Friday, April 26, 2013

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

Sixty years ago yesterday the journal Nature published a letter by James Watson and Francis Crick titled Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid (Volume 171, Pages 737-738), announcing the discovery of the double helix structure of DNA.

The 4th edition of Intermediate Physics for Medicine and Biology doesn’t discuss the structure of DNA much. As Russ Hobbie and I say in the preface, “Molecular biophysics has been almost completely ignored: excellent texts already exist, and this is not our area of expertise.” Yet, we do mention DNA occasionally. In the first section of our book, about distances and sizes, we say
“Genetic information is stored in long, helical strands of deoxyribonucleic acid (DNA). DNA is about 2.5 nm wide, and the helix completes a turn every 3.4 nm along its length.”
Problem 2 in the first chapter analyzes the volume of DNA
Problem 2 Our genetic information or genome is stored in the parts of the DNA molecule called base pairs. Our genome contains about 3 billion (3×109) base pairs, and there are two copies in each cell. Along the DNA molecule, there is one base pair every one-third of a nanometer. How long would the DNA helix from one cell be if it were stretched out in a line? If the entire DNA molecule were wrapped up into a sphere, what would be the diameter of that sphere?
A problem in Chapter 3 considers errors in DNA in the context of the Boltzmann factor.
"Problem 25 The DNA molecule consists of two intertwined linear chains. Sticking out from each monomer (link in the chain) is one of four bases: adenine (A), guanine (G), thymine (T), or cytosine (C). In the double helix, each base from one strand bonds to a base in the other strand. The correct matches, A–T and G–C, are more tightly bound than are the improper matches. The chain looks something like this, where the last bond shown is an 'error.'

A  T  G  C  G
T  A  C  G  A (error)

The probability of an error at 300 K is about 10−9 per base pair. Assume that this probability is determined by a Boltzmann factor e−U/kBT, where U is the additional energy required for a mismatch.
(a) Estimate this excess energy.
(b) If such mismatches are the sole cause of mutations in an organism, what would the mutation rate be if the temperature were raised 20° C?"
We discuss DNA again in Chapter 16, when considering radiation damage to tissue.
"Cellular DNA is organized into chromosomes. In order to understand radiation damage to DNA, we must recognize that there are four phases in the cycle of cell division ….

Figure 16.33 shows, at different magnifications, a strand of DNA, various intermediate structures which we will not discuss, and a chromosome as seen during the M phase of the cell cycle. The size goes from 2 nm for the DNA double helix to 1400 nm for the chromosome. In addition to cell survival curves one can directly measure chromosome damage. There is strong evidence that radiation, directly or indirectly, breaks a DNA strand. If only one strand is broken, there are efficient mechanisms that repair it over the course of a few hours using the other strand as a template. If both strands are broken, permanent damage results, and the next cell division produces an abnormal chromosome.19 Several forms of abnormal chromosomes are known, depending on where along the strand the damage occurred and how the damaged pieces connected or failed to connect to other chromosome fragments. Many of these chromosomal abnormalities are lethal: the cell either fails to complete its next mitosis, or it fails within the next few divisions. Other abnormalities allow the cell to continue to divide, but they may contribute to a multistep process that sometimes leads to cancer many cell generations later.”
The story of how the structure of DNA was discovered is nearly as fascinating as the structure itself. James Watson provides a first-person account in his book The Double Helix. It begins
“I have never seen Francis Crick in a modest mood. Perhaps in other company he is that way, but I have never had reason so to judge him. It has nothing to do with his present fame. Already he is much talked about, usually with reverence, and someday he may be considered in the category of Rutherford or Bohr. But this was not true when, in the fall of 1951, I came to the Cavendish Laboratory of Cambridge University to join a small group of physicists and chemists working on the three-dimensional structures of proteins. At that time he was thirty-five, yet almost totally unknown. Although some of his closest colleagues realized the value of his quick, penetrating mind and frequently sought his advice, he was often not appreciated, and most people thought he talked too much.”
The Double Helix is one of those iconic books that everyone should read for the insights it provides into how science is done, and for what is simply a fascinating story. The tale is also told from a more unbiased perspective in Horace Freeland Judson’s book The Eighth Day of Creation: The Makers of the Revolution in Biology. Let us end with Judson’s discussion of Watson and Crick’s now 60-year-old letter.
“The letter to Nature appeared in the April 25th issue. To those of its readers who were close to the questions, and who had not already heard the news, the letter must have gone off like a string of depth charges in a calm sea. ‘We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest,” the letter began; at the end, ‘It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.’ The last sentence has been called one of the most coy statements in the literature of science.”

Friday, April 19, 2013

Hyperpolarized 129Xe MRI of the Human Lung

Chapter 18 of the 4th edition of Intermediate Physics for Medicine and Biology is devoted to magnetic resonance imaging. Russ Hobbie and I discuss many aspects of MRI, including functional MRI and diffusion tensor imaging. One topic we do not cover is using hyperpolarized spins to study lung function. Fortunately, a clearly written review article, Hyperpolarized 129Xe MRI of the Human Lung, by John Mugler and Talissa Altes, appeared recently in the Journal of Magnetic Resonance Imaging (Volume 37, Pages 313-331, 2013). Below I reproduce excerpts from their introduction, with citations removed.
“CLINICAL MAGNETIC RESONANCE IMAGING (MRI) of the lung is challenging due to the lung’s low proton density, which is roughly one-third that of muscle, and the inhomogeneous magnetic environment within the lung created by numerous air–tissue interfaces, which lead to a T2* value on the order of 1 msec at 1.5 T. Although advances continue with techniques such as ultrashort echo time (UTE) imaging of the lung parenchyma, conventional proton-based MRI is at a fundamental disadvantage for pulmonary applications because it cannot directly image the lung airspaces. This disadvantage of proton MRI can be overcome by turning to a gaseous contrast agent, such as the noble gas helium-3 (3He) or xenon-129 (129Xe), which upon inhalation permits direct visualization of lung airspaces in an MR image. With these agents, the low density of gas compared to that of solid tissue can be compensated by using a standalone, laser-based polarization device to increase the nuclear polarization to be roughly five orders of magnitude (10,000 times) higher than the corresponding thermal equilibrium polarization would be in the magnet of a clinical MR scanner. As a result, the MR signal from these hyperpolarized noble gases is increased by a proportionate amount and is easily detected using an MR scanner tuned to the appropriate resonance frequency. MRI using hyperpolarized gases has led to the development of numerous unique strategies for evaluating the structure and function of the human lung that provide advantages relative to current clinically available methods. For example, as compared with nuclear-medicine ventilation scintigraphy scans using 133Xe or aerosolized technetium-99m DTPA, hyperpolarized-gas ventilation MR images provide improved temporal and spatial resolution, expose the patient to no ionizing radiation, and can be repeated multiple times in a single day if desired. Although inhaled xenon has also been used as a contrast agent with computed tomography (CT), which can provide high spatial and temporal resolution, the high radiation dose and low contrast on the resulting ventilation images has dampened enthusiasm for the CT-based technique.

Although the first hyperpolarized-gas MR images were obtained using hyperpolarized 129Xe, and images of the human lung were acquired with hyperpolarized 129Xe only a few years later, the vast majority of work in humans has been performed using hyperpolarized 3He instead. This occurred primarily because 3He provided a stronger MR signal, due to its larger nuclear magnetic moment (and hence larger gyromagnetic ratio) compared to 129Xe and historically high levels of polarization (greater than 30%) achieved for 3He, and because there are no significant safety concerns associated with inhaled helium. However, in the years following the terrorist attacks of 9/11 there was a surge in demand for 3He for use in neutron detectors for port and border security, and this demand far exceeded the replenishment rate from the primary source, the decay of tritium used in nuclear warheads. As a result, 3He prices skyrocketed and availability plummeted. Currently, the U.S. government is regulating the supply of 3He, allocating this precious resource among users whose research or applications depend on 3He’s unique physical properties. This includes an annual allocation for medical imaging, which allows research on hyperpolarized 3He MRI of the lung to continue. Nonetheless, unless a new source for 3He is found it is clear that insufficient 3He is available to permit hyperpolarized 3He MRI of the lung to translate from the research community to a clinical tool.

In contrast to 3He, 129Xe is naturally abundant on Earth and its cost is relatively low. Thus, 129Xe is the obvious potential alternative to 3He as an inhaled contrast agent for MRI of the lung. While the 3He availability crisis has accelerated efforts to develop and evaluate hyperpolarized 129Xe for human applications, it is important to understand that 129Xe is not just a lower-signal alternative to 3He, forced upon us by practical necessity. In particular, the relatively high solubility of xenon in biological tissues and an exquisite sensitivity to its environment, which results in an enormous range of chemical shifts upon solution, make hyperpolarized 129Xe particularly attractive for exploring certain characteristics of lung function, such as gas exchange and uptake, that cannot be accessed using hyperpolarized 3He. The quantitative characteristics of gas exchange and uptake are determined by parameters of physiologic relevance, including the thickness of the blood–gas barrier, and thus measurements that quantify this process offer a potential wealth of information on the functional status of the healthy and diseased lung.

Historically, polarization levels for liter-quantities of hyperpolarized 129Xe have been roughly 10%, while those for similar quantities of hyperpolarized 3He have been greater than 30%. (Recall that the thermal equilibrium polarization of water protons at 1.5T is 0.0005%—four to five orders of magnitude lower.) Given 129Xe’s lower nuclear magnetic moment, this situation has put hyperpolarized 129Xe at a distinct disadvantage relative to 3He. A recent, key advance for 129Xe is the development of systems that can deliver liter quantities of hyperpolarized 129Xe with polarization on the order 50%. This now puts 129Xe on a competitive footing with 3He, positioning MRI of the human lung using hyperpolarized 129Xe to advance quickly in the immediate future, and making hyperpolarized 129Xe MRI of interest to the broader radiology and medical-imaging communities.”
This idea of gas hyperpolarization is fascinating. How does one hyperpolarize the gas? Mugler and Altes explain:
“Although it is possible to image either 129Xe or 3He by simply placing the gas (in a suitable container) in the magnet of an MR scanner, the low density of gas compared to that of solid tissue results in a signal that is too low to be of practical use for imaging the human lung… Nonetheless, the nuclear polarization can be increased dramatically compared to that produced by the magnet of the MR scanner by using a method called opticalpumping and spin exchange (OPSE), which was originally developed for nuclear-physics experiments many years before being applied to medical imaging.

As its name implies, OPSE is, in concept, a two-step process. The first step, optical pumping, involves using a laser to generate electron-spin polarization in a vapor of an alkali metal. This process takes place within a glass container, called an optical cell…positioned within a magnetic field... A small amount of the alkali metal, typically rubidium, is placed in the cell, which is heated…during the polarization process to create rubidium vapor. The optical cell is illuminated with circularly polarized laser light…at a specific wavelength (795 nm) to optically pump the rubidium atoms. This pumping preferentially populates one of the two spin states for the valence electron, thereby polarizing the associated electron spins and resulting in electron-spin polarization approaching 100%. In the second step of OPSE, collisions between spin-polarized rubidium atoms and noble-gas (129Xe or 3He) atoms within the cell result in spin exchange—the transfer of polarization from rubidium electrons to noble-gas nuclei...”
To learn more, you can hear John Mugler discuss Hyperpolarized gas MRI in the lung on youtube.

Friday, April 12, 2013

Radon

The largest source of natural background radiation is radon gas. In Chapter 17 of the 4th edition of Intermediate Physics for Medicine and Biology, Russ Hobbie and I discuss radon.
“The naturally occurring radioactive nuclei are either produced continuously by cosmic γ ray bombardment, or they are the products in a decay chain from a nucleus whose half-life is comparable to the age of the earth. Otherwise they would have already decayed. There are three naturally occurring radioactive decay chains near the high-Z end of the periodic table. One of these is the decay products from 238U, shown in Fig. 17.27. The halflife of 238U is 4.5 × 109 yr, which is about the same as the age of the earth. A series of α and β decays lead to radium, 226Ra, which undergoes α decay with a half-life of 1620 yr to radon, 222Rn.

Uranium, and therefore radium and radon, are present in most rocks and soil. Radon, a noble gas, percolates through grainy rocks and soil and enters the air and water in different concentrations. Although radon is a noble gas, its decay products have different chemical properties and attach to dust or aerosol droplets which can collect in the lungs. High levels of radon products in the lungs have been shown by both epidemiological studies of uranium miners and by animal studies to cause lung cancer” 
In Chapter 16 we consider radon in the context of the risk of the general population to low levels of background radiation.
“The question of a hormetic effect or a threshold effect [as opposed to the linear no-threshold model of radiation exposure] has received a great deal of attention for the case of radon, where remediation at fairly low radon levels has been proposed. Radon is produced naturally in many types of rock. It is a noble gas, but its radioactive decay products can become lodged in the lung. An excess of lung cancer has been well documented in uranium miners, who have been exposed to fairly high radon concentrations as well as high dust levels and tobacco smoke. Radon at lower concentrations seeps from the soil into buildings and contributes up to 55% of the exposure to the general population.”
Given the high profile of radon in our book, I thought readers might be interested in a bit of the history of this element. A brief discussion of the discovery of radon can be found in Isaac Asimov’s book Building Blocks of the Universe. After Asimov describes the Curies' discoveries of radium and polonium from uranium ore in the late 1890’s, he writes
“When the radium atom breaks up, it forms an atom of radon, element No. 86. Radon is a gas, a radioactive gas! It fits into the inert gas column of the periodic table, right under xenon, and has all the chemical characteristics of the other inert gases.

Radon was first discovered in 1900 by a chemist named F. E. Dorn, and he called it radium emanation because it emanated from (that is, was given off by) radium. [William] Ramsay and R. Whytlaw-Gray collected the gas in 1908, and they called it niton from a Greek word meaning ‘shining.’ In 1923, though, the official name became ‘radon’ to show that the gas arose from radium…

Other gases arise from the breakdown of thorium and actinium … and have been called thoron and actinon, respectively. These are, as it turns out, varieties [isotopes] of radon. However, there have been suggestions that the element be named emanon (from ‘emanation’) since it does not arise from the breakdown of radium only, as ‘radon’ implies.”
Asimov’s Biographical Encyclopedia of Science and Technology describes the scientist who discovered radon in more detail.
“Dorn, Friedrich Ernst, German physicist
Born: Guttstadt (now Dobre, Miasto, Poland), East Prussia, July 27, 1848
Died: Halle, June 13, 1916

Dorn was educated at the University of Konigsberg and taught physics at the universities of Darmstadt and Halle. He turned to the study of radioactivity in the wake of Madame Curie’s discoveries and in 1900 showed that radium not only produced radioactive radiations, but also gave off a gas that was itself radioactive.

This gas eventually received the name radon and turned out to be the final member of Ramsay’s family of inert gases. It was the first clear-cut demonstration that in the process of giving off radioactive radiation, one element was transmuted (shades of the alchemists!) to another. This concept was carried further by Boltwood and Soddy.”

Friday, April 5, 2013

Leon Glass wins Winfree Prize

Leon Glass was honored recently by the Society for Mathematical Biology. Their website states:
“The Society for Mathematical Biology is pleased to announce that this year's recipient of the Arthur T. Winfree prize is Prof. Leon Glass of McGill University. Awarded every two years to a scientist whose work has 'led to significant new biological understanding affecting observation/experiments,' this prize commemorates the creativity, imagination and intellectual breadth of Arthur T. Winfree.

Beginning with simple and brilliantly chosen experiments, Leon launched the study of chaos in biology. Among the applications he and his many collaborators and students pursued was the novel idea of "dynamical disease" and the better understanding of pathologies like Parkinson's disease and cardiac arrhythmias. His elegant work (with Michael Guevara and Alvin Shrier) on periodic stimulation of heart cells demonstrated and explained how the interaction of nonlinearities with oscillations create complex dynamics and chaos.

The book "From Clocks to Chaos," which he co-authored with Michael Mackey, was an instant classic that illuminated this difficult subject for a whole generation of mathematical biologists. His combination of imagination, experimental and mathematical insight, and ability to communicate fundamental principles has launched new fields of research and inspired researchers ranging from applied mathematicians to medical researchers.”
Leon Glass is the Isadore Rosenfeld Chair in Cardiology at McGill University. Russ Hobbie and I cite his book From Clocks to Chaos (discussed previously in this blog) in the 4th edition of Intermediate Physics for Medicine and Biology, especially in Chapter 10 when discussing nonlinear dynamics. According to Google Scholar, the book has been cited 1800 times. Even more highly cited (over 2600 times) is Mackey and Glass’s paper Oscillation and Chaos in Physiological Control Systems (Science, Volume 197, Pages 287-289, 1977), which Russ and I also cite.

Other books and papers mentioned in IPMB include
Bub, G., A. Shrier, and L. Glass (2002). Spiral wavegeneration in heterogeneous excitable media. Phys. Rev. Lett. 88:058101.

Glass, L., Y. Nagai, K. Hall, M. Talajic, and S. Nattel (2002). Predicting the entrainment of reentrant cardiacwaves using phase resetting curves. Phys. Rev. E, 65:021908.

Guevara, M. R., L. Glass, and A. Shrier (1981). Phaselocking,period-doubling bifurcations and irregular dynamicsin periodically stimulated cardiac cells. Science 214: 1350–1353.

Glass, L. (2001). Synchronization and rhythmicprocesses in physiology. Nature. 410(825): 277–284.

Kaplan, D., and L. Glass (1995). Understanding NonlinearDynamics. New York, Springer-Verlag.
You can listen to Glass talk about cardiac arrhythmias on youtube here.