During the ten years of the DUJS’s existence, science at Dartmouth has seen breakthrough after breakthrough. Once the site of the first clinical x-ray in North America, Dartmouth College over the last decade has had a hand in the discovery of microRNA and cancer chemoprevention, and its researchers have worked to produce ethanol from biomass and to understand “dark matter.” Here we review just a few of the recent scientific accomplishments at the College.
Biology
miRNA
In 1993, Victor Ambros, a geneticist at Dartmouth Medical School, disproved the traditional paradigm that only proteins can regulate the expression of DNA. While examining defects in C. elegans larvae, he discovered a short 22 nucleotide piece of RNA, called lin-4, that was never transcribed into protein but was still able to negatively regulate expression of another gene (1, 2, 3).
Even 10 years after Ambros discovered the lin-4 RNA, the significance of his finding was still not fully realized by the scientific community. By 2001, only two of these regulatory “microRNA” (miRNA) genes had been observed, and they were both found in the genome of Caenorhabditis elegans, a worm whose name is rarely heard outside of laboratories and biology textbooks.
In fact, at the time, no one had even named this type of RNA. It was not dubbed “microRNA” until 2001, when Ambros published a paper in Science that described 15 other examples of miRNA gene regulation in the C. elegans. Furthermore, many of these miRNAs were in ancient regions of the genome that are highly conserved, and appeared to have homologs in insects, mammals, and perhaps other vertebrates. The finding demonstrated that miRNA was not simply a biological anomaly, but a prominent mechanism of gene regulation in nature (4).
In his 2001 paper, Ambros used cDNA and computational approaches to compare the two known miRNAs, lin-4 and let-7, to DNA sequences in the genomes of C. elegans and other organisms. The 15 genes that he discovered varied in expression at different times in development and appeared to have diverse functions in C. elegans. Furthermore, three of the genes had homologs in higher vertebrates. One of these homologs is expressed in the human heart and in mouse embryos, demonstrating the diversity and prevalence of miRNA (4).
Two other papers were published simultaneously in the same journal, describing other instances of miRNA regulation in worms, flies, and humans, and bringing the total miRNA count up to about 100 (4, 5, 6).
Since then, miRNA has continued to play a major role in genetics. Today, over 5,000 miRNAs have been identified in many organisms including plants, flies, worms, and vertebrates (7). A recent discovery at Dartmouth demonstrated that miRNAs may have played a major role in vertebrate evolution (8). Other labs report that miRNA is an important element in the pathology of cancer (7, 9). Since Ambros’ discovery the impact of miRNA has resounded through the world of science with a booming voice, but its humble beginnings were right here at Dartmouth.
Chemistry
Chemoprevention
It began with a simple idea: trees have long lives, and all trees produce triterpenoids. Might triterpenoids have some application in medicine (10)?
Thus began a quest by chemistry professors Gordon Gribble and Tadashi Honda, together with Dartmouth Medical School professor Michael Sporn, to revolutionize the field of chemoprevention.
Beginning in 1995, this pharmacological team set out to examine the various types of triterpenoids available commercially and naturally to see what might be applicable as a cancer treatment in vivo. Triterpenoids have long been a fixture in Asian medicine.
It was not until 1998, however, that Honda and Gribble isolated a triterpenoid that was powerful enough to function in an anti-cancer capacity. This substance, labeled triterpenoid 151 or CDDO, was able to reduce tumor growth and protect non-tumor cells. In addition, it also had the ability to reduce chronic inflammation (11).
The research group published this landmark discovery in the January 1999 edition of Cancer Research.
The anti-inflammatory function makes CDDO a “triple threat” in chemoprevention. Inflammation causes rapid cell proliferation, which increases the chance of mutagenesis and tumor development. Any reduction in inflammation, therefore, can serve to reduce the chance of mutagenesis.
Specifically, the researchers found that CDDO is capable of suppressing COX-2 and nitric oxide, two agents that commonly promote inflammation and have recently been shown to characterize the tumor microenvironment and immunological tumor promotion (11, 12). This is the logic behind use of arthritis medications in cancer treatment.
Successive publications stemming from the chemists’ work since the 1999 Cancer Research paper have indicated that CDDO can prevent lung cancer in mice and can induce apoptosis, or programmed cell death, in mouse myeloma and lung cancer cells (13).
A CDDO derivative is currently in Phase II trials with the F.D.A., with the hope that the drug could be on the marketplace by 2009 (10).
Anesthesia
As Gribble and Honda’s work shows, many of the world’s biggest discoveries lie at the intersections of the scientific disciplines. For them, it was chemistry and biology. For chemistry professor Robert Cantor, discovery lay in the overlap among chemistry, biology, and physics.
Cantor’s work has focused on the dynamics of the cell’s lipid bilayer in the context of anesthesia. Scientists have theorized that anesthetics function by binding to protein channels within the bilayer. This binding can block the ionic flow between the cell and its outer environment, thereby interrupting communication between cells (14).
Cantor sat down with DUJS in 2005 to discuss his analysis. He explained that past models of anesthesia did not take into account several important factors, including (i) the variety of viable anesthetic substances; (ii) the viability of similar anesthetics across species; and (iii) the high concentration of anesthetics needed for an in vivo effect. Cantor said these factors indicate that anesthetics could not function through a direct binding mechanism because such a specific process is at odds with the apparently non-specific nature of anesthetics (15).
Cantor, in the 2001 edition of Biophysical Journal, had hypothesized that a different mechanism must be at play. In short, he proposed that anesthetic substances enter the bilayer and change its “lateral pressure profile.” The profile describes the amount of pressure along the plane of the bilayer. As anesthetics enter the bilayer, they increase the membrane pressure, which results in conformational changes to the membrane’s proteins. The proteins are thus inactivated and the ionic flow, as with the previous model, is interrupted (14).
These conclusions have led Cantor to pursue the evolutionary implications of anesthesia. “I’ve become more interested in the why of anesthetics,” he said in the 2005 DUJS article. “A more fundamental question is why would we be anesthetized in the first place? They affect all humans, and there is nearly zero genetic diversity. If a sensitivity to a drug is narrow in a population, then any mutation that changes your sensitivity, it must affect survivability” (15).
Earth Sciences
Glacial Periodicity
The traditional theory of Milankovitch cycles asserts that the 100,000 year periodicity of ice ages is the result of gravitational attractions, orbits, and tilts of celestial bodies (16). In 2002, Mukul Sharma, an assistant professor in Dartmouth’s Earth Science department, offered a new alternative to this long-accepted theory. He proposed that changes in magnetic activity on the surface of the Sun may play a large role in glacial periodicity.
Solar activity was known to vary over shorter time periods, but cyclical fluctuations on a scale of 100,000 years had yet to be explored. Sharma devised a method of measuring these long-term fluctuations by exploiting the Sun’s effect on Beryllium-10 production in the Earth’s atmosphere. Different levels of atmospheric 10Be production on Earth reflect variances in the geomagnetic field strength and the solar modulation factor of the Sun. Sharma analyzed 10Be production data that had been derived from deep marine sediments. Using this data, he estimated solar surface magnetic activity. Because 10Be has a long half-life of 1.5 million years, Sharma was able to gather data for the last 200,000 years (17).
Sharma’s results showed not only that the magnetic activity of the Sun was variable over this period, but also that it appeared to be cyclical. In addition, the solar modulation was in phase with the 100,000 year glacial cycles. Solar magnetic intensities are believed to affect radiation and cloud formation on Earth. Thus, the variations that Sharma observed may be responsible, in part or in whole, for the Earth’s glacial cycles. While Sharma acknowledges the need for further investigation of this novel theory, it is an exciting new explanation for an ancient phenomenon (17).
Engineering
Protein Glycosylation
Many of the therapeutic proteins used in the medical world today are artificially produced and engineered using mammalian cells lines. These proteins, or glycoproteins, must often have sugar structures attached in vivo through a process called glycosylation before they can be fully functional (18).
In 2003, professor Tillman Gerngross and others at the Thayer School of Engineering genetically engineered the yeast strain Pichia pastoris to conduct human-like glycosylation. This process allows the synthesized proteins to be more uniform in structure, and also allows for more control over important protein properties, including solubility. The engineering was accomplished by deleting the non-human glycosylating gene from the yeast and incorporating its human counterpart (19).
In January 2006, Gerngross and his colleagues were able to synthesize human monoclonal antibodies in yeast, having formed GlycoFi Inc., to market their discovery by that time. GlycoFi was acquired by Merck & Co. in 2006 (20).
Cell-Mediated Production of Ethanol from Biomass
Researchers have long focused on how to develop usable fuel from cellulose biomass. Major roadblocks, however, have been that the synthesis of the fuel is often expensive, time consuming, and results in the creation of secondary products that are unnecessary and reduce the efficiency of energy provision.
Thayer School professor Lee Lynd and colleagues, however, have made significant strides toward finding a solution. The research, based on a partnership between Dartmouth and the Mascoma Corporation (a company founded in part by Lynd), is focused on producing ethanol using thermophilic organisms and what is called “consolidated bioprocessing,” where “biological conversion is solidated into a single step without added cellulase enzymes.” Cellulase enzymes are the primary substances required for the breakdown of cellulose-containing biomasses (21). In short, consolidated bioprocessing makes cellulase production, cellulose hydrolysis, hexose fermentation, and pentose fermentation a one-step process (22).
Lynd’s research has focused on the use of several organisms, including an engineered version of Thermoanaerobacterium saccharolyticum, to supply ethanol given certain biomasses. In engineering these organisms, Lynd has centered his work on reducing their production of lactic and acetic acid, substances that correlate with reduced ethanol production (22).
Environmental Science
Antarctic Cooling
In January 2002, environmental studies professor Ross Virginia, along with a team of researchers from across the country, found that average temperatures in Antarctica declined over the last decade despite a general global warming trend. They also discovered that this cooling corresponded with a 10 percent decrease in the number of soil invertebrates. The discovery, published in Nature, received widespread national attention as some pundits interpreted the results as proof that global warming does not exist.
Using weather data and lake level measurements, Virginia and his co-authors found that the air temperature at Lake Hoare in Antarctica decreased by 0.7OC from 1986-1999. Wind speed during this period also decreased, while the amount of solar radiation increased. The amount of discharge from major streams decreased while lake levels rose.
By collecting samples of nematodes, tardigrades, and androtifers from the soil, the researchers were also able to determine whether the environmental trends correlated with changes in the Antarctic biosphere. The researchers concluded that the population of nematodes and tardigrades was declining significantly.
“Given the low diversity and long generation times of these invertebrates, these declines in population represent important shifts in the diversity, life cycles, trophic relationships, and functioning of dry valley soils,” the Nature paper states (23).
Research since the 2002 paper has indicated that the hole in the ozone layer may be somewhat responsible for the Antarctic cooling. The hole causes west winds to blow toward the South Pole. This decreases the air pressure, which in turn causes a reduction in temperature (24).
Mathematics
The Quantum Drum
How is the surface of a drum like a billiards table? Alex Barnett, an assistant professor of mathematics at Dartmouth, is investigating the notion that these two systems are one and the same. The key to their similarities lies in the overlap between quantum and classical mechanics.
The quantum interpretation is analogous to a drum skin stretched over an irregularly shaped frame. When struck, the edges of the drum skin remain fixed, but the interior can oscillate at different frequency modes. In the lowest mode, the entire drum oscillates in phase as one, while at higher modes, areas of the drum oscillate differently. Theoretically, there are an infinite number of modes, with higher nodes dividing the drum surface into smaller and smaller oscillating areas (25).
In the classical system, imagine a frictionless billiard table in the same shape as the drum frame in the quantum problem. A ball follows a path over the billiard table by bouncing off of the edges. In this “chaotic” system, the path of the ball is specific to small deviations in initial conditions. In other words, two balls that begin their journeys with nearly identical initial conditions quickly diverge into wildly different paths (25).
The nature of the quantum drum is controversial at very high frequency modes. For example, it is unknown whether the oscillating patterns arrange themselves uniformly over the surface, or whether they cluster together in “scar” patterns. If the quantum modes do in fact exhibit scars, these scars may form along closed, periodic paths of the chaotic billiard ball. Barnett’s research focuses on methods of calculating the patterns for these higher nodes, and examining the connection between the classical and quantum systems (26). The consequences of these questions have practical applications in determining the behavior of heat dissipation in microchip semiconductors, and theoretical significance in the distribution of prime numbers (27). Barnett’s research was published in the January 2006 issue of Communication on Pure & Applied Mathematics, and on the cover of the January 2008 issue of Notices of the American Mathematical Society (26, 28).
Physics & Astronomy
Dark Matter and Quintessence
In 2005, Dartmouth physics professor Robert Caldwell, along with Eric Linder of Berkeley Laboratory, shed light on our understanding of dark energy. Scientists had purported “dark energy” to be the force behind the surprising 1998 discovery that the expansion of the universe is accelerating, not decelerating. The discovery shook the foundations of cosmology, since under the traditional paradigm, gravity pulls galaxies together, decreasing the rate of expansion. In order to explain the mysterious observation of accelerating expansion, scientists proposed dark energy, which would counter gravity to pull the universe apart (29).
The concept of dark energy is still poorly understood. One proposal for the nature of dark energy is Albert Einstein’s cosmological constant, which Einstein suggested in 1917, but would later call his “greatest blunder” (30). However, the cosmological constant theory received renewed interest following the accelerating expansion discovery, since it would provide the force needed to balance out gravity. The other theory was that dark energy was a dynamic force, called “quintessence.” Caldwell and Linder’s research outlined two possibilities for the fate of the universe under the quintessence model: thawing and freezing. In the thawing scenario, the acceleration of the universe will slow down and eventually stop, possibly leading to recollapse. The freezing scenario describes a state where the acceleration continues to increase, pulling galaxies further and further apart (31).
Their findings were attractive, because the models for neither of these scenarios required Einstein’s cosmological constant, which had been called into question. Particularly, the cosmological constant seemed to overcompensate for gravity, providing much more expanding force than was necessary (29). Caldwell and Linder’s ideas also provided possibilities for observational tests on the nature of dark energy (30). Their work provided new clues into the mystery behind the fate of the universe.
Acknowledgements
We would like to thank professors James Aronson, Alex Barnett, Andrew Friedland, David Glueck, and Thayer Dean Joseph Helble for their assistance in helping us review the past 10 years of science at Dartmouth.
References
1. R. C. Lee, R. L. Feinbaum, V. Ambros, Cell 75, 843 (1993).
2. V. Ambros, Nature 431, 350 (2004).
3. E. Chien, Dartmouth Undergraduate Journal of Science 9(1), 4-7 (2006).
4. R. C. Lee, V. Ambros, Science 294, 862 (2001).
5. M. Lagos-Quintana, R. Rauhut, W. Lendeckel, T. Tuschl, Science 294, 853 (2001).
6. N. C. Lau, L. P. Lim, E. G. Weinstein, D. P. Bartel, Science 294, 858 (2001).
7. E. Barbarotto et al., International Journal of Cancer 122, 969 (2008).
8. A. M. Heimberg et al., Proceeding of the National Academy of Sciences 105, 2946-2950 (2008).
9. M. Kato and F. Slack, Biology of the Cell 100, 71 (2008).
10. J. Durgin, Dartmouth Medicine (2002).
11. N. Suh et al., Cancer Research 59(2), 336-41 (1999).
12. S.J. Roberts et al., Proceedings of the National Academy of Sciences 104(16), 6770-5 (2007).
13. K. Liby et al., Clin. Cancer Res. 12(14), 4288-93 (2006).
14. R.S. Cantor, Biophys. J. 80(5), 2284-97 (2001).
15. B. Huang, Dartmouth Undergrad. Journal of Science 7, 49-53 (2005).
16. K. D. Bennett, Paleobiology 16, 11 (1990).
17. M. Sharma, Earth and Planetary Science Letters 199, 459 (2002).
18. GlycoFi Technology, GlycoFi Available at: http://www.glycofi.com/engineered_glycosylation.htm.
19. B. Choi et al., Proceedings of the National Academy of Sciences 100(9), 5022-7 (2003).
20. GlycoFi Technology, GlycoFi Available at http://www.glycofi.com/glycoproteins.htm.
21. Market Leadership, Mascoma Corp Available at http://www.mascoma.com/welcome/market_leadership.html.
22. Professor Lee Lynd, Thayer School Available at http://engineering.dartmouth.edu/biomass/.
23. P. Doran et al., Nature 415, 517 (2002).
24. Current Understanding of Antarctic Climate Change, Pew Center on Global Climate Change Available at http://www.pewclimate.org/global-warming-basics/antarctic_facts.
25. A. H. Barnett, Alex Barnett: Nontechnical Introduction to My Research (Dec. 2004). Available at http://www.math.dartmouth.edu/~ahb/nonres.html (27 Mar. 2008).
26. A. H. Barnett, Communications on Pure and Applied Mathematics 59, 1457-1488 (2006).
27. A. H. Barnett, Personal correspondence, 27 Mar. 2008.
28. Z. Rudnick, Notices of the AMS 55, 32-34 (2008).
29. G. Ellis, Nature 452, 158-161 (2008).
30. L. Yarris and E. Linder, Finding a Way to Test for Dark Energy (29 Aug. 2005). Available at http://www.lbl.gov/Science-Articles/Archive/Phys-SNAP-dark-energy.html (28 Mar. 2008).
31. R. R. Caldwell and E. V. Linder, Phys. Rev. Lett. 95:141301 (2005).