. It's just a few blocks from where we're staying.

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Are Brussel Sprouts Bad for You?

 

Probably not, and that's a good thing because I like Brussel sprouts. They may be OK for humans but they're bad for aphids [Eat up all of your Brussels sprouts -- unless you're an aphid].

I'm going to be in Brussels today. I'm looking forward to a nice meal of Brussel sprouts with beer and chocolate.

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An IDiot Software Developer Opines About Junk DNA

 
Randy "I want to believe" Stimpson is a software developer who thinks he understands biology. He has written a post where he claims Most DNA is not Junk. Doppelganger has already pointed out the most obvious faults with Randy's point of view [Software developer PROVES that there is no junkDNA*... and other stuff].I just want to comment on one small paragraph in order to clear up any confusion.

A bacterial genome has 4 million base pairs of DNA and according to Professor Larry Morgan, a bacterial genome doesn’t have junk. So I think it is safe to say that there is at least 1MB of information in the human genome.

I'm pretty sure he's referring to me. I'd like to point out for the record that bacterial genomes range in size from about 10⁶ bp up to 10⁷ bp.

All bacterial genomes have junk DNA consisting mostly of defective transposons and defective prophage. In most cases the amount of junk DNA is only a few percent of the genome.

The views expressed by Randy Stimpson are typical of those who desperately want to believe in intelligent design creationism. Junk DNA is not compatible with intelligent design creationism no matter how you cut it.

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La Tour Eiffel

 
These are my pictures of the Eiffel Tower.

It's much easier to take pictures like this from the second level 'cause you don't have to hang out near the outer railing where the risk of falling off is very high. I found that it's much better to say far away from the edge. My knees were much more stable when I did that.

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Rue du Cherche Midi

 
This is a picture of Rue du Cherche Midi right outside our apartment in Paris. The street is full of nice shops (expensive), bakeries, and small restaurants. It's perfectly situated in the middle of the 6th (6^e) arrondissement [Map].

There are lots of interesting places to see right in our neighborhood. One of the nearby cafés is shown below along with a close-up of a plaque hanging on the wall of a building in on the next street. It says that John Paul Jones died in that building in July 1792. (It seems as though the prominent men and women of the Revolutionary War were very fond of France.) Incidentally, I took a quick poll of several people in the vicinity and none of them knew who John Paul Jones was.

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Gene Genie #25

 
The 25th edition of Gene Genie has been posted at Gene Sherpas [Gene Genie is Back at The Sherpa!].

There are many posts that were submitted. I have to say, we are doing a good job of covering these genes, but probably won't get through them all. I am excited about a ton of this content. But when we move through genetic discovery, talk always falls back to personalized medicine.

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

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How Matt Nisbet Conned AAAS

 
Some of you might recall an earlier posting where I criticize Matt Nisbet for the way he organized a panel at the AAAS meeting without allowing anyone to give the other side of the issue [AAAS Panel: Communicating Science in a Religious America].I sent an email message to Professor Goldston, the panel moderator. Here's part of what I said.

I don't object to Nisbet presenting his point of view at a AAAS meeting but my respect for AAAS and your panel would be greatly diminished if the other side did not get a chance to make its case. Surely you do not want to give the impression that AAAS will only support scientists who agree with Nisbet? Surely you do not want to have a panel where the so-called "New Atheist" perspective is excluded and only religious scientists, or their close allies, are allowed to speak? Is that fair?

Please make sure that you have appropriate balance on your panel. Please make sure you don't give the impression that AAAS endorses Nisbet and his ideas about framing. The other side needs to be heard.

Mike Dunford has followed up with a posting from several days ago [Yeah, could have seen that one coming].

It's about time we realized that Matt Nisbet is not a friend of science. He needs to be strongly opposed before he succeeds in fooling any more naive scientists who might fall for his silly nonsense.

This "framing" thing has gone too far.

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Nobel Laureate: André Lwoff

 

The Nobel Prize in Physiology or Medicine 1965.

"for their discoveries concerning genetic control of enzyme and virus synthesis"

André Lwoff (1902 - 1994) received the Nobel Prize in Physiology or Medicine for his work on gene expression in bacteriophage λ. He shared the prize with François Jacob and Jacques Monod. The three men worked together at the Institut Pasteur in Paris, France, at a time when it was one of the leading centers of research in this field.

Jacob and Monod were recognize for their pioneering work on The lac Operon. Lwoff worked on the regulation of gene expression in λ. He was responsible for discovering that bacteriophage λ could enter a dormant (lysogenic) state by integrating into the E. coli genome and repressing transcription of all the genes required in the lytic stage of development.

THEME:

Nobel Laureates
The presentation speech was given by Professor Sven Gard, member of the Nobel Committee for Physiology or Medicine of the Royal Caroline Institute.

Your Majesties, Royal Highnesses, Ladies and Gentlemen.

The 1965 Nobel Prize in Physiology or Medicine is shared by Professors Jacob, Lwoff and Monod for «discoveries concerning the genetic regulation of enzyme and virus synthesis».

This particular sphere of research is by no means easy. I heard one of the prize winners, Professor Jacob, forewarn an audience of specialists more or less as follows: «In describing genetic mechanisms, there is a choice between being inexact and incomprehensible». In making this presentation, I shall try to be as inexact as conscience permits.

It has become progressively more apparent that the answer to what has hitherto been romantically termed the secret of life must be sought in the mechanism of action and in the structure of the hereditary material, the genes. This central field of research has naturally been approached from the periphery and in stages. Only in recent years has it been possible to make a serious attack on these fundamental problems.

Several previous Nobel Prize holders: Beadle, Tatum, Crick, Watson, Wilkins, Kornberg and Ochoa have worked in this sphere of research and have formulated certain basic proposals which have enabled the French scholars to continue their efforts. It has been established that one of the principal functions of genes must be to determine the nature and number of enzymes within the cell, the chemical apparatus which controls all the reactions by which the cellular material is formed and the energy necessary for various life processes is released. There is thus a particular gene for each specific enzyme.

In addition, some light has been thrown on the chemical structure of genes. In principle, they have the form of a long double chain consisting of four different components, which can be designated by the letters a, c, g, and t, and with the property of forming pairs with each other. An «a» in one of the chains has to be matched by a «t» in the other, a «g» only by a «c». However, they can be linked along the length of the chain in any order whatsoever, so that the number of possible combinations is virtually unlimited. A chain of genes contains from several hundreds to many thousands of units; such structures can easily carry the specific patterns for the million or more genes which it is estimated that a cell may have.

This model of the genes represents a coded message containing two types of information. If the double chain of a gene is split lengthwise and each half acquires a new partner, then the final result is two double chains identical to the original gene. The model thus contains information relative to the actual structure of the gene, which permits multiplication, in its turn a condition of heredity. When a cell divides, each daughter cell receives an exact copy of the parent gene. The structure of the double chain ensures the stability and permanence required by hereditary material.

But the model can also be read in another way. Along the length of the chain, the letters are grouped in threes in coded words. An alphabet of four letters allows the formation of more than 30 different words and the sequence in the gene of such words provides the structural information for an enzyme or some other protein. Proteins are also chain molecules built up from twenty or so different types of building blocks. To each of these building blocks there corresponds a chemical code word of three letters. The gene thus contains information on the number, nature, and order of the building blocks in a particular protein.

Thus it was already clear that the hereditary blueprint contained the collective structural information for all substances necessary for the functions of the living cell. It was not known how the genetic information was put into effect or transformed into chemical activity. As to the function of the genes, it was thought that they participated in a sort of procreative act when the new cell came into being, producing new substances necessary for the life of the cell, but subsequently lying dormant until the next cell division. It was presumed that the structure and formation of the chemical apparatus determined in this way defined all the regulatory mechanisms necessary for the cell's ability to adapt to changes in the environment and to respond in an adequate manner to stimuli of different types.

To begin with, the group of French workers were able to demonstrate how the structural information of the genes was used chemically. During a process resembling gene multiplication an exact copy of the genetic code is produced, termed a messenger. The latter is then incorporated into the chemical «workshop» of the cell and wound like magnetic tape onto a spool. For each word arriving on the spool, a constructional unit is attracted, which carries a complement to this word and attaches itself there just like a piece of jigsaw puzzle. The building blocks of a protein are selected in this way one by one, aligned, and joined together to form a protein with the appropriate structure.

The messenger substance is, however, short-lived. The tape lasts only for a few recordings. The enzymes are also used up in a similar way. For the cell to maintain its activity, it is thus necessary to have an uninterrupted production of the messenger material, that is to say continuous activity of the corresponding gene.

However, cells can adapt themselves to different external conditions. Thus there must exist some mechanisms controlling the activity of the genes. The research into the nature of these mechanisms is a remarkable achievement which has opened the way for the possible explanation of a series of hitherto mysterious biological phenomena. The discovery of a previously unknown class, the operator genes, which control the structural genes, marks a major breakthrough.

There are two types of operator genes. One type releases chemical signals, which are perceived by a second, receptor, type. The latter controls in its turn one or more structural genes. As long as the signals are being received the receptor remains blocked and the structural genes are inactive. Certain substances coming from outside or formed within the cell can, however, influence the chemical signals in a specific manner, changing their character so that they can no longer influence the receptor. The latter is unblocked and activates the structural genes; messenger material is produced and the synthesis of enzymes or another protein commences.

Control of gene activity is thus of a negative nature; the structural genes are only active if the repressor signals do not arrive. One can speak here of chemical control circuits similar in many ways to electrical circuits, for example in a television set. In the same way, they can be interconnected or arranged in a series to form complicated systems.

With the aid of such control circuits, the free living monocellular organism can produce enzymes when required, or interrupt chemical reactions if they are likely to cause damage; an excitatory stimulus can provoke movement, flight or attack, depending on the nature of the excitation. With such mechanisms it is possible to direct the development of cells into more complicated structures. It is particularly interesting to note that the activity of viruses is controlled, in principle, in the same manner.

Bacteriophages contain a genetic control circuit complete with emitter, receptor, and structural genes. While chemical signals are being sent and received, the virus remains inactive. When incorporated into a cell, it behaves like a normal component of the cell, and can confer on it new properties which may improve its chances of survival in the struggle for existence. However, if the signals are interrupted, the virus is activated, starts to grow rapidly and soon kills the host cell. There is considerable evidence for the view that certain types of tumor virus are incorporated into a normal cell in the same way, thus transforming it into a tumour cell.

We are easily inclined to hold an exaggerated opinion of ourselves in this era of advanced technology. Thus, we are justified in having a great admiration for the achievements in electronics, where, for example, the attempts at miniaturization to reduce component size, to lower the weight, and reduce the volume of apparatus have enabled a rapid development of space science. However, we should bear in mind that, millions of years ago, nature perfected systems far surpassing all that the inventive genius of man has been able to conceive hitherto. A single living cell, measuring several thousandths of a millimetre, contains hundreds of thousands of chemical control circuits, exactly harmonized and functioning infallibly. It is hardly possible to improve on miniaturization further; we are dealing here with a level where the components are single molecules. The group of French workers has opened up a field of research which in the truest sense of the word can be described as molecular biology.

Lwoff represents microbiology, Monod biochemistry, and Jacob cellular genetics. Their decisive discovery would not have been possible without competence and technical knowledge in all these fields, nor without intimate cooperation between the three researchers. But the mystery of life is not resolved simply with knowledge and technical skill. One must also have a gift for observation, a logical intellect, a faculty for the synthesis of ideas, a degree of imagination, and scientific intuition, qualities with which the three workers are liberally endowed.

Research in this field has not yet yielded results that can be used in practice. However, the discoveries have given a strong impetus to research in all domains of biology with far-reaching effects spreading out like ripples in the water. Now that we know the nature of such mechanisms, we have the possibility of learning to master them, with all the consequences which that will surely entail for practical medicine.

François Jacob, André Lwoff, Jacques Monod. Thanks to your technically unimpeachable experiments and your ingenious and logical deductions, you have gained a more intimate familiarity with the nature of vital functions than anyone before you has done. Action, coordination, adaptation, variation - these are the most striking manifestations of living matter. By placing more emphasis on dynamic activity and mechanisms than on structure, you have laid the foundations for the science of molecular biology in the true sense of the term. In the name of the Caroline Institute, I ask you to accept our admiration and our most sincere congratulations. Finally, I invite you to come down from the platform to receive the prize from His Majesty the King.

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A Canadian in Paris

This is where I'll be for the next few weeks. I know, it's really tough being a biochemist, but somebody has to do it.

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Goodbye Timmy's

 

Thank God, there's a Tim Hortons at the airport.

Extra large coffee and a honey cruller. Hmmmmm....

I won't be seeing any Timmy's for a very long time.

I wonder if they have bake goods and beverages where I'm going?

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Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

 
A newly published paper in PLoS Biology (Li et al 2008) finds that many transcription factors are non-specifiaccly bound to DNA and they may not be involved in regulating gene expression at most binding sites. For an explanation of why this shold not be a surprise see Repression of the lac Operon.

Here's the Author Summary of the paper.

One of the largest classes of regulatory proteins in animals, sequence-specific DNA binding transcription factors determine in which cells genes will be expressed and so control the development of an animal from a single cell to a morphologically complex adult. Understanding how this process is coordinated depends on knowing the number and types of genes that each transcription factor binds and regulates. Using immunoprecipitation of in vivo crosslinked chromatin coupled with DNA microarray hybridization (ChIP/chip), we have determined the genomic binding sites in early embryos of six transcription factors that play a crucial role in early development of the fruit fly Drosophila melanogaster. We find that these proteins bind to several thousand genomic regions that lie close to approximately half the protein coding genes. Although this is a much larger number of genes than these factors are generally thought to regulate, we go on to show that whereas the more highly bound genes generally look to be functional targets, many of the genes bound at lower levels do not appear to be regulated by these factors. Our conclusions differ from those of other groups who have not distinguished between different levels of DNA binding in vivo using similar assays and who have generally assumed that all detected binding is functional.

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Li et al. (2008) Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm. [PLoS Biology]

Goodbye Toronto

 
It's too damn cold and there's way too much snow in Toronto. I'm getting out of town for a bit. Blogging may be intermittent, especially if I'm having fun.

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This photograph was taken yesterday (Feb. 11, 2008) just outside my building. That's the Ontario Legislature.

Happy Birthday Charles Darwin

 
Charles Robert Darwin was born on this day in 1809. Darwin was the greatest scientist who ever lived.

In honor of his birthday, and given that this is a year of politics in America, I thought it would be fun to post something about Darwin's interactions with politicians. The historical account is from Janet Browne's excellent biography (Brown 2002).

William Gladstone (photo below) was an orthodox Christian. He was not a fan of evolution. In March 1877 Gladstone was leader of the Liberal party and a former Prime Minister of the most powerful country in the world. He was spending the weekend with John Lunnock—a well-known liberal—and a few other friends, including Thomas Huxley.

They decided to walk over to Darwin's House in Downe. This was 18 years after the publication of Origins and Darwin was a famous guy. The guests were cordially received by Darwin and his wife Emma. Darwin and Emma were life-long liberals and they were honored by Gladstone's visit. A few days later, Darwin wrote a note to his friend saying,

Our quiet, however, was broken a couple of days ago by Gladstone calling here.—I never saw him before & was much pleased with him: I expected a stern, overwhelming sort of man, but found him as soft & smooth as butter, & very pleasant. He asked me whether I thought that the United States would hereafter play a much greater part in the history of the world than Europe. I said that I thought it would, but why he asked me, I cannot conceive & I said that he ought to be able to form a far better opinion,—but what that was he did not at all let out.

A few years later Gladstone sent Darwin one of his essays on Homer. Darwin gratefully acknowledged the gesture.

In 1881, when Gladstone was Prime Minister again, Darwin and some of his friends petitioned Gladstone to award a pension to Alfred Russel Wallace, who was in dire financial straits at the time. Gladstone granted the request. Two months later Gladstone offered Darwin a position as trustee of the British Museum but Darwin declined. (Remember, Gladstone did not agree with Darwin about evolution, or religion.)

When Darwin died, Gladstone was instrumental in arranging for him to be buried in Westminster Abbey. The funeral was held on April 26, 1882. William Gladstone was too busy to attend. He went to a dinner at Windsor.

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Brown, J. (2002) Charles Darwin: The Power of Place (Vol. II). Alfred A. Knopf, New York (USA)

Repression of the lac Operon

There are many lesson to be learned from understanding the regulation of transcription of a well-studied system like the E. coli lac operon. Some of those lessons have consequences when we think about the problems of having large eukaryotic genomes. Read the description below and the implications that follow.

From Horton et al. (2006) p. 666

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lac repressor binds simultaneously to two sites near the promoter of the lac operon. Repressor-binding sites are called operators. One operator (O₁) is adjacent to the promoter, and the other (O₂) is within the coding region of lacZ. When bound to both operators, the repressor causes the DNA to form a stable loop that can be seen in electron micrographs of the complex formed between lac repressor and DNA (bottom figure). The interaction of lac repressor with the operator sequences may block transcription by preventing the binding of RNA polymerase to the lac promoter. However, it is now known that, in some cases, both lac repressor and RNA polymerase can bind to the promoter at the same time. Thus, the repressor may also block transcription initiation by preventing formation of the open complex and promoter clearance. A schematic diagram of lac repressor bound to DNA in the presence of RNA polymerase is shown in the figure on the right. [See Monday's Molecule #61 for another view.] The diagram illustrates the relationship between the operators and the promoter and the DNA loop that forms when the repressor binds to DNA.

The repressor locates an operator by binding nonspecifically to DNA and searching in one dimension. (Recall from Section 21.3C that RNA polymerase also uses this kind of searching mechanism.) The equilibrium association constant for the binding of lac repressor to O₁ in vitro is very high. As a result, the repressor blocks transcription very effectively. (lac repressor binds to the O₂ site with lower affinity.) A bacterial cell contains only about 10 molecules of lac repressor, but the repressor searches for and finds an operator so rapidly that when a repressor dissociates spontaneously from the operator, another occupies the site within a very short time. However, during this brief interval, one transcript of the operon can be made since RNA polymerase is poised at the promoter. This low level of transcription, called escape synthesis, ensures that small amounts of lactose permease and β-galactosidase are present in the cell.

In the absence of lactose, lac repressor blocks expression of the lac operon, but when β-galactosides are available as potential carbon sources, the genes are transcribed. Several β-galactosides can act as inducers. If lactose is the available carbon source, the inducer is allolactose, which is produced from lactose by the action of β-galactosidse (Figure 21.18). Allolactose binds tightly to lac repressor and causes a conformational change that reduces the affinity of the repressor for the operators. [see Regulation of Transcription] In the presence of the inducer, lac repressor dissociates from the DNA, allowing RNA polymerase to initiate transcription. (Note that because of escape synthesis, lactose can be taken up and converted to allolactose even when the genes are repressed.)

Electron micrographs of DNA loops. These loops were formed by mixing lac repressor with a fragment of DNA bearing two synthetic lac repressor–binding sites. One binding site is located at one end of the DNA fragment, and the other is 535 bp away. DNA loops 535 bp in length form when the tetrameric repressor binds simultaneously to the two sites.

The strength of binding between a protein and a ligand is measured by an equilibrium binding constant (K_B). In the case of lac repressor binding to its specific strong binding site (O₁) K_B = 10¹³ M^-1. This is very high, in fact it is one of the tightest DNA bindings known in biology. What this means is that lac repressor will sit on the operon and repress transcription for at least 20 minutes under normal conditions.

However, the repressor will eventually fall off (dissociation rate constant k_-1 = 6 × 10^-4 s^-1) and, as described above, the operon will be transcribed once (escape synthesis). A new repressor molecule finds the operator sequences very quickly because lac repressor binds non-specifically to DNA (K_B = 4 × 10⁴) and slides along the DNA searching for the operator in a process called one dimensional diffusion (association rate constant k₁ = 10¹⁰ M^-1 s^-1). Even though the lac repressor only remains bound non-specifically for a few seconds, it is able to search about 2000 bp looking for a specific binding site.

Given the huge difference between the specific and non-specific binding constants, the cell only needs about ten molecules of lac repressor to ensure that the operator sequences are bound almost all of the time. At any given time nine of these molecules will be bound to random pieces of DNA in the genome and the other one will be bound to the lac operon.

Similar repressors and activators work in eukaryotic cells to regulate transcription. But in eukayotic cells we have a much bigger problem. First, there are very few regulatory proteins that have as strong a specific binding constant as lac repressor. Second, there is much more DNA in a eukaryotic cell. The consequences of having a large genome are: (a) it takes these DNA binding proteins much longer to find their specific binding site, and (b) at any one time, many more of the regulatory proteins are soaked up in non-specific binding to DNA. In eukaryotic cells with an abundance of junk DNA a typical regulatory protein has to be present at about 20,000 copies per cell in order to have a decent chance of biding to its specific regulatory site for a significant length of time. (Recall that only ten molecules of lac repressor are needed in E. coli.)

Given the properties of DNA binding that we have discovered and characterized in bacteria and bacteriophage, we can calculate that escape synthesis in eukaryotic cells in likely to be much more of a problem than in bacterial cells. Furthermore, accidental transcription of random bits of DNA is almost certainly going to be common in a cell with a large bloated genome. This is because RNA polymerase also binds non-specifically to DNA and also because the larger the genome, the more likely you are to encounter promoter and regulatory sequences that just by chance happen to be close matches to real functional sequences. This is a very important concept and one that is not widely appreciated. Based on our knowledge of basic biochemistry we expect that there will be random, infrequent transcription of a large percentage of the genome. These transcripts are merely a consequence of the properties of DNA binding proteins and they have no biological significance.

Some of these problems in eukaryotes are mitigated by a separate level of regulation at the level of chromatin structure. Large regions of the chromosome can be masked from DNA binding proteins by formation of a tight heterochromatic complex of nucleosomes and DNA. Less compact complexes are formed in non-active regions of the genome where the DNA is less accessible but not invisible. When genes in a region are transcribed, the chromatin opens out into an open complex where the DNA is easily accessible to regulatory proteins. This solves some of the problems discussed above but it is only a partial solution. We know for a fact that the concentrations of regulatorty proteins are high (20,000 copies) and a growing amount of evidence points to frequent accidental transcription.

©Laurence A. Moran and Pearson Prentice Hall

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Horton, H.R., Moran, L.A., Scrimgeour, K.G., perry, M.D. and Rawn, J.D. (2006) Principles of Biochemisty. Pearson/Prentice Hall, Upper Saddle River N.J. (USA)