Fall 2012: Volume 5, Issue 1

The Amherst

ELEMENT Volume 5, Issue 1

Fall 2012

Letter from the Editors Thank you for picking up this semester’s copy of the Element! We would like to thank all of our writers and editors for helping us this semester.

This issue features articles about biology (A Summer At Harvard Stem Cell Institute by Haneui Bae ‘13 and Skin to Neuron: Controlling Neuronal Fate by Kevin Mei ‘16), medicine (NIH’s Solution to Bottlenecks in the Drug Development Pipeline by Ji Hoon Lee ‘16), chemistry (Organic Chemistry For Dummies by Xiao Xiao ‘16 and Arsenic: Portrait of a Killer by Alice Li ‘13), and environmental science (A Fiery Debate on Western Forests by Anna Rasmussen ‘13). While we are excited to bring you articles from a number of different scientific fields, we would also like to continue to diversify what the Element has to offer. We would also like to feature more articles in the future, in order to better represent the breadth of scientific research and interests of Amherst students. So if you want to tell the campus about research you did or if you have some topic related to science that you’d like to learn and write about, please join us next semester!

Thanks for reading, and enjoy the issue!

Sincerely,

Alice Li

Maile Hollinger

News-In-Brief Maile Hollinger ‘15 Using Music to Fine-Tune Synthetic Silk Fibers For years, scientists have tried to replicate the strength and durability of spider silk in the laboratory – but now, musical composition might have a hand in creating biosynthesized materials such as silk. Using a field known as category theory, researchers and composers at MIT and Tufts have translated the structures of some artificial silks into musical compositions.

Preliminary research has shown that strength and cohesiveness of the material translated into musical characteristics such as tempo and fluidity. Researchers on this project hope to take their results a step further and use category theory to predict the properties of biosynthesized materials before they are even produced, saving money and time in the process.

Nobel Prize winner Dr. Joseph Murray dies at 93 Dr. Joseph E. Murray, most known for his contribution to transplant surgery as the lead surgeon during the first successful organ transplant in 1954, passed away due to hemorrhagic stroke on November 26th. He was awarded the Nobel Prize in 1990

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for his continued work in pioneering organ transplants, which included the first organ transplant from a non-related individual.

He will be remembered for his contributions not only to the field of transplant surgery but also plastic surgery, as he was credited with the development of procedures to repair congenital face defects in children.

A Therapeutic Treatment for Alzheimer’s?

Researchers at the University of Zurich have found that turning off signaling molecules known as cytokines in the immune system has reduced abnormal protein deposits that cause Alzheimer’s. In this study, mice with Alzheimer’s were treated with an antibody that turned off the immune molecule p40, and then abnormal protein deposits were measured in the brains of these mice. Levels of the abnormal protein amyloid-β (which plays a central role in Alzheimer’s) were reduced by approximately 65 percent in this study. Profs. Heppner and Becher – the scientists who headed the study – remain hopeful that inhibition of p40 can be brought to human patients soon as a therapeutic approach to alleviating Alzheimer’s.

Table of Contents

The Amherst Element Staff Editors-in-Chief Alice Li Maile Hollinger Associate Copy Editors Anna Rasmussen Ji Hoon Lee Kevin Mei Xiao Xiao Haneui Bae Emily Jackson David Nam Narendra Joshi Feature Contributor Maile Hollinger Layout Emily Jackson David Nam Xiao Xiao Narendra Joshi Haneui Bae

Cover Feature 1

Neurons in the Lateral Hypothalamus

Haneui Bae ‘13

24 Glowing Embyoid Bodies

Haneui Bae ‘13

Features

2 News-in-Brief

Maile Hollinger ‘15

Letters

4 NIH’s Solution to Bottlenecks in the Drug Development Pipeline

Ji Hoon Lee ‘16 7 Arsenic: Portrait of a Killer

Alice Li ‘13 10 A Fiery Debate on Western Forests

Anna Rasmussen ‘13 14 Organic Chemistry For Dummies

Xiao Xiao ‘16 20 Skin to Neuron: Controlling Neuronal Fate

Kevin Mei ‘16

Summer Research

17 A Summer of Research and Fun at Harvard Stem Cell Institute

Haneui Bae ‘13 Get Involved!

Send questions, comments, letters, or submissions to theAmherstElement@gmail. com.

The opinions and ideas expressed in the Element are those of the individual writers and do not necessarily reflect the views of the Element or Amherst College. The editorials are a product of the opinions of the current editors-in-chief of the Element. The Element does not discriminate on the basis of gender, race, ethnicity, sexual orientation, scientific background, age, or hair color.

Research findings published in the Element are not intended for wide distribution or for the reader’s profit. As a member of the Amherst community, please use the information and data presented in the Element judiciously.

Cover Picture: These are immunofluorescent pictures of mouse brain section and stem cell tissue culture. Please see p.17 for more information!

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Letters

NIH’s Solution to Bottlenecks in the Drug Development Pipeline National Center for Advancing Translational Sciences

Ji Hoon Lee ‘16 The Drug Development Bottleneck “Scientists discover potential cure for cancer.” “Novel drug candidate shows promise against Alzheimer’s.” “New nanoparticles shrink tumors in mice.”—These titles are just few of the many news articles we spot online on a regular basis. For avid readers of these articles, we know that they all conclude the same way, with something along the lines of, “We predict that this therapeutic strategy will be implemented in clinics across the nation in ten to fifteen years.” Given the urgency of those in need, ten or fifteen years is an inordinate amount of time. Even more alarming, these cures are often never to be heard of again after the initial scientific breakthroughs are cast into an ephemeral limelight.

The problem lies deep within the system. The current therapeutic development pipeline—a long, winding road between the discovery of a potential therapeutic compound in a lab and the implementation of approved drugs in the clinic—is called the “valley of death” in the trade. In this “valley,” about 5,000-10,000 potential compounds must go through preclinical trials on animal models, clinical trials on humans, and a rigorous review by the Food and Drug Administration (FDA). Even without consideration for drug failures after post-marketing surveillance, only 1 out of 10,000 pharmaceutical drugs is approved by the FDA (Fig. 1).

Meanwhile, pharmaceutical companies must face the triple threat of exorbitant investment sums ranging up to $1 billion, a lengthy timeframe of about 13 years, and a 98% failure rate.1 The resulting bottleneck in the therapeutic development pipeline makes the

successful approval of a drug nearly impossible.

An example of a difficulty within the pipeline is the preclinical drug toxicity test. These tests show that up to fifty percent of drugs that are judged non-toxic in animals are toxic to humans.2 What’s more, drugs that may be harmless to humans but toxic to animals are eliminated during this phase. The highly inaccurate and inefficient pre-clinical test is just one example of the bottleneck that may prevent potentially groundbreaking drugs from reaching the market.

The question then becomes: how can we increase the productive potential of the therapeutic pipeline and get more effective medicines for clinical use? Can we introduce new innovations that will increase the rate of drug output?

What is NCATS? Recognizing the need for a better system of translational science (science that serves specific therapeutic applications such as developing drugs, diagnostics, and devices), the National Institutes of Health (NIH) announced the establishment of the National Center for Advancing Translational Sciences (NCATS) for the fiscal year 2012. The new translational center is to be a catalyst for removing the bottleneck in the pipeline through collaboration with both private and public sectors.

“We need a place to actually look at the whole process of translation in a way that can consider how it might be reengineered, consider how we can make a difference by partnering with both

Figure 1: The drug development pipeline

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Letters advocacy groups and with industry,” says Thomas Insel, the former acting director of NCATS, in a recent interview with ScienceInsider. “Consider where the opportunities are for great innovation that are not just related to schizophrenia or autism or bipolar illness but that are really generic. They go across all of medicine.”3 NCATS has several advantages unique to its identity as a public translational science center. Rare and neglected diseases, for which there are relatively few effective treatments, often garner little interest from pharmaceutical companies that find it not worth the investment. As a public center, NCATS’ Office of Rare Diseases Research can coordinate and foster research in the field and fill the dead zone between the public and private sectors. Furthermore, NCATS can manipulate, or “reengineer,” the process of drug Figure 2: 3-D human tissue chip development to increase its approved drug output. In NCATS’ Prospects this sense, NCATS will provide an interesting experimental ground Despite much controversy at its outset, what the center to observe how intramural and extramural sectors can work promises to bring the public in the future is indubitably positive. together to reach a common goal, by approaching the pipeline To address the aforementioned problem of pre-clinical toxicity itself as the scientific problem.4 testing, NCATS, in collaboration with several governmental organizations, proposed to develop a 3-D human tissue chip that The NCATS Controversy will allow for more precision in toxicity tests. The tissue chip is Despite potential benefits, the establishment of NCATS was an elegant combination of the new induced pluripotent stem initially met with much skepticism from the scientific community. cell (iPS) technology and a microscopic chip that will resemble “As originally described, NCATS sounded very much like a drug the 3-D, in vivo conditions of the human organ systems (Fig. 2). development scheme that was going to be an underfunded research This technology allows us to take a sample of an individual’s cells, organization,” says Bruce Cronstein M.D., the director of the transform them inside the chip into a desired organ tissue, and test Clinical and Translational Science Institute at New York University therapeutic compounds to see an extremely accurate picture of the School of Medicine. “Changes in research programs…would mean drug’s behavior in the human body. Because the current method that some areas of medical research would be neglected, such as of drug testing involving animals is highly unreliable, human tissue community-based health research.”5 chips will spur a paradigm shift in predicting the outcome of the Indeed, some industrial scientists also expressed worry drug in humans.7 that NCATS will reduce NIH’s commitment to basic science In addition, NCATS aims to develop effective models for and draw its attention to drug development.3 “People were engendering novel insights into existing drugs, such as finding worried about contamination from pharma and whether a new therapeutic uses for abandoned and approved drugs—“drug government agency could develop new drugs any better than the rescue and repurposing.” Due to their severe side effects or lack pharmaceutical industry,” adds Dr. Cronstein. “But that reflected of potency in treating the initially targeted disease, pharmaceutical a misunderstanding of the nature of the center. It’s never been companies abandon the production of many drugs.8 However, the intended that it be the sole developer of a drug from finding deluge of recent discoveries that reveal the molecular mechanisms a target to getting licensure for a therapy.”5 In response to the of these drugs allows us to investigate new uses for them, such as skepticism, NCATS has also committed itself to “reinforcing— uncovering their potencies in treating other disorders. Both the not reducing—NIH’s commitment to basic research” as one of private sector and the public benefits from this research, because its top priorities.4 the companies can simply remanufacture the drugs without much Even with these assurances, funding for the new center poses further approval. a major concern. All but 2% of the $575 million in funding for Due to these hopeful plans, Congress passed funding for NCATS comes from pre-existing NIH programs and is not new NCATS in December 2011. “Congressional support for the money from an external source. “The amount of new funds going National Center for Advancing Translational Sciences marks a to NCATS is a very small amount indeed,” defends Francis S. major milestone in mobilizing the community effort required Collins M.D., Ph.D., the director of NIH. “We are trying to be to revolutionize the science of translation,” says Dr. Collins. very careful about this. We believe we could do a lot with modest “Patients suffering from debilitating and life-threatening diseases resources at this point simply by putting the focus on bottlenecks do not have the luxury to wait the 13 years it currently takes to [in the drug development pipeline].”6 translate new scientific discoveries into treatments that could save or improve the quality of their lives. The entire community must work together to forge a new paradigm, and NCATS aims to catalyze this effort.”9 The Amherst Element, Vol 5, Issue 1. Fall 2012

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Letters References 1. Collins, F. S. (2011). Reengineering Translational Science: The Time Is Right. Science Translational Medicine, 3(90), 90cm17.

2. Greaves, P., Williams, A., Eve, M. (2004). First dose of potential new medicines to humans: how animals help. Nat Rev Drug Discov., 3(3), 226-36.

3. Kaiser, J. (2012, Jan 10). Acting Director Thomas Insel Explains New NIH Translational Center’s Aims and Structure. Retrieved from http://news.sciencemag.org/scienceinsider/2012/01/ acting-director-thomas-insel-exp.html 4. Research. Retrieved from http://www.ncats.nih.gov/research/ research.html 5. Boughton, B. (2011). New Translational Research Center Generates Controversy Among Scientists. Clin Transl Sci., 4(5), 309, doi: 10.1111/j. 152-8062.2011.00354.x.

6. Wadman, M. (2012, Mar 20). NIH director grilled over translational research center. Retrieved from http://blogs.nature. com/news/2012/03/nih-director-grilled-over-translationalresearch-center.html 7. Kaiser, J. (2011, Sep 16). White House Boosts Translational Medicine, Drug Chip Project. Retrieved from http://news. sciencemag.org/scienceinsider/2011/09/white-house-booststranslational.html 8. Kaiser, J. (2011, Jun 24). NIH’s Secondhand Shop for Triedand-Tested Drugs. Retrieved from http://www.sciencemag.org/ content/332/6037/1492.full 9. NIH establishes National Center for Advancing Translational Sciences. (2011, December 23). Retrieved from http://www.nih. gov/news/health/dec2011/od-23.htm Figure 1: http://www.immunetrics.com/applications/drugdiscovery.php Figure 2: http://www.ncats.nih.gov/research/reengineering/ tissue-chip/projects/awards-2012.html

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Letters

Arsenic Portrait of a Killer Alice Li ‘13 Few people like to think they encounter poison on a daily basis.

Names of poisons such as arsenic conjure images from films featuring murder mysteries or plots of medieval intrigue—situations that seem far removed from twenty-first-century reality. But recent studies have shown that arsenic remains prevalent in food today, in products ranging from fruit juices to rice.

A paper published in May 2012

by Jackson et al. conducted arsenic analysis on three commercially available brown rice syrups, fifteen infant formulas without organic brown rice syrup (OBRS), two toddler formulas with OBRS, 29 cereal bars (13 with OBRS), and three flavors of a highenergy performance product. The study found arsenic in all products with OBRS, and the baby formulas Figure 1: Rice and rice products are surprising sources of arsenic. that included OBRS as an ingredient contained more than 20 times the How does arsenic poisoning actually work? As it turns out, amount of arsenic compared to the arsenic has a wide range of toxic effects. It has been known to baby formulas without it.1 inactivate enzymes involved in cellular energy pathways. By atUnsettling as it may be to realize that we might be consumtaching to ADP (adenosine diphosphate) in place of a third phosing arsenic in our everyday food, it turns out that this developphate group, arsenic disrupts the generation of ATP (adenosine ment is only another addition to the long history humankind has triphosphate), a high-energy compound crucial for cellular activshared with this poison. ity.3 It has been classified as a carcinogen that can cause mutations in DNA, as well as interfere with DNA repair processes.4 “The Inheritance Powder” While arsenic poisoning may have been difficult to distinguish Arsenic is a naturally occurring metalloid element, number from natural causes of death, it was not quite as easily disguised if thirty-three in the periodic table of the elements. It occurs in autopsies were performed on a corpse. Reliable toxicological tests two forms, organic (carbon-containing) and inorganic, with the for arsenic have existed since 1846. Arsenic decomposes slowly in organic form being much less lethal than the inorganic form. the body, allowing it to be detected long after the time of death; Arsenic has historically been popular as a murder weapon— furthermore, arsenic slows down the natural decomposition of by one estimate, arsenic was used in almost 40 percent of all 2 human tissue, essentially “mummifying” the body.2 poison murders in France between 1835 and 1880. It acquired the nickname “inheritance powder” because of its use by those The Poison Hiding In Plain Sight who wished to dispose of unwanted relatives. In the form of Arsenic is ubiquitous, both in the environment and in the white arsenic (arsenic trioxide, As2O3), it became a powder that human body. It is the 20th most abundant element in the Earth’s was easily mixed into food and drink with very little effect on crust, 14th in seawater—and, unexpectedly, 12th in the human taste. Moreover, the symptoms of arsenic poisoning were often 5 body.

It is essential for the proper growth and reproduction of mistaken for natural diseases, including influenza, cholera, and some animals, including chickens, and the average person who heart disease.2 The Amherst Element, Vol 5, Issue 1. Fall 2012

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Letters weighs 154 pounds contains a full 7 mg of arsenic.6 Arsenic has been widely encountered throughout human history outside of homicides. Greek physicians such as Hippocrates and Galen advertised it as a therapeutic agent, and it continued to be used as a medicine during the Victorian Era, when a 1% arsenic trioxide preparation called Fowler’s solution was widely prescribed as a health tonic. It was also used to treat syphilis. Predictably, use of arsenic as a medicine often led to detrimental side effects; increased risk of cancer was eventually linked to use of Fowler’s solution, and arsenic treatments of syphilis could lead to gangrene and subsequent limb amputation.6 Arsenic was used in everything from beauty products to rat poisons, and white arsenic’s resemblance to flour and sugar led to an unfortunate number of accidental poisonings. In one case, a group of mourners ate rice pudding before the funeral service; the rice pudding had been accidentally made from arsenic rather than sugar, however, with the result that many of the mourners fell ill during the procession to the burial ground and narrowly avoided joining the deceased in the grave.7 Arsenic was also an ingredient in several colored chemicals, notably Scheele’s green (a copper arsenite, CuHAsO3) and Emerald green (a combination of copper acetate and copper arsenite, also known as Schweinfurt green, Paris green, or Vienna green). These chemicals were used to color artists’ paints, wallpaper, soap, lampshades, children’s toys, candles, and even clothes and cake decorations. Unsurprisingly, a

Figure 2: A dress whose green color was derived from an arsenic-based dye.

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Figure 3: Arsenic trioxide, also known as “white arsenic.” number of illnesses and deaths occurred due to children sucking on objects that had been painted with these arsenic compounds and people breathing in arsenic that diffused from wallpaper into the air.6,7 Arsenic Today: A Hazard...and a Cure?

We may be fortunate enough to no longer wear arsenic-laced clothes or use arsenic-based paints, but as the study by Jackson et al. suggests, arsenic continues to be a major health hazard.

In the 1970s, public health officials in Bangladesh decided to install wells that tapped into sources of clean water deep below ground in order to combat water-borne illnesses such as cholera, typhoid, and dysentery. At first, their efforts seemed to work, as infant mortality and disease incidence dropped. Yet other disease symptoms began to appear—symptoms that were eventually traced to arsenic poisoning. Only then did health officials discover that the wells had tapped into water sources that were naturally filled with arsenic.8 Given that arsenic can be present in groundwater and soil, it seems slightly less shocking that rice can become a source of inorganic arsenic. As it turns out, rice is unusually efficient among crops for its ability to take up arsenic, due in part to its ability to absorb the mineral silicon, which happens to be similar enough in structure to arsenic that arsenic can be readily absorbed as well.9 Considering that rice is a major staple in diets worldwide, it seems fair to ask exactly how much we should be concerned about levels of arsenic in our food.

Can arsenic ever be beneficial to humans? The question seems absurd at first glance, but surprisingly, arsenic trioxide—the same white arsenic that has been a favorite murder weapon throughout history—has been shown to be effective in treating acute promyelocytic leukemia (APL), a blood cancer. Arsenic trioxide induces apoptosis, or programmed cell death, of promyelocytic leukemia cells.10 The exact mechanisms are not yet well understood, but the case of arsenic trioxide suggests that medicinal benefits can exist where we least expect them.

Letters Arsenic has been pervasive throughout human history up until the modern day as an agent of death, both on purpose and by accident. While it remains a genuine hazard to human health in the environment and in our food, it has also unexpectedly become a medical ally in the ongoing fight against cancer, reminding us that even the deadliest toxins may help us save lives.

References 1. Jackson, B. P., Taylor, V. F., Karagas, M. R., Punshon, T., & Cottingham, K. L. (2012). Arsenic, Organic Foods, and Brown Rice Syrup. Environmental Health Perspectives, 120(5), 623-626. doi:10.1289/ehp.1104619.

2. Blum, D. (2010). The Poisoner’s Handbook: Murder and the Birth of Forensic Medicine in Jazz Age New York. New York, NY: The Penguin Group.

3. Ratnaike, R. N. (2003). Acute and Chronic Arsenic Toxicity.

Postgraduate Medical Journal, 79(933), 391-396. doi:10.1136/ pmj.79.933.391.

4. Abernathy, C. O., Liu, Y. P., Longfellow, D., Aposhian, H. V., Beck, B., Fowler, B., Goyer, R., Menzer, R., Rossman, T., Thompson, C., & Waalkes, M. (1999). Arsenic: Health Effects, Mechanisms of Actions, and Research Issues. Environmental Heatl Perspectives, 107(7), 593-597.

5. Marcus, S. (2012, May 11). Arsenic Toxicity in Emergency Medicine. Retrieved October 12, 2012 from http://emedicine. medscape.com/article/812953-overview 6. Emsley, J. (2005). The Elements of Murder. New York, NY: Oxford University Press Inc. 7. Daily Mail. (2010). Found in Wallpapers, Dresses and Even Libido Pills: Arsenic, the Victorian Viagra That Poisoned Britain.

Retrieved October 11, 2012 from http://www.dailymail.co.uk/ health/article-1245809/Found-wallpapers-dresses-libido-pillsArsenic-Victorian-Viagra-poisoned-Britain.html 8. Blum, D. (2010, October 13). How to Poison a Small Country.

Retrieved October 11, 2012 from http://www.wired.com/ wiredscience/2010/10/how-to-poison-a-small-country/ 9. Blum, D. (2012, June 8). The Arsenic Diet. Retrieved October 11, 2012 from http://www.wired.com/wiredscience/2012/06/ the-arsenic-diet/ 10. Yedjou, C., Tchounwou, P., Jenkins, J. & McMurray, R. (2010).

Basic Mechanisms of Arsenic Trioxide (ATO)-Induced Apoptosis in Human Leukemia (HL-60) Cells. Journal of Hematology & Oncology, 3:28. doi:10.1186/1756-8722-3-28.

Figure 1: http://www.sxc.hu/photo/1391019 Figure 2: http://articles.latimes.com/2010/jun/27/image/la-igdiary-eco-20100627 Figure 3: http://commons.wikimedia.org/wiki/File:Arsenic_ trioxide.jpg

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Letters

A Fiery Debate on Western Forests Anna Rasmussen ‘13

The Pole Creek Fire burned hot and fast through dense that burned almost 1.5 million acres.4 Fires affect forests as well as pockets of beetle-killed trees when it erupted on September 9th of people’s daily lives, and their power and importance should not be this year, putting my hometown in central Oregon on guard. Four underestimated. cars were destroyed and several hikers were forced to quickly escape the area.1 Our neighborhood was put on pre-evacuation notice as Dealing with Fire the fire came within just a few miles. We have been evacuated in Forest fires are a natural part of many ecosystems. Lightning the past for encroaching fires, and luckily our neighborhood has is a major ignition source for forest fires, and has been causing come out relatively unscathed. Growing up in a community that fires long before humans started fighting them. Fire ecology varies deals with forest fires from forest to forest on a regular basis has and depends on the greatly influenced my typical climate of passion for the topic the region. Some because I have seen ecosystems are both the positive well adapted to fire and negative effects because, historically, of fire. I have seen fires occurred fairly beautiful plants frequently.

Other and baby trees that ecosystems have flourish after a fire as longer time spans well as the hundreds between fires and of thousands of thus have a different acres of dead forest, composition. Some waiting for the next plants depend on lightning strike. fire to open cones, The Pole Creek remove competitors, Fire has had both or keep tree densities ecological and at a healthy level economic impacts for that particular on the town of ecosystem. Common Figure 1: The Pole Creek fire burning near Three Creeks Meadow.

Sisters, Oregon. management practices This particular fire in dry Western forests burned intensely in areas with dense standing or fallen dead aim to reduce tree density, remove low vegetation that act as ladder trees, but also acted as an “underburn” over half of its burn area, fuels, and create open “park-like” stands.5 Techniques such as clearing out smaller fuel sources but not severely damaging full thinning, mowing, and controlled burns are used to reduce fuels. grown trees.2 While not ecologically devastating, the Pole Creek Today, it is widely accepted that human activities, such as Fire did negatively impact tourism in Sisters, harming the small fire suppression, logging, grazing, and climate change, are greatly businesses that depend on a successful summer season to keep altering forest ecosystems and often cause a loss of biodiversity. running. Plumes of smoke hung around town for over a month, Forest fire intensity and size has been increasing in recent decades raising health concerns. Senator Wyden visited Sisters after the due to human activity and climate change.6 In the West there is fire and discussed the loss of biofuels for the community.3 The a great debate raging about whether current fire prevention high school has been using slash (small cuts of wood including methods such as thinning and prescribed burns are actually logs and branches) from thinning projects as biofuel for heat, and beneficial for forests. A recent study by Mark Williams and Bill the popularity of biofuel in Sisters is growing.3 The fire burned Baker has fueled the debate on how to manage forests. Williams twenty-seven thousand acres of forest and cost $17 million to and Baker found that high intensity stand replacement fires in fight.4 In total, Oregon spent $250 million to fight fires this year dry forests were more “normal” than is currently accepted. Their

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Letters research uses land surveys from the late 19th century and tree ring data to make models of past fire history. Current management practices of dry forests are greatly influenced by the Southwestern model, which purports an image of open, park-like forests with high frequency, low intensity fires.5 Williams and Baker argue that this is an unrealistic image and management practices should be changed to reflect a more accurate understanding of fire history.

This publication raises an important issue: current policies are trying to make a one-size-fits-all solution for a multifaceted problem. The West has a great range of forests, low to high elevation, mixed to single-species stands, wet to dry forests that have adapted to different fire frequencies and intensities. No single management method will benefit all of these systems.

Fire: Past, Present, and Future Williams and Baker (2012) reject three common hypotheses about dry forests, including: 1. Dry forests are uniformly composed, have low tree density, and contain little undergrowth; 2.

High-severity fires are rare, low-severity fires are common; and 3.

High-severity fires have increased over the last century and a half.7 They state at the end of their paper: “If the goal is to perpetuate native biological diversity, it is appropriate to restore and manage spatial and temporal variability in forest structure and fire severity, including substantial areas of dense forests and high-severity fire, across dry western forests in the United States.”7 There are a great variety of dry ecosystems, some of which have had high-

severity fires historically. Using uniform management practices, which typically promote decreasing tree density and removing understory to prevent high intensity fires, may have other biological consequences. However, it is also important to consider that what was “normal” does not necessarily mean it is the way of the future.

The safety of human populations, protection of resources and carbon stores, and climate change will influence how we tackle forest management.

Another extensive study by Marlon et al. (2012) looked at 3000 years of charcoal data and combined historical descriptions of fire as well as small-scale studies of recent times to characterize fire activity. They found that fire activity was directly correlated with climate from 500CE until the mid 1800s.8 For the last 150 years, however, fire activity has not followed the typical pattern because of human activity such as land clearance, railroad construction, and fire suppression.8 This undermines the validity of William’s and Baker’s argument that the land surveys used in their study were of forests unaffected by human activity, but brings to light a more pressing issue. Humans have greatly reduced fire activity because of fire suppression, grazing, and altering forest ecology.

This has led to a “fire deficit” that has greatly altered forest makeup and could have far-reaching consequences in the future as our climate continues to change. Fuel buildup and changes in forest composition could greatly alter forest types throughout the West, especially as fires continue to increase in size and intensity.8

Figure 2: The Pole Creek Fire lighting up the night.

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Letters improper management leads to wasting biofuels and timber. If we Climate Change Forests are a natural resource for their inherent beauty, want forests to recover in our lifetime we need to recognize their biodiversity, habitat creation, recreational purposes, role in climate importance in climate control, as havens of biodiversity, and as control, and energy and raw material sources. Our way of life renewable and natural resources, and we must actively restore and depends on healthy forests. Management practices should consider manage them. historical trends in forests, but also the effects of climate change on forest ecology and composition. Climate greatly influence fire frequency and intensity. For example, Wild Fire Area Burned (WFAB) is significantly related to climate change but varies depending on ecosystem type.9 Fire activity in northern and mountain ecosystems is greatly impacted by hot and dry weather conditions, which deplete fuel moisture, increasing ignition probability and fire spread. On the other hand, in southwestern and arid ecosystems moist conditions play a more important role than warmer temperatures in fire seasons because moisture leads to more undergrowth that can easily dry and fuel fires in a drier year. This is a prime example of the vast differences between Figure 3: Standing dead trees from a previous fire contrast against the thick smoke from the Pole ecosystems and how a one-size- Creek Fire fits-all approach to managing and understanding fire behavior is not helpful. Climate is a major Maintaining healthy, safe, and diverse factor in fire behavior, and understanding climate effects on ecosystems Williams and Baker are not the first to criticize restoration specific ecosystems can help make better management practices, 9 efforts by the government. A recent study by Schoennagel and whether it is fuel reduction or adapting forests to climate change.

Nelson (2010) studied fuel treatments under the National Fire Forests are also an important part of climate regulation as Plan.

About 1% of Western forests have been treated under they sequester carbon from atmospheric CO2. As the climate the plan, costing $6 billion.11 Many treatments have occurred in changes and forest fires become more frequent, carbon loss in 10 areas in great need of restoration, but some have also occurred in western forests will increase. Post-disturbance restoration of areas without uncharacteristic fuels buildup.11 These researchers forests and management practices that facilitate forest adaptation 10 point out the danger of focusing solely on fuels reduction and to climate change are increasingly necessary. Forest composition ignoring the role of climate change and the growing forest-urban has greatly changed in many Western forests, and in some cases interface.

The effectiveness of fuel reduction in areas that need overcrowding occurs, weakening trees’ resistance to disease, pests, it should not be overlooked, however.

Fuel treatments have been and fire. Having worked in the woods with the forest service, I very effective at reducing tree mortality due to fire as shown in a have seen a startling number of dead or dying forests. These dead study of the Tripod Fire by University of Washington and the US trees are often a result of mountain pine beetle infestations or 12 Forest Service.

Forest thinning and fuel treatments also allowed past intense fires. Dying forests are a major problem for several firefighters to bring the Pole Creek Fire under control when it was reasons. Accumulation of down and dead woody material creates closest to the town of Sisters and mitigated damage from the fire.2 large amounts of fuel for future fires to rip through and slow Reducing fuel availability has a place in forest management and the reforestation process. Forests are also an important source should continue to be used to ensure healthy forests and public of carbon storage and trees are primary producers in many ecosystems. Trees are also an important natural resource, and safety.

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Letters Human activity has greatly altered the structure of our forests.

Now we must find the delicate balance between allowing fire to play its natural role in ecosystems, helping forests get back to a state where they can cope with fire in some cases, and maintaining safety for people in the surrounding area. This can only happen through accurate and encompassing research, an informed and educated public, and proactive management of our forests.

References 1. Cornelius, J. (2012, September 11). Fire turns Bend couple’s weekend hike into adventure. The Nugget Newspaper. Sisters, OR, USA. Retrieved from http://www.nuggetnews.com/main.as p?Search=1&ArticleID=20178&SectionID=130&SubSectionID =235&S=1 2. Fire has varied impact on forest. (2012, September 25).The Nugget Newspaper. Sisters, OR, USA. Retrieved from http:// nuggetnews.com/main.asp?SectionID=130&SubSectionID=235 &ArticleID=20251&TM=78523.42 3. Cornelius, J. (2012, October 16). Senator Wyden talks energy in Sisters. The Nugget Newspaper. Sisters, OR, USA. Retrieved from http://www.nuggetnews.com/main.asp?Search=1&ArticleID=20 327&SectionID=7&SubSectionID=88&S=1 4. Burns, J. (2012, October 9). Oregon’s long, costly fire season nears end. KTVZ. News website. Retrieved October 28, 2012, from http://www.ktvz.com/news/Oregon-s-long-costly-fireseason-nears-end/-/413192/16922632/-/on6b31z/-/index.html 5. Guerin, E. (2012, September 17). Fire scientists fight over what Western forests should look like. High Country News. Retrieved from https://www.hcn.org/issues/44.16/fire-scientists-fightover-what-western-forests-should-look-like 6. Westerling, A. L., Hidalgo, H. G., Cayan, D. R., & Swetnam, T. W. (2006). Warming and earlier spring increase Western U.S. forest wildfire activity. Science, Vol, 313, 940–843.

7. Williams, M. A., & Baker, W. L. (2012). Spatially extensive reconstructions show variable-severity fire and heterogeneous structure in historical western United States dry forests. Global Ecology and Biogeography, 21(10), 1042–1052. doi:10.1111/ j.1466-8238.2011.00750.x 8. Marlon, J. R., Bartlein, P. J., Gavin, D. G., Long, C. J., Anderson, R. S., Briles, C. E., Brown, K. J., et al. (2012). Long-term perspective on wildfires in the western USA. Proceedings of the National Academy of Sciences, 109(9), E535–E543. doi:10.1073/ pnas.1112839109 9. Littell, J. S., McKenzie, D., Peterson, D. L., & Westerling, A. L. (2009). Climate and wildfire area burned in western U.S. ecoprovinces, 1916–2003. Ecological Applications, 19(4), 1003– 1021. doi:10.1890/07-1183.1 10. Raymond, C. L., & McKenzie, D. (2012). Carbon dynamics of forests in Washington, USA: 21st century projections based on climate-driven changes in fire regimes. Ecological Applications, 22(5), 1589–1611. doi:10.1890/11-1851.1

11. Schoennagel, T., & Nelson, C. R. (2010). Restoration relevance of recent National Fire Plan treatments in forests of the western United States. Frontiers in Ecology and the Environment, 9(5), 271–277. doi:10.1890/090199 12. Prichard, S. J., Peterson, D. L., & Jacobson, K. (2010). Fuel treatments reduce the severity of wildfire effects in dry mixed conifer forest, Washington, USA. Canadian Journal of Forest Research, 40(8), 1615–1626. doi:10.1139/X10-109 Figure 1: Taylor, J. (Photographer). (2012). Taken off the Cold Springs Turn Off [Photograph], Retreived October 28, 2012, from: http:// www.nuggetnews.com/main.asp?SectionID=129&TM=37048.42 Figure 2: Wester, J. (Photographer). (2012). Untitled [Photograph], Retreived October 28, 2012, from: http://www.nuggetnews.com/ main.asp?SectionID=129&TM=37048.42 Figure 3: Iraci, T. (Photographer). (2012). Untitled [Photograph], Retreived October 28, 2012, from: http://www.firehouse.com/ news/10782531/oregons-pole-creek-fire-continues-to-grow

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Organic Chemistry for Dummies The Survival Manual for Organic Chemistry Courses in Amherst

Xiao Xiao ‘16

Try this question: how many isomers, including stereoisomers, does a compound of C8H18 have?

Sounds hard? I agree wholeheartedly. Isomers: Organic chemistry is known for its breadth, Compounds with depth and complexity. Hence it has earned same molecular formula but the dubious honor of being a killer class different in any university or college (according to structural formulas rumors, students come out crying from some organic chemistry exams). I will break down the reasons why organic chemistry is hard and share with you some of the strategies I have adopted while preparing for my exams.

Organic chemistry and why is it hard – in general: Organic chemistry is the study of carbon-based compounds.

We can expect to encounter topics such as preparations, Characterization: characterizations, syntheses and Determination of structure compound properties. For most of the organic compound via spectroscopic techniques us, the transition between Chem161 to Chem-221 proves to be daunting because of issues such as lack of preparation and the requirement of a different mindset. However, once you have managed to deal with the following three concerns, you will see a marked improvement in Wait what? A freshman your understanding and giving out suggestion mastery of the content. on a course he has yet to take? Sounds really Difficulty 1: legit: Memory I am a freshman from Singapore, The opening where the high schools follow question about C8H18 the British General Certificate of seems to require a lot of Secondary Education (GCSE)memory. First, there is Advanced Level curriculum. We are the issue of memorizing expected to learn organic chemthe definitions of terms istry courtesy of the curriculum. such as isomers and In addition, I have taken some stereoisomers. Next, we university-level chemistry courses need to understand the before, where organic chemistry chemical makeup of an knowledge is a requirement. octane (C8H18), which requires mastery of the concept of nomenclature as well. Finally, we have to make sure that while drawing out the variations we do not miss or repeat isomers.

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Although just memorizing all of the isomers is certainly one way to get a correct answer, that is neither the most efficient nor the recommended method. Organic chemistry should not be studied by memory alone, as there is simply too much material to remember. The beauty and intricacy inherent in organic chemistry will be gone if we proceed via a brute-force memorization path.

If we spend a little time pondering, we will notice that by capitalizing on the ‘systematicity’ of the problem solving there is, in fact, minimal memorization involved. For instance, we can start with the straight-chain 8-carbon variation, which is simply octane.

Then we can go on to 7-carbon chain with a methyl substituent somewhere. This is also a nice time to start considering stereoisomers since Chiral center: chiral centers will start to show up. An atom that forms a non-superimposable Hence, we can transform a chemistry spatial mirror image problem into a math problem. Of of itself by connecting course we will need our chemistry to different atoms via knowledge to eliminate repetitions but bonding we have just reduced the amount of information we need to remember. As succinctly put into words by a current organic chemistry student: “if you can understand the concepts, there is no need to memorize.”

However, some basic memorization cannot be avoided. This is unfortunate but some techniques can help: specifically, the idea of compartmentalization and categorization.

These are just fancy terms for breaking down the materials into big chunks with common characteristics or similarities. We can

Figure 1: A partial mindmap framework with limited compounds

Letters remember the other terms in the same category more efficiently if we manage to memorize one of them due to their similarities. It is going to be tough even for someone with photographic memory. Therefore, in the spirit of categorization and compartmentalization, a mind-map of reaction flow and reaction scheme will simplify the task significantly. Group organic compounds with similar functionality or easily transformable functional groups in a cluster so that they help in the memorization process. Furthermore, the mindmap production process itself is a good way to review the materials regarding reactions and syntheses.

Difficulty 2: Different Figure 2: Another framework. Writing out the full structural formula is recommended for better skill set visual perception.

The first shock that we In short, some people are just naturally adept at manipulating may encounter is the lack of mathematics involved, unless one considers counting the number a molecule in their mind. For most of us, a model set comes in of atoms for each element. As simple as that sounds on paper, handy. Once we have done enough problems with the help of organic chemistry derives its notorious reputation as a “weeder” a model set, manipulating the molecule in the mind will not be class for that single reason. The lack of math is replaced by a as difficult. However, it is important that while manipulating the requirement for a completely different skill set, which includes 3D physical models, we engage in the exact same process in our mind. visualization and manipulation of molecular models, derivation of The models are there only as a guide. It will be meaningless if isomeric structures, and spectra interpretation. Once the second you only perfunctorily twist and turn the models and copy down organic chemistry course arrives, the skill set will then grow to the final structure in my notebook. The crux lies in the thinking include synthesis and retro-synthesis, interconnection with process as it conditions and familiarizes your brain so that by the time exams start, you will be confident even without the models. biochemistry, and most importantly, mechanism drawing.

Isomerism branches off into different types of isomerism If all this sounds unfamiliar to you, please do not worry. You right from the start, such as structural, functional and optical are not alone. The lack of prior exposure to these skills is exactly isomerism. In addition to the systematic approach explained earlier, the reason why organic chemistry can be so hard to appreciate and they have a certain hierarchy, which can be helpful. For example, conformational isomerism is a subset of stereoisomerism. It understand. is easier to memorize concepts like isomerism if you can figure We definitely need a different approach towards organic out their relative positions on the hierarchy. Alternatively, more chemistry questions as compared to questions from Chem-161 exposure helps (get started on those additional problems at the or even 155/151. Organic chemists speak in a foreign language back of textbook or from the Q Center.) with a handful of letters such as C, H, O, N and P coupled with Spectra-reading refers to the some lines and arrows. Organic chemistry questions, in general, NMR: Nuclear magnetic no longer have answers that can be derived easily. As Professor interpretation of various spectra, resonance: A technique of Bishop—one of the chemistry professors at Amherst College— such as those of NMR, IR, UV and using the magnetic nuclei has stated, it is often necessary to start with some scratch work mass spectrum (do not worry if of certain elements to emit to see where the initial approach leads. Thus, professors are often those sound like some FBI codes electro-magnetic radiation eager to see students with the courage to explore and experiment. instead of organic chemistry at for the purpose of spectra the moment). Primarily, we hope production Read: prepare a lot of paper. to identify a compound and its structure by using the aforementioned techniques. Hence those Sub-section: Learning the specific skills The ease of mastering 3D visualization and orientation of four spectra need to be read in tandem; i.e., when you are stuck molecules is determined by each student’s ‘affinity’ for this skill. with the NMR, switch to the IR spectrum with whatever details you already have. It is common that the hints and clues from one The Amherst Element, Vol 5, Issue 1. Fall 2012

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Letters spectrum will trigger something more from another spectrum.

That, in turn, will prompt further revelation of the structure when brought back into the original spectrum.

Reaction synthesis and retro-synthesis have their foundations in the different types of organic Retro-synthesis: reactions. In short, you are supposed Question solving techto design a kind of recipe to prepare nique of transforming an end product. Chemistry lecturers target molecules of typically impose several conditions synthesis into smaller regarding the permissible starting and simpler precursors materials just to increase the difficulty by working backwards and add some fun. Those mind-maps that cross-link different reactions and compounds together will be a wonderful study tool. We will often notice recurring patterns in the synthesis route towards certain classes of compound after some practice. That is a sign that we have truly internalized and mastered the content. Again, in order to discover those patterns, more practice questions are needed.

The connections to other disciplines under the chemistry umbrella may appear intimidating but as long as we remember that it is still chemistry, we will be fine. The underlying chemical principles do not change, which means that the structure of a particular compound always grants it its particular property. This holds true even if we encounter questions involving amino acids, lipids or carbohydrates. Zoom in on the chemical relationship between functional groups and structures.

Finally, mechanism drawing is yet another ‘affinity’-type skill that may make life seem unfair. Some general rules to consider include electron flow and the role of catalysts. Electrons always flow from electron-rich regions to electron-poor regions. Finally, they may Electron sink: or may not end up in an electron sink. As Molecules or atoms a result, if there is any counter-intuitive that can accept a step in your proposed mechanism, you lone pair of electrons may wish to go back and check before proceeding further. It is best to illustrate the role of a catalyst in an example. If an acidic catalyst is added for a particular reaction— let’s say ester hydrolysis—and you are supposed to provide a mechanistic explanation, there should be minimal negative charges in your proposed intermediate steps in order to reflect the acidic environment. Furthermore, the Carbonyl carbon: first step of the overall mechanism The carbon in the funcshould always involve the acid, which tional group of C=O, the in this case means the protonation carbonyl group of the carbonyl carbon.

Difficulty 3: Time Labeling time requirement as something particular to organic chemistry is kind of biased since practically all courses at Amherst require considerable time input. However, the importance of practicing organic chemistry diligently on a daily basis cannot be stressed enough. All new skills require mastery and mastery only

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comes from consistent practice. Practice takes time. As Professor Kan compared the studying of organic chemistry to that of sports practice, time is a factor that has a direct relation to your grade.

Just as a new tennis player can only hope to improve by practicing every day, organic chemistry too relies on an accumulation of effort and experience.

Technically, if time is fixed as a constant, the only way to increase productivity is by being more efficient. In terms of organic chemistry, that translates to being fully focused in lecture. Being focused in lecture will have an effect on your material appreciation, absorption and retention. Thus you will often experience lots of a-ha moments when you hit the books. On the contrary, if you let your mind wander off while the lecturer is speaking, you have to make up that time dedicated for material understanding in your preparation time. That takes more time than having somebody who is well versed, such as the professors, explaining the concept to you while you are alone. In addition, that time during preparation could have been better used for reinforcement of understanding.

The 10 cardinal rules: 1. Be brave and explore – courtesy of Prof. Bishop 2. Be disciplined – courtesy of Sam Ubersax ‘15 3. Prepare for war – courtesy of Sam Ubersax ‘15 4. Try to make organic chemistry enjoyable – courtesy of Hyunsun (Sunnii) Roh ‘15 5. Understand why your answer is correct/wrong – courtesy of Hyunsun (Sunnii) Roh ‘15 6. Complete a mind-map that works for you 7. Adopt a new mindset towards learning organic chemistry 8. Always zoom in onto the area-of-interest when approaching an organic question 9. Establish links between different organic topics since they cannot stand alone 10. Read this article completely p.s. The correct answer to the question on C8H18 is 24.

Acknowledgements I would like to thank Professor Anthony Bishop, Sam Ubersax and Hyunsun Roh for their support. They have been wonderful interview subjects. In addition, I would like to thank Ms. Magdalena Zapedowska from the writing center for her advice and guidance in the editing process. Finally, I would like to thank the Amherst Element members for their comments and suggestions for this article.

Reference Klein, David. Organic Chemistry. 1. Baltimore: Wiley, 2012. 1014.

Print.

Summer Research

A Summer of Research and Fun at

Harvard Stem Cell Institute

Haneui Bae ’13

This summer I did a 10-week summer internship program at Harvard Stem Cell Institute. To summarize this very long account in one word: Amazing. If you want to know why, please read on. If you don’t know anything about stem cells, also read on.

My Encounter with Stem Cells As some of you may know already, this year’s Nobel Prize in Physiology or Medicine was awarded to Shinya Yamanaka for the “discovery that mature cells can be reprogrammed to become pluripotent.”1 This Nobel Prize has more meaning for me than any other years, because I had just spent the past 10 months studying Yamanaka’s seminal paper in 2006 and learning all about the new field of induced pluripotent stem (iPS) cells that he pioneered. In June, people in my Harvard lab actually ran into Yamanaka at the ISSCR (International Society for Stem Cell Research) conference in Japan. They took a picture with him and proudly displayed the photo as their profile pictures on Facebook throughout the summer. iPS cells are a special type of stem cells. Many of you probably have heard of embryonic stem (ES) cells. ES cells are a population of cells in an embryo of a developing organism that has the potential to differentiate into any type of cells in the body, such as muscle cells, skin cells or neurons. This ability is called pluripotency. As the embryo develops, however, the cells lose their pluripotency. Or people thought so until Yamanaka discovered in 2006 that he can reprogram terminally differentiated skin cells back into the pluripotent stage by inducing the expression of four genes, now called Yamanaka factors, in the cell.2 This cell is now the iPS cell.

But less than a year ago, I did not know anything about stem cells, let alone Yamanaka or the iPS cells. Last semester, I took a Smith College course called “Stem Cells and their Amazing Potentials,” taught by Professor Michael Barresi. In the class we had Skype conferences with many leading stem cell researchers around the nation, including Dr. George Daley of Harvard Stem Cell Institute and Dr. Rudolf Jaenisch of the Whitehead Institute, and created an educational 20-minute documentary as a final project. Despite the numerous hours of sleep I lost to keep up with its intense workload, it was one of the best classes that I have taken during my years at Amherst. (I definitely encourage everyone to take it!)

The class focused on the implications of this new iPSC technology. The technology has tremendous potential not only for medicine and regenerative therapies, but also more immediately for the study of disease pathology.3 The study of human disease has been limited due to the unavailability of human experiments and the failure of animal models to properly mimic human disease.

Now we can take easily accessible skin cells from patients with different diseases, reprogram them into iPS cells, differentiate them into any cell type we want, and study the progression of the disease in a petri dish. Throughout the semester we read about various ways scientists across the nation have taken this technology and applied it to diseases such as autism and Parkinson’s disease.4,5 This sparked an interest in me. I had been reading about these amazing accomplishments, but I wanted to see it for myself.

I learned about the Harvard Stem Cell Institute internship program from an Element article a few years ago, written by Christina Wright ’11 (“Turning Lead into Gold: The Alchemy of induced Pluripotent Stem Cells” Volume 3, Issue 1. Contact the Element to read this article!)

Schier Lab, Eggan Lab, and My Project Because of my interest in Neuroscience and iPS cells, I was accordingly placed in a lab where I could pursue both of my passions. My PI (Principal Investigator), Alexander Schier, uses patient iPS cells to study narcolepsy, a sleep disorder characterized by sleep attacks and abnormal sleep patterns. Narcolepsy is caused by death of a population of hypothalamic neurons that secrete neuropeptide hypocretin (also known as orexin).6 I worked with a postdoctoral fellow named Florian on this project. (And because he was also part of the Eggan lab, which works much more extensively with iPS cells, I spent much of my time in the Eggan lab as well.)

Specifically, Florian was working on developing a protocol to differentiate iPS cells into specific types of hypothalamic neurons. The hypothalamus contains diverse populations of neurons that regulate fundamental physiological processes of the body, such as feeding, sleeping, and energy expenditure.7,8 These neuron populations secrete different kinds of neuropeptides, such as melanin-concentrating hormone (Mch), hypocretin (Hcrt), and proopiomelanocortin (Pomc). Loss or abnormal function of these neurons can lead to human diseases like obesity and narcolepsy.6,9 It has been difficult to study the mechanisms of diseases associated with the hypothalamus, largely because of the inaccessibility of its neurons. However, with iPSC technology, we can now take a skin cell donation from a narcoleptic patient, and reprogram it into an iPS cell line. The next challenge then is how to direct the differentiation of these iPS cells into hypocretin-secreting hypothalamic neurons. Florian was working on this protocol when I came into the lab this summer. He experimented with different growth conditions for his human embryonic stem (hES) cell cultures to see which condition best mimicked the actual developThe Amherst Element, Vol 5, Issue 1. Fall 2012

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Summer Research Antibody

Merge

PomcGFP EBs

PmchCre-rbMch

HcrtGFP-msHcrt

DATCre-rbTH

Reporter

Figure 1: Different transgenic reporter mouse brains sections were stained with their respective antibodies. I found that the reporter expressions were co-localized with antibody staining, confirming the correct targeting of the reporter construct. mental environement, and produced the most hypocretin neurons.

The ultimate goal of the lab is to study the mechanism of disease in patient iPSC-derived hypothalamic neurons, but in order to get to these “exciting experiments,” he had to create the set of necessary tools.

My project over the summer was to help him create these tools. The differentiation in cell cultures does not happen uniformly. To identify the neuron types of interest in vitro without killing and staining the cells with an antibody, researchers use transgenic ES cell lines expressing a reporter, like GFP and tdTomato, under cell-type specific promoters. Florian had several transgenic mouse reporter lines for different neuropeptides like Pomc, Hcrt, and Pmch. I used immunofluorescence staining to confirm the correct expression of the reporters in the mouse brain sections. Then I cultured the ES cells isolated from these mice in different chemical conditions to differentiate them into hypothalamic neurons.

I was able to quantify and confirm the reporter and antibody colocalization, and successfully differentiated one Pomc-reporter mES cell line into reporter-positive cells with clear neuronal morphology. (Figures 1 and 2)

Stem Cells Beyond I thoroughly enjoyed my project and the fact that I worked in such close proximity to iPS cells. However, as I interacted with other people in my lab and other students in the program, I quickly

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Figure 2: After 26 days of differentiation, I found positive reporter expression (green) in cells with clear neuronal morphology.

Blue is a nuclear stain.

realized that there is a huge variety to stem cell research. Here, I want to describe some of the projects pursued by my friends over the summer.

Teddy – Eggan Lab Teddy’s project was a classic example of iPSC disease modeling. The Eggan Lab uses the iPSC technology to study ALS (amyotropic lateral sclerosis). The lab has created various iPSC lines from patients with familial cases of ALS, and had successfully differentiated them into lower motor neurons, cell types that are affected in ALS. Teddy’s project was to study the altered mitochondria trafficking in the iPSC-derived motor neurons using live imaging techniques. The iPSC technology allowed him to easily observe how the disease develops and affects the function of human motor neurons, usually difficult to obtain for study.10 Sam – Domian Lab Teddy and I worked with neurons mainly, but there are many other stem cell research focusing on other cell types as well. My awesome roommate Sam worked in lab at Mass. General Hospital (MGH), working with cardiomyocytes, or heart cells. Many labs have tried to differentiate ES cells or iPS cells into cardiomyocytes, which can then be used for disease modeling or even heart transplantation for cardiac patients. However, under standard culture conditions, ES cell-derived cardiomyocytes are immature, resembling fetal heart cells. Recently her lab had found a protein whose overexpression may promote these immature heart cells to

Summer Research undergo further differentiation and become fully mature cardiomyocytes. Her project was to test this hypothesis.10 Sara – Carmargo Lab So far I have only discussed pluripotent stem cells (ES and iPSC cells) but there are other types of stem cells that are not pluripotent, but multipotent. Multipotent cells can give rise to only certain types of cells. For example, hematopoietic stem cells can give rise to various types of blood cells, but not neurons or skin cells. Multipotent cells exist in fully developed organisms (a.k.a. us) and regenerate our tissue when it is damaged. Sara worked with hematopoietic stem cells in the Carmargo lab at Children’s Hospital Boston. Sara worked on discovering novel factors that promote hematopoietic cell expansion, using FACS (Fluorescence-activated cell sorting) analysis.10 Katie – Chaikof Lab Stem cells are also used for engineering of medical devices.

Katie worked in the Chaikif lab at Beth Israel Deaconess Medical Center, which works on tissue engineering using stem cells. Specifically, Katie’s project involved developing a hernia patch seeded with human mesenchymal stem cells. Stem cells will help the patch integrate more quickly and robustly with the host tissue, decreasing the chances of infections and high hernia recurrence rates, common following abdominal wall repairs.10

Figure 3: HSCI interns took a day trip to the Spectacle Islands one weekend. We played tag football on the hill and came down to the beach to cool down. From left, Sara, Yucheng, Maureen (program coordinator), Frankie, and Xiang are spelling out the word HSCI. - Photo Credit Frankie Wong

The Internship Beyond As amazing as the lab work was, my summer experience at HSCI was so much more than what I did in the lab. I made friends from all around the country. The program had a diverse range of interns, from rising sophomore to seniors, neuroscientists to engineers, and from variety of schools around the country. Despite the short time we had to get to know each other, we have become surpringly close. HSCI hosted many social events where we could talk and have fun outside of the lab. We watched the London Olympics Opening Ceremony together, had several potlucks, and took a daytrip to the Spectacles Islands. (Figure 3) There were weekly morning classes taught by Willy Lensch, the director of the program and an amazing harmonica player.

The classes covered the general history of stem cell research as well as practical skills like how to efficiently read a scientific paper.

On some mornings, guest speakers came to talk about their life and research.

One of the most inspiring guests was Brooke Ellison. Brooke was paralyzed from the neck down after a car accident at 11. Overcoming her difficulties, she has graduated from Harvard University with a magna cum laude and since then become an inspiration for many. She now is now working on stem cell research advocacy and education. When we talked to her over Skype, I was struck by how cheerful and hopeful she was. Her personal experiences and the stories of others like her were a great reminder of the human faces of stem cell research.

References

Acknowledgements Great thanks to my HSCI friends who helped me write about their research projects, and Frankie for the photo above!

1. http://www.nobelprize.org/nobel_prizes/medicine/laureates/2012/# 2. Takahashi, K. & Yamanaka, S. Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell, 126: 663-676 (2006).

3. Zhu, H. et al. Investigating monogenic and complex diseases with pluripotent stem cells. Nature Review Genetics, 12: 12:266-275 (2011).

4. Marchetto, M.C. et al. A model for neural development and treatment of Rett Syndrome using human induced pluripotent stem cell. Cell, 143: 527-539 (2010).

5. Solder, F. et al. Parkinson’s Disease Patient-Derived induced Pluripotent Stem Cells Free of Viral Reprogramming Factors. Cell, 136: 964-977 (2009).

6. van den Pol, A. Narcolepsy: A Neurodegenerative Disease of the Hypocretin System? Neuron, 27: 415-418 (2000).

7. Kim M.S. et al. Hypothalamic localization of the Feeding effect of Agouti-related peptide and a-melanocyte-stimulating hormone. Diabetes, 49: 177–182 (2000).

8. Sakurai, T. The Neural circuit of orexin (hypocretin): maintaining sleep and wakefulness. Nature Neuroscience, 8: 171-181 (2007).

9. Dhillo, W.S. & Bloom, S.R. Hypothalamic Peptides as drug targets for obesity. Current Opinion in Pharmacology 1: 651-655 (2001).

10. Abstract Brochure of the 2012 Harvard Stem Cell Institute HIP Symposium, August 9, 2012, Cambridge, MA.

My experiences at HSCI were amazing, and it definitely shaped what I want to do after graduation. I’m sure you will enjoy it as much as I did. I encourage anyone to apply for the internship!

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SKIN TO NEURON CONTROLLING NEURONAL FATE Kevin Mei ‘16

Introduction to Seam Cells Most people think of differentiated cells as being in their final state. They are stuck in their cell type, be it neuron, muscle, skin, etc. and won’t divide anymore. Here, I describe an interesting phenomenon in the model organism Caenorhabditis elegans in which a skin cell will give rise to a neuron. C. elegans are small, transparent nematode worms that are ideal for genetic manipulation because their entire genome has been sequenced and a fate map is known for every one of its cells.1 This means that from the fertilized egg onwards, scientists know how every cell will divide and into what cell type each will differentiate into.

Figure 1: Upon hatching, C. elegans have 10 seam cells on a lateral side: H0-H2 in the head, V1-V6 throughout its midbody, and T in its tail.

to stem cells.

The V5 seam cell lineage V5.p produces an anterior daughter cell that becomes a neuroblast (see Fig. 2). Further divisions in the V5 lineage give rise to the PVD and PDE neurons of the C. elegans and supporting glial cells. PDE is a neuron that senses the presence of bacteria and slows the worm down, thus letting it know when it should feed. [3] PVD responds to mechanical stimulus and detects pain,4 and is responsible for the worm’s response to harsh touch and extreme temperatures. Glial cells are cells that support neurons.

Collectively, PDE, PVD, and the glial cells are referred to as the postdeirid (Fig. 3).

Over high school, I did research on the seam cells in the Hobert Lab at Columbia University Medical Center. My research used genetic techniques to isolate mutants in which PVD or PDE hadn’t formed. First, I used the chemical ethyl methanesulfonate (EMS), which causes mutations in DNA, to create many worms that were missing the postdeirid. I isolated these worms and then tried to find which genes had been mutated to cause loss of the postdeirid. Because the latter wasn’t accomplished, I won’t present the research results. However, there are several genes that are already known that determine whether the seam/skin cells will divide and become neurons. Let’s look at these mechanisms to

C. elegans have a special type of skin cell known as seam cells.

C. elegans have a row of seam cells on their left and right lateral sides. Upon hatching, the worms have three pairs of seam cells in the head (H0-H2), six throughout the mid-body (V1-V6), and one in the tail (T) (see Fig. 1). Seam cells are functionally differentiated skin cells and perform functions similar to the hypodermis, its layer of skin, such as secreting cuticles. They are interesting because they behave like stem cells in their self-propagating division pattern.2 Seam cells divide to give an anterior (V.a) and posterior (V.p) daughter cell. The anterior cell becomes a hypodermal cell that joins the hpy7 syncytium, a layer of hypodermal cells, while the posterior daughter becomes another seam cell.

Indeed, in this way, the division of the seam cells contribute to the growth of C. elegans: one daughter cells adds to the skin layer, while the other daughter becomes another seam cell that will continue dividing.

Seam cells will also give rise to neuroblasts, which are neuron precursor cells. Unlike fully differentiated neurons, neuroblasts still have the ability to divide.

This ability of seam cells to give rise to different cell Figure 2: The lineage of V5. Anterior daughter are denoted with a V.a and types while self-propagating is what makes them akin posterior daughters are denoted with a V.p.

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Letters human fibroblast cells (which are already differentiated) by using genetic techniques and introducing four transcription factors responsible for “stem cell” type.5 The problem is that it’s hard to specify which cell type a stem cell should differentiate into. The hope is that by learning some of the genes responsible for neuronal fate, we may able to use genetic techniques to turn a skin cell directly into a neuron. lin-32 is one major transcription factor that plays a role in neuronal fate.6 Keeping in mind that in null mutants, the normal gene no longer expresses itself and thus, its normal function is Figure 3: A C. elegans worm with the postdeirid present. PVD is shown in green and PDE is no longer in effect- worms with null shown (faintly) in red right next to PVD. These are the cell bodies- axons are too thin to be mutants of lin-32 are shown to be missing the postdeirid, indicating that seen. I isolated mutant worms in which these neurons are missing. one of the normal functions of lin32 is to specify that “this cell will be a understand how the phenomenon of skin to neuron differentiation neuroblast.”

Further research has shown that V5.pa never becomes may occur. a neuroblast, but becomes a hypodermal cell—the “normal” fate Regulating the V5 cell fate: transcription for anterior daughters of seam cells.

LIN-32, the protein product of lin-32, forms a dimer with factors another protein HLH-2 to regulate neuronal cell fate.7 Meanwhile, Transcription factors, proteins that control which genes are another transcription factor, lin-22, represses lin-32 in all the V expressed or not expressed, are considered the most important cells except V5. Because of this activity, the postdeirid is only regulators in genetics. Transcription factors include the Hox genes, formed in V5.

In mutants of lin-22, lin-32 is no longer repressed which determine the patterning and type of body structure in in V1-V4 and the seam cells may all adopt the same lineage as V5, humans and other vertebrates. If we’re going to investigate how developing postdeirids (Fig. 4). neuronal fate is controlled, and then how neuronal fate arises from We see that a set of factors work together in regulating cell our differentiated skin cells, we’ll most likely have to focus on and fate; we need to have a more complete or general picture of work with transcription factors. genetic interactions to understand neuronal differentiation. Like Yamanaka, who recently won the 2012 Nobel Prize for Yamanaka et al.’s stem cells, it’s probably only a few “necessary” his work, et al. was able to induce pluripotent stem cells, cells genes (perhaps lin-32) that seam cells have which make them that have the ability to differentiate into other cell types, from “different” from “regular” skin cells. Identifying and understanding those genes will enable us to Figure 4: In V1, the seam cells divide to continiously give hypodermal cells that contribute to the worm’s hypodermis. In lin-32 mutants, the V5 lineage adopts the same fate as the V1 lineage because lin-32 is no longer functioning to differentiate the cell different from the other V cells. lin-22 suppresses lin-32. In lin-22 mutants, V1-V4 may all adopt the same fate as V5 and form postdeirids because lin-32 is now functioning in all the V cells.

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Letters

Figure 5: Heterochronic mutants can cause repetitive lineages such as one shown above. V5.pp adopts the fate of the anterior daughter and this same division continues, creating extra postdeirids. know why seam cells, again functionally differentiated skin cells, are able to give neurons. My research was still dealing with the “indentification” part.

Heterochronic genes and timing What makes skin cells turn into neurons? Well, in the V5 lineage, the change happens only after a certain number of divisions, implicating timing as a factor. Heterochronic genes are genes that regulate the timing of divisions. C. elegans hatch at L1 stage and go through four larval stages (L1-L4). lin-28 is a heterochronic gene responsible for the proper timing of entry into L2 phase. Mutations in lin-28 cause worms to skip L2 and go directly into L3 stage.8 Since PVD and PDE are formed in L2, mutants of lin-28 are missing the postdeirid. There are many other such genes with varying effects on the seam cells. Some cause early differentiation of the seam cells while other delay it. Some cause repeats of divisions so that extra cells are formed (Fig. 5).

Anothing control of timing is when genes are turned on, rather than the effects of genes on timing. The gene mab-5 is activated several times through the life span of a C. elegans worm to direct neuronal fate. mab-5 itself also specifies neuronal fate like lin-32 but early expression of mab-5 actually inhibits postdeirid formation.9 Intercellular signaling An example of communication between cells is Wnt signaling.

Wnt signaling in C. elegans polarizes seam cells and controls their asymmetric divisions.10 It lets the seam cells know which will be the anterior daughter and which will be the posterior daughter.

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We can see how this is important as only anterior cells become hypodermal cells while posterior daughters become seam cells.

Also, the postdeirid with PVD and PDE both come from anterior daughters. When polarity is confused, strange scenarios occur (Fig. 6): Wnt mutants often have ectopic neurons, meaning they are out of place, missing neurons, or extra neurons.

In a study by Wrishnik et al., it was found seam cell contact is necessary for postdeirid development.9 When cells fail to touch, Wnt signalling is activated to turn on the Hox gene mab-5, previously mentioned, whose premature expression surpresses the postdeirid.

In both timing and intercellular signaling, we want to know what genes are activated or deactivated when cells signal to each other or after a certain stage. These are the genes that enable seam cells to produce neuronal cells.

Significance of V5 cell fate regulation Stuyding the V5 cell fate is interesting because it is an exception to differentiation: seam cells are still able to change their cell fate.

Understanding this event helps us understand differentiation in general. Yamanaka et al. found that a few genes make stem cells, “stem cells.” What makes a neuron, a “neuron?” And with this knowledge, can we induce neurons from stem cells or already differentiated cells?

Knowing how genes control differentiation and neuronal fate helps us gain a better understanding of developmental defects, neurodegenerative diseases, and stem cells. There are applications to cancer, which results from the failure of cells to differentiate properly and therefore proliferate excessively.

Letters

Figure 6: An example of when anterior/posterior polarity is confused. The posterior cell (V5.pap) that would usually produce glial cells now adopts the fate of the anterior cell (V5.paa) and produces extra PVD and PDE instead.

Moreover, it would be interesting to be able to turn cells of one type into another, such as skin cells, which are plentiful, into neurons, which are difficult to regenerate and more complex in terms of structure.

Genes, and genes for differentiation especially so, are conserved throughout species. Hox genes, transcription factors responsible for patterning, are ubiquitous. Genes that specify cell fate in C. elegans have their homologs (genes related by origin) and analogs (genes related by function) in the fruit fly D. melanogaster, mice, and humans. The mechanisms and models found in C. elegans can be (and are) applied to us. I’ve focused on the seam cell V5, and even then, have focused on only a few genes and mechanisms that control V5’s cell lineage. It may take bioinformatics to keep track of all the variety of factors that control neuronal fate and how they relate and interact, but it should be kept in mind that it takes only a few pieces to solve big problems.

References 1. Sulston, J. E. and H. R. Horvitz. “Post-embryonic cell lineages of the nematode C. elegans.” Developmental Biology (1977): 56, 110-156.

2. Altun, Z.F. and D.H. Hall. Epithelial system, seam cells. Ed. Laura A. Herndon. 14 June 2010. 1 September 2011 <http:// wormatlas.psc.edu/hermaphrodite/seam%20cells/mainframe. htm>.

3. Bounoutas, Alexander and Martin Chalfie. “Touch sensitivity in Caenorhabditis elegan.” Pflugers Arch (2007): 691-702.

4. Smith, CJ, et al. “Time-lapse imaging and cell-specific expression profiling reveal dynamic branching and molecular determinants of a multi-dendritic nociceptor in C. elegans.” Developmental Biology (2010): 18-33.

5. Takahashi, Kazutoshi and Shinya Yamanaka. “Induction of pluripotent stem cells from mouse embryonic and adult fibroclast cultures by defined factors.” Cell (2006): 663-676.

6. Zhao, C. and S. Emmons. “A transcription factor controlling development of peripheral sense organs in C. elegans.” Nature (1995): 74-78.

7. Portman, D. and S. Emmons. “The basic helix-loop-helix transcription factors LIN-32 and HLH-2 function together in multiple steps of a C. elegans neuronal sublineage.” Development (2000): 5415-26.

8. Ambros, V. and H Horvitz. “Heterochronic mutants of the nematode Caenorhabditis elegans.” Science (1984): 409-16.

9. Wrischnik, L. and C. Kenyon. “The role of lin-22, a hairy/ enhancer of split homolog, in patterning the peripheral nervous system of C. elegans.” Development (1997): 2875-88.

10. Eisenmann, D.M. “Wnt signaling.” 25 June 2005. wormbook.

1 November 2011 <http://wormbook.org/chapters/www_ wntsignaling/wntsignaling.html>.

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Science at amherst: Interterm courses

WORKSHOP IN ENVIRONMENTAL LEADERSHIP

An Introduction to the Principles, Practices,

Jan E. Dizard and Katie MacDonald

and Procedures of 737 Turbine Flight

Department of Environmental Studies, Amherst College

Henry Parker Hirschel

January 13 (evening); January 14-18 (8:45am-4:30pm); January 19

Department of Astronomy, Amherst College

(9am-1pm)

January 15 - 22 (no class Sunday or MLK Day), 12:30pm – 3:00pm,

Location: O’Connor Commons (Jan. 14-15); Friedmann Room (Jan.

field trips (2) will be all day

16-18)

Location: Merrill 220

Wind Turbine Seminar and field trip

EMT-B Course

Henry Parker Hirschel

Molly Scott, Mariah Servos, Joshua Haswell

Department of Astronomy, Amherst College

ACEMS

Seminar: Sunday January 20th / Field Trip (Berkshire East Ski

Dates and times TBA

Area) January 21st Location: Merrill 220

SUSTAINABLE FORESTRY AND AGRICULTURE: OPERATIONAL CHALLENGES AND SOLUTIONS

Celestial Navigation

Bob Saul ‘80

Henry Parker Hirschel

Center for Community Engagement

Department of Astronomy, Amherst College

January 8-17, 1:00pm - 3:30pm, Tuesdays and Thursdays only

Monday January 7 - Monday January 14 (no class Sunday), 1:00 pm

Location: Webster 220

- 3:30 pm Location: Merrill 220

Superfluidity and liquid helium 4 Michael Ray

THE BIONIC BICYCLE: A SEMINAR AND TEST RIDE Henry Parker Hirschel Department of Astronomy, Amherst College Wednesday January 23, 12:00 pm - 2:30 pm Location: Merrill 220

Department of Physics, Amherst College Dates and times TBA