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Thursday, September 27, 2007

Nations must fight climate change like terrorism, Rice says

From CNN [ Nations must fight climate change like terrorism, Rice says].
WASHINGTON (CNN) -- U.S. Secretary of State Condoleezza Rice on Thursday told delegates to a global climate change conference that countries around the world must work together to combat climate change, much as they cooperate against terror and the spread of disease.

"No one nation, no matter how much power or political will it possesses, can succeed alone," she said. "We all need partners, and we all need to work in concert."

Rice said the United States takes climate change seriously, "for we are both a major economy and a major emitter."

Other nations have been critical of the Bush administration's policy on climate change after the United States withdrew from the 1997 U.N. Framework Convention on Climate Change, known as the Kyoto Protocol. More than 150 countries signed the Kyoto agreement, which mandates limits on emissions.

Fight climate change like we fight terrorism. Work together, but drop out of Kyoto. No further comment is necessary. It saddens me that my Prime Minister is falling for this nonsense.

[Photo Credit: CBC News]

Who's Reading Sandwalk Right Now?

I was curious about when people were reading Sandwalk. Sometimes I get into chat mode with some of you in the comments section. It seems that some people have a schedule similar to mine.

Then I got to thinking. Maybe everyone in Europe reads during the night and everyone in Australia during the day—or some such permutation. So I took a snapshot of where my readers are at different times of the day/night.

Here are the results for 1PM, 5PM, 11PM, and 6AM respectively. There doesn't seem to be a pattern except that most of you are asleep between midnight and 6AM your time. It looks like you're surfing the internet most of the time you're awake! (BTW, who's that person in Hawaii? I'd like to visit you. Do you have a spare room?)

Polycystic Liver Disease

Polycystic liver disease (PLD) is associated with the formation of multiple cysts of various sizes in the liver. Sometimes it causes enlargement of the liver and abdominal pain but in most cases there are no symptoms and the patient may be unaware of any problem.

This disease is not the same as the often fatal polycystic kidney disease (PKD) [OMIM 173910] although patients suffering from kidney failure due to PKD will often have cysts in their liver as well.

PLD is inherited as an autosomal dominant trait, which means that you will have liver cysts even if you only inherit one mutant allele from one parent. There are probably several different genes that can be affected but two genes have been identified and characterized [OMIM 174050]. One of them is the SEC63 gene on chromosome 6q21 [OMIM 60648][Entrez Gene 11231]. This gene encodes one of the components of the ER membrane translocon. This is the pore through which newly synthesized is threaded following attachment of the ribosome/signal-recognition-particle complex [Signal Hypothesis] [Human Genes Involved in the Signal Hypothesis Pathway]. The defect in SEC63 probably interferes with sorting and secretion of proteins in the liver and this is what causes the cysts.

The Online Medelian Inheritance in Man (OMIM) database at Johns Hopkins University is one of the best databases in the world.
The known alleles are null mutations meaning that they disrupt synthesis of the protein. It appears that the presence of one defective copy of the SEC63 gene has no effect on normal development or secretion in most tissues but does have a non-lethal effect in liver cells.

The other gene that's associated with polycystic liver disease is PRKCSH, a gene that encodes the β subunit of glucosidase II [OMIM 177060]. This protein plays a role in the glycolsylation of proteins in the endoplasmic reticulum [glycosylation]. Since glysosylation is requried for protein sorting and secretion, it is likely that interference in that process is resposible for liver cycsts. This is the same process that's defective in SEC63 mutants.

[Photo Credit: OSF Heathcare]

Human Genes Involved in the Signal Hypothesis Pathway

The Signal Hypothesis describes the mechanism whereby proteins that are destined to cross a membrane are synthesized. One of the key components of this pathway is Signal Recognition Particle or SRP. The structure of SRP is shown below from a paper by Maity and Weeks (2007)

Most of SRP is composed of an RNA molecule called 7SL RNA. It is shown as red and yellow helices in the bottom figure. The secondary structure is depicted in the top right-hand corner of the figure. There are six different proteins in SRP. All of them are bound to the RNA in one way or another. The six proteins are SRP9, SRP14, SRP54, SRP68, and SRP72. The numbers refer to the molecular mass in kilodaltons.

There are three genes for 7SL RNA. They are all found on chromosome 14 (above). Two of them are closely linked and the third one is somewhat farther away.

The genes for the protein components are:

The three membrane components are the SRP receptor, the translocon (formerly known as ribophorin), and the signal peptidase. There are two subunits in the SRP receptor, α (docking protein) and β. The human genome contains a single gene for SRP receptor α subunit called SSPR (SSPRα). The genome has two separate genes for the β subunit called SSRB and SSR2.

The translocon is composed of three proteins; SEC61, SEC62, and SEC63. The SEC61 protein has three subunits; α (genes SEC61A1 and SEC61A2), β (gene SEC61B), and γ (gene SEC61G).

Finally, there are three subunits of the signal peptidase complex encoded by SPCS1 (signal peptidase complex, subunit 1), SPCS2, and SPCS3.

There are 20 genes required for effective translocation of proteins with a signal sequence (only the SRP are shown on the chromosome maps). Additional proteins are required to assist in the translocation (chaperones) and in glycosylation of the protein once it enters the lumen of the endoplasmic reticulum.

Maity, T.S. and Weeks, K.M. (2007) A threefold RNA-protein interface in the signal recognition particle gates native complex assembly. J. Mol. Biol. 369:512-24 [PubMed]

Iranian Army Is a Terrorist Organization - What's This All About?

The New York Times reports on a recent US Senate resolution.
The Senate approved a resolution today urging the Bush administration to designate Iran’s Islamic Revolutionary Guard Corps as a foreign terrorist organization, and lawmakers briefly set aside partisan differences to approve a measure calling for stepped-up diplomacy to forge a political solution in Iraq.

Since last month, the White House has been weighing whether to deem the entire Revolutionary Guard as a terrorist group or to take a narrower step focused only on the Quds Force, an elite unit of the corps. Either approach would signal a more confrontational posture by declaring a segment of the Iranian military to be a terrorist organization.
Saying that it's "confrontational" is putting it mildly. Is there a logical reason for doing this? Here's what General Petraeus says,
It quoted General Petraeus as saying it is “increasingly apparent to both coalition and Iraqi leaders that Iran, through the use of the Iranian Republican Guard Corps Quds Force, seeks to turn the Shiite militia extremists into a Hezbollah-like force to serve its interests and fight a proxy war against the Iraqi state and coalition forces in Iraq.”
Ahhh .... now I get it. We have a case where foreign soldiers in Iraq might be helping certain militia groups in order to serve its own interests and fight a proxy war against its perceived enemies. All soldiers who do that are terrorists, right?

Makes a lot of sense to me.

As an aside, I note that the US Congress is a lot more confident about military intelligence these days. I guess the fiasco of Colin Powell's UN Presentation on February 6, 2003 has been forgotten in light of a vastly improved intelligence gathering network. We can now be confident that all pronouncements about the evil axis countries are accurate, right?

[Photo Link: U.S. Special Forces Secure Tribal Sheikhs Meeting In Diyala Google.]

Conservative Think Tanks

Conservative think tanks have been wrong about so many things in the recent past it's a wonder anybody still pays attention. Bill Maher gets it in a show that aired last winter.

[Hat Tip: Canadian Cynic.]

Wednesday, September 26, 2007

Plants, not Fungi, Are Most Closely Related to Animals?

The American Society for Biochemistry & Molecular Biology has drawn up guidelines for a new curriculum in undergraduate education. The complete recommendation can be found at Recommended Curriculum for a Program in Biochemistry and Molecular Biology in the Journal Biochemistry and Molecular Biology Education (BAMBED).

Under the list of "Skills that biochemistry and molecular biology students should obtain by the time they have finished their undergraduate program," there are a number of motherhood type statements. One of them is "Ability to assess primary papers critically." We've been discussing these required skills for the past few months. I've questioned the wisdom of teaching undergraduates how to critically evaluate the scientific literature because I think it's a skill that only comes after a lot of experience in the discipline.

There are many confusing papers out there and it's difficult to decide what's right and what's wrong. We can give students our opinion but that's not the same as teaching them how to critically evaluate a paper.

Here's an example of how difficult it is to read the scientific literature. A recent paper by John Stiller (2007) promotes the idea that plants are more closely related to animals than fungi. Here's the abstract.
Evolutionary relationships among complex, multicellular eukaryotes are generally interpreted within the framework of molecular sequence-based phylogenies that suggest green plants and animals are only distantly related on the eukaryotic tree. However, important anomalies have been reported in phylogenomic analyses, including several that relate specifically to green plant evolution. In addition, plants and animals share molecular, biochemical and genome-level features that suggest a relatively close relationship between the two groups. This article explores the impacts of plastid endosymbioses on nuclear genomes, how they can explain incongruent phylogenetic signals in molecular data sets and reconcile conflicts among different sources of comparative data. Specifically, I argue that the large influx of plastid DNA into plant and algal nuclear genomes has resulted in tree-building artifacts that obscure a relatively close evolutionary relationship between green plants and animals.
This position is contrary to a whole lot of work that has been published over the past several decades. I don't think very much of this paper and neither do John Logsdon of Sex, Genes & Evolution [Promoting Plants at the Expense of Fungi?] and Ryan Gregory of Genomicron [Discovery wants to "demote" fungi]. Read their blogs to see why we're skeptical about this paper.

How do you explain this to undergraduates? How can you teach them to critically evaluate such a paper when, on the surface, it seems perfectly reasonable and the data seems sound? I submit that most of us work within a model of how we think the history of life has developed over millions of years. That model is based on reading hundreds of papers and getting a "feel" for the data. Some papers are rejected and some are given more credence and this is based on all kinds of intangibles—including the reputation of the authors. Can undergraduates be taught such a thing? I don't think so.

Tangled Bank #89


The latest version of the Tangled Bank has been posted on Aardvarchaeology [Tangled Bank #89].

Nobel Laureate: Günter Blobel


The Nobel Prize in Physiology or Medicine 1999.
"for the discovery that proteins have intrinsic signals that govern their transport and localization in the cell"

Günter Blobel (1936- ) received the Nobel Prize in Physiology or Medicine for The Signal Hypothesis and Signal Recognition Particle.

The Presentation speech was delivered on Dec. 10, 1999 by Professor Ralf Pettersson of the Nobel Committee at Karolinska Institutet. The drawing depicts the first version of the Signal Hypothesis in 1971 from the Nobel Lecture.

Your Majesties, Your Royal Highness, Ladies and Gentlemen,

Imagine a large factory that manufactures thousands of different items in millions of copies every hour, that promptly packages and ships each of them to waiting customers. Naturally, to avoid chaos, each product requires a clearly labeled address tag. Günter Blobel is being awarded this year's Nobel Prize in Physiology or Medicine for having shown that newly synthesized proteins, analogous to the products manufactured in the factory, contain built-in signals, or address tags, that direct them to their proper cellular destination.

An adult human is comprised of approximately 100,000 billion cells, all of which are structurally similar. A striking feature is that each cell contains small compartments or organelles. Organelles are bounded by impermeant, lipid-rich membranes that ensure the physical and functional separation of vital biochemical processes. This compartmentalization enables cells to be compared to a large city in which each public function is housed in a separate building. The blueprint for all cellular processes is maintained in the genome located in the cell nucleus, the City Hall of the cell. Energy production takes place within mitochondria, the power plant of the cell; the breakdown and recycling of waste takes place in the lysosome etc. The production of new products, proteins in the case of the cell, is carried out by ribosomes in a process resembling an assembly line. There is indeed a feverish amount of activity within cells. Every second, thousands of protein molecules are degraded and replaced by new ones. How does a newly made protein get to its correct intracellular location, and how do proteins enter into and move across the membranes surrounding individual organelles? These two central questions occupied the minds of scientists during the 1960s.

Günter Blobel has provided the answer to both these questions. In 1967 he joined the renowned cell biology laboratory headed by George Palade at the Rockefeller University in New York. Palade, who received the Nobel Prize in 1974, had defined and charted the route that secretory proteins take from their site of synthesis within the cell to the cell surface. Secreted proteins are made in the cell in association with a membrane system called the endoplasmic reticulum.

Blobel began by examining how a newly synthesized secretory protein is targeted to and then translocated across the endoplasmic reticulum membrane. Based on the results from a series of elegant experiments, Blobel put forth the so-called "signal hypothesis," in a preliminary form in 1971 and a mature final form in 1975, to explain how this process takes place. The signal hypothesis postulated that newly made proteins contain built-in signals, address tags or zip codes, that target proteins to the endoplasmic reticulum and that subsequently lead them across the reticulum membrane through a specialized channel. Proteins that are translocated across to the other side are packaged for subsequent transport to the cell surface.

To test this hypothesis, Blobel developed an ingenious experimental test tube system, which enabled him to individually study each step of the process. The system which relied on components obtained from mouse, rabbit, and dog cells, laid the foundation for the development of the field of molecular cell biological research. In the following 20 years, Blobel and his co-workers characterized this complex process in great detail. The original signal hypothesis, in all its essential parts, has stood the test of time and proven to be correct.

Blobel extended his studies and was able to demonstrate that proteins destined to become transported to other organelles, or that become integrated into different cellular membranes, also contain specific address tags and so-called "topogenic" signals. The guiding principles that Blobel has helped to elucidate are universally applicable and highly conserved. They have remained almost unchanged during the course of evolution, functioning in yeast, plant, and animal cells.

Perhaps the most important consequences of Günter Blobel's discoveries is that we now understand the fundamental principles guiding the formation and maintenance of cell and organelle structure. The signal hypothesis provides a framework to understand the mechanisms underlying many hereditary diseases and other disease processes in which specific proteins become mislocalized. In addition, these discoveries have enabled the pharmaceutical industry to turn cultured cells into efficient mini-factories for the production of protein-based drugs, such as insulin, growth hormone, coagulation factors, etc.

Günter Blobel, your discovery that proteins contain built-in signals that direct them to their correct destination within cells and across membranes has had a profound impact on our understanding of how a cell and its organelles are assembled and maintained. Your work has also laid the foundation for modern molecular cell biology. On behalf of the Nobel Assembly at Karolinska Institutet I wish to convey to you my warmest congratulations and I now ask you to step forward to receive your Nobel Prize from the hands of His Majesty the King.

Bayblab Supports MMP

Vote for MMP

Good for Bayblab. Read a short summary of the issue at [Electoral Reform: Referendum 2007].

To be fair, it's only kamel (the smart one ) who supports MMP. We don't know if the other bloggers at Bayblab are onside yet.

Will the IDiots Make the Same Mistake with RNA that They Made with Junk DNA?

Robert Crowther (whoever that is) posted a similar question on the Intelligent Design Creationis blog of the Discovery Institute. His question was Will Darwinists Make the Same Mistake with RNA that They Made in Ignoring So-Called "Junk" DNA?.
One interesting thing that leapt out at me when reading this was the fact that, while many scientists now realize that it was a mistake to jump to the conclusion that there were massive amounts of "junk" in DNA (because they were trying to fit the research into a Darwinian model), they are on the verge of committing the same exact mistake all over again, this time with RNA.
In order to understand such a bizarre question you have to put yourself in the shoes of an IDiot. They firmly believe that the concept of junk DNA has been overturned by recent scientific results. According to them, the predictions of Intelligent Design Creationism have been vindicated and all of the junk DNA has a function.

Of course this isn't true but, unfortunately, there are some scientists whose level of intelligence is not much above that of the typical IDiot [Junk DNA in New Scientist] [The Role of Ultraconserved Non-Coding Elements in Mammalian Genomes].

Now the IDiots have turned their attention to RNA. They fell hook line and sinker for the hype about functional sequences in junk DNA and they're falling just as easily for the hype about new RNAs. They believe all those silly papers that attribute function to every concevable RNA molecule that has ever been predicted or detected in some assay.

The IDiots were wrong about junk DNA and they're wrong about RNA. The answer to my question is "yes," the IDiots will make the same mistake. You can practically count on it. The answer to Crowther's question is "no." Most (but not all) scientists did not fall for the spin on junk DNA and they realize that the vast majority of our genome is junk. In the long run, they will not fall for the claim that most of the junk DNA is functional because it encodes essential RNA molecules.

Canada Ranks #9 on the Corruption Scale!

According to Transparency International Canada is in 9th place in terms of corruption. I think our dismal showing is because university Professors don't ask for bribes like they do in other countries. We should change that. From now on an "A" is going for $1000 and if you want a "B" it will only cost you $600!

[Hat Tip: Gene Expression]

Signal Recognition Particle

The signal recognition particle binds to ribosomes at the site of the exit tunnel and interacts with the N-terminal end of newly synthesized protein. If the protein contains a signal sequence then protein synthesis is temporarily arrested. The complex is directed to the membrane surface and the end of the protein is inserted through a pore in the membrane. Protein synthesis then continues and the newly synthesized protein is inserted into the endoplasmic reticulum in eukaryotes or across the plasma membrane in bacteria [The Signal Hypothesis].

In all species (bacteria and eukaryotes) the signal recognition particle is composed of a conserved ~300 nucleotide RNA molecule (7SL/7S RNA) and several (usually six) proteins. Only one of the proteins is common to both bacteria and eukaryotes (Hainzl et al. 2007). The organization of the mammalian SRP is shown above (Maity and Weeks, 2007).

There are two distinct regions of SRP. The large subunit consists of nucleotides 101-255 of the 7S RNA molecule. The RNA is folded into the secondary structure shown on the left (Mauty and Weeks, 2007). In this diagram, the linear nucleotide sequence is connected by solid lines with arrows and the dashed lines depict hydrogen bond interactions between bases that are brought into proximity by the secondary, and tertiary, structure of the RNA molecule.

Four proteins (SRP19, SRP54, SRP68, SRP72) are bound to the large subunit. SRP54 is the only protein found in all species. The large subunit recognizes the signal peptide and binds to the membrane receptor.

The other subunit is called the Alu subunit. The significance of this name will become clear in another posting. The RNA component consists of nucleotides 1-100 and 256-299 arranged in a single double helical structure. Proteins SRP9 and SRP14 bind to the Alu subunit. The Alu subunit is responsible for arresting protein synthesis.

SRP is an important cellular component and it plays a crucial role in protein synthesis and protein trafficing. It's also a good example of a ribonucleotide particle present in all species. Most people don't appreciate the fact that many small RNAs are an integral part of the cellular machinery. Other examples are the telomerase complex and RNAse P. These small RNAs have been known for a long time. The recent publicity about other types of small RNAs has unfortunately conveyed the impression that this is a new discovery.

The structure of SRP has not been fully worked out but a great deal is known about the various components. A model of the complete mammalian signal recognition particle, incorporating the known structures of the RNA and the various proteins, is shown below (Halic and Beckmann, 2005).

Hainzl, T., Huang, S. and Sauer-Eriksson, A.E. (2007) Interaction of signal-recognition particle 54 GTPase domain and signal-recognition particle RNA in the free signal-recognition particle.
Proc. Natl. Acad. Sci. (USA) 104:14911-6. [PubMed]

Halic, M. and Beckmann, R. (2005) The signal recognition particle and its interactions during protein targeting. Curr. Opin. Struct. Biol. 15(1:116-125. Review. [PubMed]

Maity, T.S. and Weeks, K.M. (2007) A threefold RNA-protein interface in the signal recognition particle gates native complex assembly. J. Mol. Biol. 369:512-24 [PubMed]

A Synthetic Anticoagulant Related to Heparin

Heparin (left) is an oligosaccharide bound to a very specific protein to form heparin proteoglycan. The physiologically important oligosaccharide is called heparan sulfate. It is found on the surface of normal endothelial cells and it is this molecule that binds antithrombin III. The interaction of heparan sulfate and antithrombin III inhibits blood clotting [Inhibiting Blood Clots: Anticoagulants].

It is very difficult to synthesize heparan sulfate so the synthetic drug is quite expensive. The results of a number of studies indicated that the exact structure of each of the sugar residues (rings) was very important for proper anticoagulant activity as was the position of the sulfate groups (those with "S" that are bound to the rings).


Blood Clotting
A recent paper by Chen et al. (2007) shows that simpler forms of the heparin-like oligosaccharide have significant anticoagulation activity. They started with a compound called N-sulfo heparosan, which is prepared from bacterial oligosaccharides by a combination of enzymatic and chemical steps. This starting material was then modified using various recombinant enzymes to produce a large class of heparin-like molecules. One of these derivatives, recomparin (below left) (Lindhardt and Kim, 2007) had significant anticoagulation activity. (Click on the figure to enlarge.)

The result is significant because recomparin does not have the modified rearranged sugar (iduronic acid, IdoUA)that was previously thought to be essential for anticoagulation activity. The modification of the oligosacchraide to create the iduronic acid residues was complicated an inefficient. Thus, the new recomparin drug will be much cheaper to make.

Chen, J., Jones, C.L. and Liu, J. (2007) Using an Enzymatic Combinatorial Approach to Identify Anticoagulant Heparan Sulfate Structures. Chemistry & Biology 14: 972-973.

Lindhardt, R.J. and Kim, J-H. (2007) Combinatorial Enzymatic Synthesis of Heparan Sulfate (review of Chen et al. 2007). Chemistry & Biology 14:972-973.

Theme: Blood Clotting



Blood Clotting
March 26, 2007
Monday's Molecule #19. Warfarin—an anticoagulant and a rat poison.

March 27, 2007
Vitamin K. Vitamin K plays an important role in blood clotting.

March 28, 2007
Nobel Laureates: Dam and Doisy. Dam: "for his discovery of vitamin K" Doisy: "for his discovery of the chemical nature of vitamin K"

April 2, 2007
Monday's Molecule #20. Heparin—an anticoagulant.

April 2, 2007
Blood Clotting: The Basics. Fibrinogen and how it forms clots.

April 4, 2007
Nobel Laureate: Arne Tiselius. ""for his research on electrophoresis and adsorption analysis, especially for his discoveries concerning the complex nature of the serum proteins"

April 4, 2007
Blood Clotting: Platelets. What are platelets and how do they form blood clots?

April 4, 2007
Blood Clotting: Extrinsic Activity and Platelet Activation. Description of the activity of thrombin and the activation of blood platelets.

April 5, 2007
Blood Clotting: Intrinsic Activity. The role of factors VIII and IX. Deficiencies in Factor VIII cause hemophilia A an X-linked form of hemophilia that was common in European royal families descending from Queen Victoria.

April 8, 2007
Genes for Hemophilia A & B and von Willebrand disease. Locations of the F8, F9 and vWF genes on human chromosomes X and 12.

April 12, 2007
Inhibiting Blood Clots: Anticoagulants. How does heparin inhibit blood clotting?

April 15, 2007
Human Anticoagulant Genes. Mapping the genes for anticoagulant factors.

April 16, 2007
Dicumarol and Warfarin Inhibit Blood Clotting. The role of vitamin K in blood clotting.

September 26, 2007
A Synthetic Anticoagulant Related to Heparin. Synthesis of a new anticoagulant to replace heparin.

April 26, 2008
Fibrin and Blood Clots. What does a blog clot look like?

May 10, 2008
On the Evolution of the Blood Clotting Pathway.
Ian Musgrave explains Russel Doolittle's latest results.