Issue 13 by Elements Magazine

The Scientific Magazine of the University of Puget Sound

Digging Deep Reveals a Naked Mystery

Status Update from The Allium Where Will Curiosity Take Us? Good Vibrations: The Physics of Guitar Sound Issue 13, Spring 2013

University of Puget Sound

See Back Cover! 1

Letter From The Editor

Part I: Unconventional Introduction

Welcome to Elements Magazine from UPS! Now on number thirteen, With handmade illustrations, intriguing articles, and student photos, This issue is the best I’ve ever seen.

Enjoy our hard-work and this amazing spread! Sincerely, Claire (aka “Rhymin’”) Simon Editor-in-Chief

Part II. Ode to Issue 13, We Went BOLD

In this issue, we break the boundaries of topsoil And explore the tunnels of peculiar semi-naked creatures. While underground, be sure to examine the roots, Beneficial microbes and fungi dwell in those plant features. Curiosity on Mars breaks the boundary of our planet, Student research expands our understanding of pain, And a tiny organism also known as a “water bear” Can survive in outer space conditions, it’s insane!

Part III: Elements of Elements

Stepping away from the rhyme for a moment, I want to highlight this spring issue in a broader perspective. At Elements, a magazine that roots itself in balancing presentation, accuracy, as well as accessibility, it is challenging to strike the right pitch. Deciding when to simplify or add complexity in science writing seems to pit readability against accuracy within every paragraph.

For images, which are worth a thousand words, things get proportionally more complicated. In a textbook or scientific publication, figures are a manifestation of a particular concept, yet in a magazine they must also be visually pleasing and accessible to our readers. For example, a photo of a perfect snowflake may give insight into the beauty of crystallization while at the same time deceive the viewer-these “perfect” snowflakes rarely occur in nature. One should particularly notice the diverse display of images in this issue. There are hand-drawn illustrations, computer generated figures, and a plethora of student photos. We hope this issue challenges your perception of any image or figure you encounter in a text book, article, or magazine. Not every line, shape, or blade of grass is exactly as it seems. We also hope it adds to your appreciation of the hard work and effort behind what appears to be an effortlessly great photo. For some, this takes a lifetime. For us at Elements, it takes one hardworking semester. So it figures, we are awesome.

Part IV. Rhyming Again for the Final Goodbye

It is most of the staff’s and my final year at UPS and Elements Magazine. This is an attempt to condense the greatness of our experience together Of deadlines, weekly meetings, challenges, friendships, Fun, growth, and way, way too much fruit leather. Huge appreciation to everyone involved in this and every issue! Your participation, dedication, and enthusiasm is inspiring That means you, math nerds smeared with pie, dangling photographers, Everyday supporters, and all the editors who work without tiring.

“Mad Lab” Elements Staff Front: Chelsea Clark, Claire Simon, Kira Thurman Back: Maggie Shanahan, Jay Goldberg

Credits

Editor-in-Chief: Claire Simon Head Copy Editor: Chelsea Clark Head Layout Editor: Kira Thurman Staff Editors: Maggie Shanahan & Jay Goldberg Front Cover Illustration: Mary Wexman Table of Contents Photo: Marisa Lopez Allium Cover: Claire Simon CosmoNerds: Rachel Edgar and Daniel Guilak CosmoNerd Photo/Layout: Chris Putnam/Mel Kohler Front Cover Species Plant/Fungi Identification Key (from left to right): Oregon grape, Sword Fern, Western Trillium, HorsetailWestern Trillium, Amanitas, brown mushroom 1, Blue Gum (Eucalyptus), shelf shroom (top), light brown mushroom 2

Acknowledgments We would like to thank the following organizations and individuals: the ASUPS Media Board, Tamanawas for loaning us their computers and software, and UPS Photo Services for curbing our Wikimedia usage!

Contact & Publishing

e-mail: elements@pugetsound.edu web: http://clubs.ups.edu/clubs/elements mail: ASUPS - Elements, University of Puget Sound, 1500 N Warner St. #1017, Tacoma, WA 98416 Published by QC Graphics LLC 1819 Central Avenue S, Suite 80, Kent, WA 98032 This issue was published on paper from well-managed forests, controlled sources and recycled wood or fiber.

Elements Magazine

Photo by Bryce Bunn

The creativity from fellow students is amazing. It shows how science and art readily combine, It has inspired this unusual form of a letter And compelled me to make parts of it rhyme.

As Elements and I go on to new and separate adventures I will surely keep in touch. All I can say is that I will miss this. Everyone at Elements, it has been clutch.

Table of Contents Naked Mole-Rats Bare it All: Stories from Underground

My Love Affair with the Eastern Newt

Mission to Mars: Getting the Best of our Curiosity

Defining Science: It’s an Asteroid… It’s a Meteor… It’s a Meteorite

Katie Moran

Michaela Alden Kira Thurman

David Santillan

Friends with Benefits: Symbiotic Relationship Between Plants, Bcteria, and Fungi

Physics and the Fretboard: Getting in Tune with Your Guitar

Delayed Effects of Stress: The Relationship Between Stress and Headaches

PB & A: Peanut Butter and Antibotics Fill Stomachs, Fight Infections

Gossiping Gardens: What do the Trees Have to Say?

Back from the Brink: Researchers identify proteins that allow tardigrades to enter “reversible death”

THE ALLIUM Mad Labs

21 22

Pointed Observations

“I’m Just Too Viscous, Mr. Bowen”

They Said WHAT?: Little known sayings from widely known scientists

CosmoNerd Citations FLIP! Back Cover: Contest Winner, Sharon Styer Photo Contest Winners Honorable Mentions: Staff favorites Ode to the Images in Science Claire Simon

26 27

Spencer Gordon Angelica Kong Chelsea Clark Becca Long

Jay Goldberg

Michaela Alden

Maggie Shanahan and Chelsea Clark Mary Wexman

Lauren Fellows

Kira Thurman and David Santillan

FLIP!

University of Puget Sound

31 30 29

Naked Mole-Rats Bare it All Stories from underground

K atie M oran

ontrary to their name, naked mole-rats (Heterocephalus glaber) are not moles, rats, or even naked. You probably recognize these little guys from childhood visits to the zoo, or because they make great sidekicks for teenage secret agents like Kim Possible. They are known for their giant teeth and excellent digging skills, and they have been known to periodically yell things such as, “Booya!” ...or maybe that was just in the cartoon. Naked mole-rats are small rodents that live in extensive underground tunnels in Eastern Africa. They are in the same order as rats (Rodentia) but belong to a distinct family (Bathyergidae) of mole-rats including the blind mole-rat, cape mole-rat, star-nosed mole-rat, and common mole-rat. These rodents are not truly naked because they have special sensory hairs that stick out from their body to help them navigate their dark tunnels, much like the whiskers of a cat. Naked mole-rats are like professors: the more you learn about them the more interesting they become, and they look really weird when they’re not in their natural habitat. Perhaps part of the reason they live underground is because they are so strange in appearance. Their eyes are beady and useless, their ears are covered over with skin to

keep the dirt out, and their Wikimedia Commons A naked mole-rat aka “sand puppy” eating skin is the color of a nude crayon. But looks aren’t everything. The fascinating story of the naked mole-rat begins with their unique lifestyle. The mole-rats live in a community of about 80 individuals who share communal living spaces as well as different jobs that make the colony run smoothly.` They are eusocial animals, meaning they have a queen and distinctive social roles within their colony such as workers, breeders, and diggers. Eusociality is more typically seen in insects, such as bees, and the only other mammals that live this way are African Mole-Rats.2 Workers, who go out digging in search of tubers and roots in the ground for food, are the smaller individuals. Some of the larger individuals act as guards, remaining in the nest to defend the colony from predators. Though unconfirmed, there is some speculation that there is a special job for a select few naked mole-rats that do nothing all day but eat so that they will be large enough to plug

Mole-Rat Manor: extensive tunnels house colonies of up to 80 individuals. Diggers, sweepers, and volcanoers excavate the tunnel system while other naked mole-rats forage for food, care for offspring, and guard the nest.

Elements Magazine

up the tunnels in the case of a flood. Other mole-rats, both male and female, share the responsibility of caring for the young.1

injury.

Additionally, naked mole-rats have an extremely long life span in comThe queen of the naked mole-rats is the female in charge of populat- parison to other animals of similar size and livelihood. Naked moleing the whole colony with the help of a harem, a small selection of rats can live to be upwards of 30 years old whereas a typical mouse males that provide the best genes. She is the only reproductively ac- only lives for about a year.6 This is a huge discrepancy and many labs tive female in the colony. Her presence represses the sexual maturity are studying naked mole-rats to learn more about how they are able to of her subjects, so that the queen truly is the only one who can re- remain physically and neurologically healthy for such a long time. For produce.3 She is more aggressive than the other mole-rats, and larger one, naked mole-rats do not go through normal senescence, or cellular since she must carry litters of almost 30 offspring!2 To make room for aging mechanisms. In contrast to the typical aging processes that octhe fetuses, the queen’s vertebrae lengthens by 32% so that she gets cur in most mammals, naked mole-rats show few signs of age-related longer instead of wider, giving her the ability to continue roaming the mortality until very late in life.8 This unique aging process is accompatunnels even while she is pregnant. The queen’s presence in the tunnels nied by an ability to reproduce well into the third decade of their lives. Another thing is important for prothat keeps moting the order in Naked Mole-Rats and No Cancer: them living the colony; her smell for a long alone can instill fear Contact inhibition is the process by which cells stop growing and dividing when time is that in the workers, makthey come in contact with other cells. For example, normal cells will stop proliferating they do not ing them dig more once they fill up the bottom of a culture dish with a single layer of cells. However, cancer get cancer. efficiently. Evidence cells do not exhibit proper contact inhibition processes and thus continue to proliferate, Even when of this comes from resulting in many layers as the cells grow on top of each other. Ultimately, this leads to researchers studies that record the the formation of tumors. Humans exhibit single level contact inhibition, meaning that try to force amount of digging an the signals to stop dividing only occur once, when crowding has reached a threshold. Naked mole-rat cells, on the other hand, have two levels of contact inhibition, includcancerous individual does in the ing a contact inhibition process occurring at very low cell density, which has been growth in presence or absence termed “early contact inhibition.” As a result, naked mole-rat cells do not even form naked moleof the queen’s odor.3 the dense single-layer of cells that human cells do, but halt growth before this point. The rats (by geThe queen also barextra level of contact inhibition may be a large contributing factor in suppressing tumor netically rels through the tungrowth and thus preventing cancer in naked mole-rats.7 modifying nels, trampling some them to have of her subordinates predisposias she goes about tions to canher daily business. cer or by muThis trampling is not tating their physically detrimencells in vitro), tal, but it shows the they do not queen’s dominant role see the same in the colony. scale of cancer The complex set of tunnels the naked mole-rats inhabit is another fasgrowth that is observed in other model organisms. Mutations to the cinating aspect of their lifestyle. Tunnels can extend up to two miles p53 and pRB pathways almost always lead to cancer in mouse cells, long and are almost completely excluded from the world above, with but do not cause cancer in naked mole-rats.7 Researchers are looking all of the tunnels closed off from the surface. Naked mole-rats live into the cellular mechanisms that provide this apparent cancer immuin an almost completely hypoxic environment. They can survive with nity. One such mechanism is the contact inhibition pathway in naked extremely low levels of oxygen, which is abnormal for most mammals. mole-rats, which is distinct from the one found in humans (see figure Within the tunnels there are special chambers for communal sleepabove). Naked mole-rat cells do not form tumors in part because they ing, eating, and pooping, and there is even a special ‘daycare’ chamber cease proliferation when they get too crowded. This process, called where the babies are raised.4 contact inhibition, occurs earlier in naked mole-rats compared to This mammal’s ability to survive in such unique conditions is interest- other mammalian cells, and it could contribute to the prevention of ing to many medical researchers. For researchers who focus on brain cancerous tumor growth in this species.8 injury after strokes or heart attacks, the hypoxic survival mechanisms To us, it seems like naked mole-rats would have a hard life. Humans of the naked mole-rat are of interest because it may help us to underspend time, energy, and even hire professionals to secure an environstand or improve the treatment of human brains. Unlike the brains ment sunny and wide open to breathe fresh (oxygenated) air; an enof naked mole-rat, human brains cannot survive long with low levels vironment that is quite opposite of the dark naked mole-rat tunnels. of oxygen. It is believed that naked mole-rats can survive these poor Humans also strive to clothe themselves sufficiently, soak up sunlight, living conditions because their brains remain in an immature state, revel in high-excitement and high-stress situations, and in many cases similar to a fetal brain, as levels of oxygen available in utero are low.5 revolt against the absolute rule of a monarch. Though these human It is not surprising that brains are very different before birth, but it characteristics are not necessarily a direct cause for cancer, the dark, is interesting to consider that they are changing in response to oxynon-stressful, and immortal story of the naked mole-rat might have a gen. Understanding more about the brain’s response to oxygen after lot to tell us about our own health. birth may provide useful in developing ways to prevent or treat brain Figure by Chelsea Clark and Claire Simon

University of Puget Sound

My Love A ffair with the E astern Newt by

M icha el a A lden

Photos by Michaela Alden

very summer in the Adirondacks, I observe all kinds of wildlife, but the highlight of my trip is always the tiny, mellow, unbelievably orange Eastern Newt (Notophthalmus viridescens). These newts are part of the family Salamandridae and can be found in deciduous and coniferous forests throughout the eastern United States and adjacent parts of Canada.

Elements Magazine

The Eastern Newt has a unique life cycle. An individual begins life in an aquatic larval stage, develops into the familiar terrestrial form known as a â&#x20AC;&#x153;red eft,â&#x20AC;? then returns to the water as an adult. The red eft stage lasts for 2-7 years and makes up about half of the life span.

Although the number of Eastern Newts has declined due to habitat degradation, they are still so abundant in their range that they are not considered to be threatened. This means that they are easy to find if you know when and where to look.

During its red eft stage, the newt is nocturnal and may be found wandering through leaf litter on rainy nights, snacking on small invertebrates. In fact, they are thought to play an important role in controlling the populations of small insects like mosquitoes.

Wikimedia Commons

When they develop into adults and resume life underwater, they lose the reddishorange coloration and turn yellow-olive, though their bright red spots remain (see below). As adults, they can grow up to five inches in length.

If you want to pick up a newt, be sure to keep it moist, handle it gently, and put it back close to where you found it. Itâ&#x20AC;&#x2122;s best to keep handling to a minimum and wash your hands afterward because, as bright coloration often indicates, the newts secrete toxins from their skin when threatened. This is a defense mechanism that makes them unpalatable to predators like birds, mammals, and fish.

University of Puget Sound

Mission to Mars by

Getting the Best of our Curiosity

K ira Thurman

Why Mars?

ince NASA’s first glimpse of Mars in 1965 with the Mariner 3 flyby mission, the Red Planet has been a mystery. While strangely resembling Earth in composition, the surface of Mars is similar to the moon, pockmarked with craters created by space debris crashing into the surface. Mars is also similar to Earth in that it has polar ice caps, an atmosphere (while it is extremely thin), and a slight tilt, causing seasons. Many scientists want to explore Mars, as they believe it could explain the history of climate change, which could be useful for Earthly applications. As human beings we are naturally curious and want to find more about this strange planet that could have once resembled Earth. Past and present missions Over the years, NASA has sent numerous missions to Mars. From Mariner 3, where we learned the surface of Mars is not covered in liquid water, to now, with rovers and orbiting satellites, we continue to learn more about this mysterious Red Planet. The rovers are perhaps the most iconic and well-known missions to Mars. Since 2003 Spirit and Opportunity have been searching the Red Planet. The newest Martian mission, the Mars Science Laboratory (MSL) mission, housed in the Curiosity rover, now joins these two rovers on the surface of Mars. They are tasked with finding out more information about Mars and relaying that information back to Earth.1

What sets Curiosity and MSL apart from the other rovers is the sophisticated instruments on board. While Spirit and Opportunity are still roving on Mars, despite the fact they were only scheduled to be operational for a year, Curiosity is larger, more sophisticated, and has more tools. Before it could analyze anything, Curiosity had to travel to and land on Mars.1 Going to Mars Curiosity’s space journey started on November 26, 2011 at 7:02 a.m. PST. The rover was launched in an Atlas V-541 rocket as Curiosity is twice as heavy as Spirit and Opportunity and is three times larger. The Atlas V-541 rocket was chosen due to its ability to lift the heavy rover, The 541 signifies the diameter of the nose cone (payload, where Curiosity is housed), the number of solid rocket boosters and the number of engines respectively. Thus, the diameter of the nose cone is five meters, there are four solid rocket boosters and one engine.1 The timing had to be perfect to allow for safe passage for the rover. If the launch was not timed out properly, the rover would not be able to reach Mars and would be lost in space forever. The launch window for Curiosity was from November 25- December 18, 2011. The launch window is calculated for when Earth is the closest to Mars. This allows for the least amount of space travel, reduces the amount of fuel required to propel the spacecraft, and creates a less costly mission.1 Due to its size, when Curiosity reached Mars, it employed a new landing technique, rather than the “bouncing” technique employed by both Spirit and Opportunity. Because Curiosity is so much larger, both in mass and in volume, this “bouncing” technique was not a good option. Instead, using new precision-landing techniques, Curiosity successfully landed on August 5, 2012 at 10:32 p.m. PDT.1,2

Wikimedia Commons

The first stage of this new landing technique was guided entry where small rockets were used to guide though Martian atmosphere. An on board system steered the rover to the pre-determined landing sight. Next a parachute (see figure) was deployed to slow the spacecraft down. Parachutes were used with previous missions, however, this one had to be much larger. During a pow-

Elements Magazine

Research The first rock touched by Curiosity had an unexpected composition that was different from rocks found on previous missions. This rock is more varied in composition and resembles rocks found in volcanic regions on Earth. Analysis of soil samples show the Martian soil composition to be similar to basaltic soils from Hawaii’s volcanoes. Another milestone and something for the history books is that on February 20, 2013, Curiosity became the first instrument to drill into the interior of a rock beyond Earth. This rock was named “John Klein” after the first deputy project manager of MSL, who passed away in 2011.5,6,7 The Curiosity mission has not been without its setbacks. In late February, Curiosity suffered from a memory glitch. Because there are two computers on board, the rover was still able to function during this problem. The source of the glitch has yet to be determined but, Curiosity recovered in early March.8 In mid-March, the MSL team reported that Curiosity found “evidence of water-bearing minerals in rocks near where it had already found clay minerals inside a drilled rock.” 9 Wikimedia Commons

While there is not yet evidence of little green men on Mars, Curiosity still has much to find. Curiosity’s power sources will last at least a Martian year (about 687 Earth days) hopefully enough time for the mission to demystify Red Planet.10

Self portrait of Curiosity on Mars

ered descent, mini thrusters guided the spacecraft to nearly zero velocity and stabilized the spacecraft. Finally a sky crane lowered Curiosity by tethers to the surface. The mobility system turned on so Curiosity could essentially rove as soon as its wheels hit the ground. Once the on board system sensed touchdown, the tethers were cut and the sky crane flew away where it crashed at full force safely away from the rover.1,2,3 Gadgets and Gismos The MSL has many nifty gadgets and gismos on board. Many of these were gifts from other agencies around the world. The Russian Federal Space Agency donated a neutron-based hydrogen water detector, the Spanish Ministry of Education and Science donated a meteorological package and the Canadian Space Agency donated a spectrometer. All of the gifts from different agencies are important because, although the USA and NASA are the ones responsible for Curiosity, MSL, and the mission, it is still a mission that will benefit all of us on Earth.1 The rover has many parts. The 6 wheels and camera mounted on a mast (like Spirit and Opportunity) allow Curiosity to rove and take pictures. A laser vaporizes thin layers of surface rock to allow it to analyze the underlying elemental composition. Onboard chemical testing chambers also analyze rock and soil samples. A suite of other scientific instruments analyzes organic molecules, in particular looking for life supporting elements (Nitrogen, Phosphorus, Sulfur, and Oxygen). The rover is powered by the radioactive decay of Plutonium.1,4

Defining Science It ’s an A steroid… It ’s a M eteor … It ’s a M eteorite by

D avid S antill an

here is a haze of confusion over the differences between an asteroid, meteor, and meteorite; in reality these outer space rocks have very few differences and a lot in common. An asteroid is a small, inactive body of rock, which orbits the sun. A meteor is a fragment of an asteroid that is absorbed in the Earth’s atmosphere, also known as a shooting star. The only distinction between a meteor and a meteorite is that a meteorite is a meteor that has safely passed the Earth’s atmosphere and has come to impact the Earth’s surface. There is constant fascination with the different rocks our galaxy has to offer; now you have the tools necessary to decide whether or not it is actually a meteor or a meteorite . . . or perhaps it is truly Superman.

University of Puget Sound

Friends with Benefits Symbiotic Relationships Between Plants, Bacteria, and Fungi by

S pencer G ordon

Wikimedia Commons

lants allow all of us to survive on our earth, and they are a vital part of almost every land-based ecosystem. Most people donâ&#x20AC;&#x2122;t know that plants are dependent on their underground buddies, mycorrhizal fungi, as well as bacteria. Mycorrhizal fungi only grow with plant roots, and more than 80% of plants depend on them.1 Bacteria act as important mediators of this symbiotic relationship. Mycorrhizal fungi have an arrangement with plants so that they share resources and rely on each other completely for certain dietary needs. The fungus helps the plant acquire the necessary amount of water and nutrients each day. As humans, we need our daily vitamins, which we get through eating certain foods that we buy at the grocery store. The fungus does all of the shopping the plant needs in exchange for a fee, which is typically carbohydrates. However, different fungi can charge different fees. Plants have evolved with fungi for the entirety of their existence and over those generations have developed relation-

10 10

The totally hot threesome beneath our feet

ships with specific fungi. In some cases, a fungal strain that is symbiotic with one plant could even be parasitic to another.1,2 Mycorrhizal fungi enter the root cells of plants and, through that intimate connection, exchange carbohydrates and other

Elements Magazine

nutrients. Mycorrhizae can also grow through the soil to connect multiple plants, creating an underground highway for nutrients. Generally, when people think of fungi, they think of a single mushroom sticking up from the ground or coming out of an old stump, but there is more to them than meets the eye. These structures sticking up from the ground are just where the fungi produce spores for reproduction, and they make up just the tip of the iceberg. Most of their biomass is underneath the ground in an extensive, web-like network of mycelia.1,2

Some bacteria also have the ability to regulate plant growth and possibly whether or not the plant will accept the fungus as a guest. Bacteria share multiple hormones with plants and thus have a very strong influence on how these plants behave. The mechanisms for the transmission and cellular communication occurring in this relationship have yet to be fully explored. Given the crucial role of bacteria-fungus symbiosis in the growth of some crop species, manipulation and application of these symbionts may potentially increase both crop yields and tolerance to many different kinds of natural and man-made problems.1,2

Illustrations by Maggie Shanahan and Chelse Clark

Single-celled organisms called bacteria have been discovered as integral players in this symbiotic relationship. Bacteria have been observed living inside certain kinds of mycorrhizal fungi and play a very significant role in fungal growth and structure. Through scanning electron microscopy, bacteria have been seen digesting the outer layer of some fungi, while other studies have found bacteria to be required for fungal spore germination. The bacteria could be using their ability to germinate fungal spores

as a way to farm the fungus for food. Certain bacteria have been labeled as biodegraders due to their ability to break down fallen trees, leaf fall, and many other compostable substances.2

Mycorrhizal fungi extend structures called mycelia into the root cells of plants, and bacteria inhabiting mycelia facilitate the exchange of carbohydrates and other nutrients.

University of Puget Sound

Physics and the Fretboard by

Getting in tune with your guitar

A ngelica K ong

ne of the most popular instruments in Western culture is the guitar, and it has been a huge influence on the pop culture of music. While it’s safe to say that many people could identify the sound and appearance of this instrument, fewer are familiar with the physical aspects of the guitar. Little do some guitar players know that they are really playing with math and science! Fret spacing, harmonics and instrumental tuning can be explained by physics. Fret Spacing Frets are the little metal bars on a guitar’s fretboard that mark where a string can be held down to produce a certain note. The number of frets a guitar has varies depending on whether it is electric, acoustic, classical, etc, but what’s important is the spacing between each fret, which is essentially the same on every guitar.

C#. Continuing this pattern (D, D#, E, F, etc), we eventually arrive back at C, this time an octave higher. In the end, what we have is a whole octave equally divided into twelve different notes. Basically, the frequency of a sound wave determines the tone that is produced. A higher frequency results in a higher pitch, while low frequencies result in lower pitches. We find that the frequency ratio between the sound waves a half-step apart is an interval of 1.05946. In other words, if we play a note and then multiply its sound wave frequency by 1.05946, we get a note a half-step higher. For example, we could play the note C,multiply the note’s frequency by this interval, and then we would end up with a C#. Since middle C has a frequency of 261.6 Hz,2 multiplying 261.6 by 1.05946 equals a new frequency of 277.15 Hz, and the corresponding note C#.

This is where the guitar design called the “rule of eighteen” comes from. It turns out that 1.05946 happens to be extremely close to The distance between each fret is a half-step.1 If holding down the fraction 18/17, and so the total distance from the start of a certain fret gives the note C, moving up one fret will play a the fretboard to the bridge is divided equally into eighteen. The first fret is placed at 1/18 of the total distance. The remaining distance is again divided into Guitar In Action! Holding down a fret decreases the length of the string, producing a eighteen equal portions, and different sound wave frequency and creating a different note. the second fret is placed 1/18 of this distance. The process repeats, and as a result, the fret spacing decreases as you move up the fretboard.1 Harmonics

Photo by Claire Simon

Most people identify harmonics as a light ringing sound, but what exactly are harmonics and how does that sound occur? In fact, the harmonics are part of the overtone series.3 Suppose we have a note created by natural means (by using instruments, as opposed to computers and electronic music). We hear not only the sound wave of the desired note, or fundamental pitch, but also the overtones. Overtones occur at frequencies other than the fundamental pitch and are only heard subtly, but they contribute to the overall sound produced when a string is strummed.3 Playing harmonics all comes

Elements Magazine

down to isolating these overtones. If you visualize these sound waves as a sine graph, there are several nodes along the graph where the waves intersect with the x-axis.4 Now if you imagine the x-axis as the guitar string, then these nodes are the places along the string where you can strum harmonics. When you play a guitar string without compressing the string at any frets, you hear the fundamental pitch, in addition to all of its overtones. By finding a place along the guitar where there is a node and lightly damping the string in that spot, most of the sound waves that result are muted, except for the ones that intersect the node.2 As a result, the waves that intersect the node become isolated and are the only sound waves that can be heard, creating a light ringing tone called harmonics. Tuning

Photos by Claire Simon, Kira Thurman, and Angelica Kong

If two sounds of different frequencies are played at the same time, their vibrations will interfere with one another. This causes a pulsation, called a beat, between the two tones.4 Pulsations can be heard as long as the two different tones are continuing to sound together. However, the pulsations will disappear when the two frequencies of the notes match a harmonic ratio. Therefore, this method of paying attention to the beats can be used to tune instruments. For example, as long as the desired note is being played in the background, a violinist can start to play a string and adjust the pitch to match the original note until the beats disappear. At that point, the two frequencies being played sound in pure unison, and there is no more interference between the two matching wave frequencies.3 This method of tuning can be quite effective. In most cases though, it’s not so effective for tuning guitars. In order to hear the beat pulsations between the frequencies of two sounds, the sounds have to be sustained for several seconds. When a guitar string is played, though, the note diminishes fairly quickly, which doesn’t provide enough enough time to listen for beats. Luckily, with the help of modern technology, there may be a way we can hear beats on a guitar after all! Using an amplifier with an electric guitar might allow us to sustain the notes long enough to hear these beats. If that’s not really your style though, there is always the invention of electric tuners! It’s up to you. But the moral of the story is, do try this at home.

The 5th, 7th, and 12th frets are where three nodes are located on the guitar string, and where harmonics can distinctly be heard.

University of Puget Sound

Delayed Effects of Stress

The relationship between stress and headaches S tudent R ese arch

C helse a C l ark

eadache pain affects a large portion of the population and can be very disabling for those who experience it. Headache consultations constitute about 4% of general practioner visits in the medical field, and one of the most common reasons for referral to a neurologist is headache pain.1 ‘Primary headaches’ refers to headache disorders for which no other cause can be attributed.2 ‘Secondary headaches’ are caused by some other condition, and they often produce very extreme, even life-threatening acute pain. However, the pain from primary headaches should not be overlooked – primary headaches often greatly reduce quality of life and result in significant longterm disability.

Over the past year, I worked with Dr. Roger Allen in the Physical Therapy Department at Puget Sound to study the impact of stress on fluctuations in headache pain. Stress is known to be a contributing factor in many headache disorders.2,3,4-8 The body responds to various environmental conditions with a stress response, which activates the hypothalamic-pituitary axis to protect the body. When this stress response is chronically activated, the body can be worn down, eventually resulting in disease.4 Stress can affect headaches in many ways. It may in some cases trigger fluctuations in pain, or it may be a predisposing factor to having headaches. Frequent headaches can also play a role in creating more stress for a patient, potentially resulting in negative feedback loops. In particular, stress can be one of the components causing infrequent, episodic headaches to become a chronic problem.9 The exact relationship between stress and

Figure by Chelsea Clark

In general, most headache patients experience fluctuations in headache pain intensity, duration, and frequency. There are many known factors that influence this variability. For example, many foods can serve as triggers, and alcohol, weather, exercise, and

stress can also have an effect.2,3

A plausible mechanism for the ten-day delay in pain onset following a stressful event shows the release of thyroxine by the hypothalamic-pituitary-thyroid (HPT) axis.

Elements Magazine

Correlations between daily stress and pain levels 0-14 days later. Subject 1 (left) showed a strong positive correlation for stress and pain ten days later, while Subject 2 (right) showed a strong negative correlation (Clark, unpublished data).

headache pain is poorly understood, but stress likely directly influences the processes that produce and modulate pain.4 Although the mechanisms may not yet be clearly understood, it is clear that stress is an important factor in the mediation of headache pain.

and CRPS showing a ten-day delay in pain following a stressful event. This subject showed high correlations between stress and headache pain levels ten days later. This suggests that stress may impact chronic headache pain in a similar way that it does other chronic pain syndromes, such as FS and CRPS.

Previous studies have found a ten-day delay in the onset of pain flares following a stressful event in patients with other chronic pain disorders, including fibromyalgia syndrome (FS) and complex regional pain syndrome (CRPS).10-13 Using serial lag correlations, these studies reported low correlations between stressful events and same day pain but high correlations between stressful events and perceived pain intensity occurring ten days later.

However, the data from Subject 2 did not follow the same trend as Subject 1. A strong negative correlation was found, meaning that high levels of stress led to a decrease in pain ten days later, instead of an increase in pain as seen before. This suggests a different mechanism for pain modulation in response to stress for Subject 1 compared to Subject 2. As we still see a strong correlation for a ten-day lag, it is possible that for this patient, increased stress leads to a decrease in HPT activity, causing less thyroxine to be produced. If less thyroxine is being produced, we would expect to see a decrease in free thyroxine levels ten days later, and thus decreased pain perception.

The delay in pain onset was also shown to correlate with the release of a thyroid hormone called thyroxine.13 When an individual experiences stress, the hypothalamic-pituitary-thyroid (HPT) axis is activated, ultimately stimulating the thyroid gland to release thyroxine (T4) and triiodothyrodine (T3).4 Thyroxine is immediately bound and inactivated by thyroxine-binding globulins (TBGs) for ten days following release by the thyroid.14,15 This means that when the HPT is activated by stress, thyroxine is released but does not become active in the body until ten days after the stressful event. High thyroxine levels can lead to increased anxiety as well as increased nerve excitability, which can both contribute to an increase in perceived pain levels.16 My study aimed to build off of this information and to expand the research to headache pain. My project investigated the relationship between headache pain and stress to see if the results describing the ten-day delay in pain onset for other chronic pain disorders (FS and CRPS) also apply to chronic headache pain. Two subjects completed the study. The subjects were given a daily paper and pencil questionnaire for a period of 10 weeks, which was completed in the evening before the patients went to sleep. This questionnaire was used to assess the average level of stress throughout the day, pain at its worst during the day, and level of functioning. Our results varied widely between the two subjects studied. For Subject 1, the results were consistent with previous work on FS

There is some debate over whether stress leads to an increase or decrease in thyroid hormone release. For example, in a review of the HPT axis responses to stress, Selye concludes that thyroid hormone release can either increase or decrease, depending on the species and type of stressor.15 The findings of my study show differences in the bodyâ&#x20AC;&#x2122;s reaction to stress. The root cause of these differences has yet to be determined, but it is worth investigating in the future. The findings of this study have many implications for headache patients and their therapists, as well as other healthcare providers. For patients, it is often frustrating to manage seemingly random fluctuations in headache pain. The results of this study suggest that highly stressful events may lead to elevated pain perception ten days later, or decreased pain perception ten days later, depending on the individual. Healthcare providers may be able to help patients to determine if their pain fluctuations follow this trend, which will allow them to better understand their individual pain and thus manage treatment accordingly. Research Advisor: Dr. Roger Allen, PhD, PT at University of Puget Sound

University of Puget Sound

PB & A:

Peanut Butter and Antibiotics Fill Stomachs, Fight Infections by

B ecca L ong

n 1928, Sir Alexander Fleming discovered penicillin, the first recognized antibiotic, which became a go-to cure for many maladies.1 After the discovery of this medical marvel, antibiotics became extremely popular. In general, an antibiotic is a substance produced by a microorganism that is aggressive to the growth of other microorganisms when used in high concentrations. These microorganisms destroy infections and can cure diseases, but the story is not that simple. When humans consume antibiotics, some bacteria survive the initial kill-off, and natural selection favors bacteria that are resistant to the drug.

resistant Tuberculosis around the world.2 Super-bugs are also becoming a huge problem in hospitals where sick patients living in close proximity have an increased risk of acquiring infections.3 The super-bugs are stubborn, and it seems that the only way to kill them is more drugs. Though the dangers of antibiotic use have caused heated debate, not all antibiotics are evil. They may even help combat malnutrition.

This double trouble team of medicine and nourishment is proving to be a literal lifesaver for children in developing countries.

Photo by Claire Simon using Wikimedia Commons

Ironically, the increasing use of antibiotics leads to mutated “super-bugs,” which are resistant to the antibiotics manufactured to kill them. These emerging super-bugs are often deadly. There are 16 million cases of antibiotic

A group of doctors from Washington University in St. Louis studied malnourishment in “Project Peanut Butter,” which showed doctors that food wasn’t enough to cure malnutrition.1 Studies conducted in Malawi revealed that severe malnutrition may involve more complicated damage to the stomach, which can lead to infections. Therefore improving diet may not provide adequate treatment for malnourished individuals.

Project Peanut Butter focuses on areas with intense poverty, like Malawi, where individuals suffer from a form of malnutrition called kwashiInnovative antibiotics: Using pills and peanuts a research team supplements peaorkor. Kwashiorkor is caused by senut butter with amoxicilin to treat stomach infections and malnutrition in Malawi. vere lack of protein, but diets rich in protein and fat are not enough to heal the damage done by malnutrition.4 The team from Washington University in St. Louis learned that supplementing peanut butter with high doses of amoxicillin helps fight stomach infections. So as the protein in the peanut butter combats the effects of kwashiorkor, the antibiotics tackle the infections in the stomach. This double trouble team of medicine and nourishment is proving to be a literal lifesaver for children in developing countries. As hospitals became breeding grounds for super-bugs and the use of antibiotics in food increases, it’s hard not to wonder if antibiotic use should be limited. But antibiotics do serve a noble purpose today, just like they did when they first appeared in Sir Fleming’s laboratory: to kill and to cure.

Elements Magazine

Gossiping Gardens What do trees have to say?

J ay G oldberg

hile talking trees may seem like something out of the mind of J.R.R. Tolkien, they are a very real phenomenon. Many plant species are able to communicate with their community members, be them plants or insects, friends or enemies. Unlike the Ents of Middle Earth, real plants do not communicate with a spoken language, but a vastly more complex one composed of chemicals. Simply put, they communicate with odor. The odors of plants are composed of a wide range of volatile (gaseous) compounds.1 Some of these chemicals, such as nicotine and methanol, are familiar. However, the majority of these substances are frequently unknown outside the field of odor science, despite their relative ubiquity in the natural world. One such substance is caryophyllene, a chemical found in the odor of oregano,2 clove,3 basil,4 hops,5 hemp,6 and many other plants. Just as people change the tone of their voice or the choice of their words depending on their physical or emotional state, plants too can vary the chemicals they produce and thus the messages they send to their surroundings. Plants produce certain volatile chemicals in response to various stresses such as light, heat, and herbivory. The chemicals produced in response to feeding by herbivores are known as herbivory induced plant volatiles, or HIPVs.1

Photo by Danny Kessler

HIPVs can send a diverse array of information to a plantâ&#x20AC;&#x2122;s neighbors. Even a single chemical released by a plant can say different things to different organisms. Some components of HIPVs send a cry for help, recruiting predatory insects to feed on the plantâ&#x20AC;&#x2122;s attackers.1 A class of HIPVs known as green leaf volatiles are produced by a plethora of plants when under attack by herbivores. While you might not be familiar with green leaf volatiles by name, you most likely know the smell of freshly mown grass, for which they are responsible. Since these chemicals are often indicative of damaged plants, herbivores can eavesdrop on their scent, following a trail of green leaf volatiles to an easy meal. Distressed plants release yet another HIPV, methyl jasmonate, alerting nearby plants to prepare defenses for the coming attack.7 Methyl jasmonate is able to accomplish this because it is derived from a plant hormone, jasmonic acid, This tobacco leaf (Nicotiana attenuata) called a predatory Geocoris bug (brown) to remove the herbivorious Manduca catepillars (green) eating it.

University of Puget Sound

Wikimedia Commons

While this slug is munching away on a leaf, the plant has already produced signals called herbivory induced plant volatiles (HIPVs) to send a cry for help.

which regulates the plantâ&#x20AC;&#x2122;s defenses. Once a plant receives methyl jasmonate it is quickly converted into jasmonic acid, thus promoting the production of anti-herbivory defenses. Many scientists question whether or not this is an altruistic act on the part of the plant. It is believed that it may actually be the plantâ&#x20AC;&#x2122;s way of quickly signalling to distant sections of its own body, as volatiles can disperse across long distances much faster than internal messenger molecules. Still, the neighbors manage to also get the message and benefit from it.

As humans, we are unable to hear the constant chatter of the plants around us. Next time you sniff a flower, pick a berry, or mow your lawn, try to listen with your nose.

Photo by Jay Goldberg

The blend of chemicals released varies depending on the part of the plant in question. The odors of leaves, flowers, stems, and roots will vary according to what the plant needs to say. Many flowers have a specialized scent to attract pollinators, whereas the scent of roots can promote the growth of beneficial microbes while suppressing the growth of harmful ones.8 Some root volatiles have even been suggested to function in attracting animals that feed upon pathogenic fungi and microorganisms.9

Many ants have symbiotic relationships with plants and are especially attune to the smell of their voices.

Elements Magazine

Back

from the brink

Researchers identify proteins that allow tardigrades to enter “reversible death” by

M icha el a A lden

ardigrades, also known as “water bears,” are the ultimate polyextremophiles. They are able to withstand extreme temperatures, high pressure, ionizing radiation, and low levels of oxygen. These tiny invertebrates, about a millimeter in length, are the only multicellular organisms known to tolerate the radiation and vacuum of outer space.1 Their near-indestructibility at every stage of development has allowed them to colonize a variety of extreme habitats including deserts, high mountains, and polar regions, although they are most commonly found in moss.2 There are over 900 species of tardigrades and they constitute their own phylum in the superphylum Ecdysozoa.2

One of the extreme conditions tolerated by tardigrades is extreme water loss, also known as desiccation. They endure this by entering a state called anhydrobiosis (meaning life without water). During anyhdrobiosis, a tardigrade curls up into a form called a “tun,” halting its metabolism, reproduction, and development for as long as harsh conditions persist. As long as water is replenished within about four years, they reanimate and resume normal function.2 Anhydrobiosis occurs in a variety of bacteria, protists, metazoans and plants. The ability of anhydrobiotic organisms to tolerate a loss of up to 95% body water is interesting to biologists because water makes up the bulk of all living cells and normally

University of Puget Sound

protects macromolecules from damage. There are many practical reasons to investigate the mechanisms that prevent and repair this damage; research in this area has implications in vaccinology, cryogenics, organ storage, agriculture, and astrobiology.3,4

How did these new protein families get their names? After discovering the presence of these proteins, the researchers investigated their locations within cells. To do this, they tagged the proteins with green fluorescent protein (GFP) and observed the fluorescence under a microscope to see where the proteins were located. They found that CAHS proteins existed mostly in the cytoplasm (ambient cellular fluid), while most SAHS proteins showed up outside of the cell, an indication that they had been secreted. These discoveries led to the identification of CAHS as ‘cytoplasmic’ and SAHS as ‘secretory.’ Because of the proteins’ locations, the researchers speculate that CAHS proteins contribute to protection of cytoplasmic components, while SAHS proteins contribute to protection of secretory organelles such as the Golgi apparatus. Wikimedia Commons

How is it possible for cells to survive in such harsh conditions? A study carried out by Yamaguchi and colleagues (2012) approached the question using proteomics, the branch of molecular biology dealing with determining the proteome (the entire complement of proteins expressed by the DNA of a cell, tissue, or organism).5 The researchers knew that many anhydrobiotic organisms express high levels of Late Embryogenesis Abundant (LEA) proteins in response to desiccation. According to the water replacement hypothesis, LEA proteins expand to stabilize membranes and shield DNA from damage when water is scarce. Thinking that tardigrades may employ similar proteins, Yamaguchi and colleagues looked for heat-soluble proteins in the anhydrobiotic tardigrade Ramazzottius varieomatus, a species known for high desiccation tolerance.

did not resemble any known proteins and were dubbed the Cytoplasmic Abundant Heat Soluble (CAHS) protein family. When faced with dehydrated conditions, these proteins change structure in a way similar to LEA proteins.

The proteins of interest were those Finally, the researchers compared that remain folded and functional the abundance of these proteins after exposure to heat, like LEA in hydrated and dehydrated proteins do. To isolate such proteins, tardigrades. They found no sigthe researchers collected a “prenificant difference in abundance, heat”’ protein fraction from 500 which suggests that these proindividuals using centrifugation, teins are constitutive—meaning heated the sample to 95°C, then that they are continuously excollected the fraction of proteins pressed regardless of whether that were still intact with another or not the tardigrade is under round of centrifugation. These reenvironmental stress. DNA daScanning Electron Microscope image of a tardigrade, also known as a “water bear” maining heat-soluble proteins were tabase searches showed that the analyzed using gel electrophoresis, DNA encoding these five novel a technique that separates proteins proteins is conserved among taraccording to size. The proteins were then separated into their digrades, but not in other anhydrobiotic invertebrates like aramino acid components with the help of trypsin, a protein-dithropods, nematodes, and rotifers. It is thought that tardigrades gesting enzyme found in the digestive system. Mass spectrosevolved these genes independently from other phyla. copy, which detects elements based on their signature emission This study represents important progress in understanding the wavelengths, was used to determine the types and amounts amazing survival tactics of these unique animals. The mechaof amino acids present in each protein. A computer program nisms of anhydrobiosis and other forms of cryptobiosis are still compared these amino acids against the genome of R. varieonot well understood, so there are many possible directions for matus and traced each protein back to its DNA sequence. continued research. We could learn a lot from our tiny, indeWith this technique, the researchers did not find LEA prostructible friends. teins—but they did discover five new proteins that had never been described before. Two of them are similar to mammalian fatty acid binding proteins (FABPs), but lack enough key features of FABPs that they are considered new proteins. This Check out this time-lapse video of a tardigrade converting itself two-protein set was named the Secretory Abundant Heat Solinto a tun and re-emerging (by YouTube user ddhorikawa): uble (SAHS) protein family. Three other heat-soluble proteins www.tinyurl.com/bbqn73a

Elements Magazine

The Allium Timeline About

Lives in Every Grocery Store

705

Place

More Life Event

The Allium 22 hours ago

Pearl The Allium 22 hours ago

The Shallot

Photos

Activity Log

#makingpeoplecry Onions making puns: punions. Onions on youtube: http://www.youtube.com/watch?v=CD-q-PKKbyE

From The Dirt

Friend Photos from Wikimedia Commons

Friends 3 Status

Studies at University of Puget Sound

Friends

About

Update Info

Hot Saute

Red Sweet

The Allium, youâ&#x20AC;&#x2122;re the best comedic section and bff a grown bulb like me could ask for. Last weekend was the best weekend of my life. Funions 4 eva!! Promise not to take the following section seriously? Tomo letâ&#x20AC;&#x2122;s go sit on a bleu cheese burger in The Sub. <3 <3

University of Puget Sound

21 21

By Maggie Shanahan and Chelsea Clark

Unknown Breakthrough Ecological Phenomenon

Fill in the Blank:

By Dr.________(Your last name), Ph.D.* *University of Puget Sound

ABSTRACT (1) (2) are indigenous to (3) but they have spread throughout (4). In their native habitat, this species forages for (5). However, expansion to new habitats could lead to dietary changes. This study was done to explain the effects of novel diets on the behavior of wild (1). Specimens were collected from the (6), and kept in a (7) environment for (8) days. Specimens were divided into two groups. The control group was fed (5) and the treatment group was fed (9). Immediately after eating (9), the treatment group began to (10). The control group remained (11) throughout the experiment. Due to human error, (12) of the subjects escaped. The p value was found to be (13), so we consider these results to be significant. The results corroborate the (14) phenomenon, in which (15) (16) on (17), suggesting that (18) diets induce a (19) neural response in (1). Future studies should consider the effects of (9) on closely related species such as (20), in order to deepen our understanding of the (14) phenomenon.

22 22

Elements University ElementsMagazine of Magazine Puget Sound

1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20.

Animal (plural) ___________ Latin-sounding name 足足足_______ Country ___________ Country ___________ Food ___________ Destination __________ Adjective __________ Number __________ Food __________ Verb ____________ Adjective____________ Percent____________ Decimal less than 1 _________ Someone in the room_______ Noun (plural) _________ Verb__________ Noun__________ Adjective__________ Adjective__________ Animal__________

P o i n t e d

O b s e r v a t i o n s

Comics by Mary Wexman

University of Puget Sound

“I’m Just Too Viscous, Mr. Bowen” A geology rhyme By Lauren Fellows

geologist named Bowen went out for a walk And on his stroll came across a unique rock With a glassy surface that seemed almost new And was black as pitch the whole way through “Obsidian,” he said with much dismay, Please tell me how you got this way.” And even without a mouth or teeth Obsidian hm-hhm’d and began to speak “I can’t form crystals,” came its reply “They’re far too much work for one such as I” And Bowen pondered this, and thought “He has to crystallize someway, he ought.” Bowen smiled, for a suggestion he knew, And asked Obsidian these questions two: “Have you tried it in a pluton?” “Have you tried it… on a futon?” Obsidian’s resent its stoic surface belied Grumpily it gathered its words and replied: “I will not crystallize in a pluton I will not crystallize on a futon I’ll never get these crystals growin’ I’m just too viscous, Mr. Bowen.”

“Well then,” thought Bowen, “what have we here? A rock that won’t crystallize? How very queer!” As Bowen thought, more suggestions he found He picked the obsidian up from the ground. “Have you tried it with more water? Have you tried it… with an otter?” “I will not crystallize with more water I will not crystallize with an otter 24 24

I’ll never get these crystals growin’ I’m just too viscous, Mr. Bowen.” Bowen rubbed his chin in thought “My theories can’t all be for naught.” “Have you tried it with low pressure? Have you tried it… with a tape measure?” “Now you’re talking,” Obsidian replied, “Take out the pressure, and you might find That over many years, (you’ll have to wait) Fine-grained crystals will start to take shape. “But that’s far too much work,” Obsidian adds, “A lazy rock like me is much better off glass.” Bowen considered, and pondered, and asked “You say that you are happy as glass But say we add water, at low pressure too, Wouldn’t those conditions be better for you?” Obsidian thought about this for a bit Before replying with a rock’s impeccable wit: “But those crystals, too, take a while to be made, You’ll be long dead by then, I’m afraid.” Bowen laughed, “Of course, how silly of me! That these things take time is geologists’ creed! You seem quite happy as you are now One day you’ll grow crystals--it won’t matter how.” And so Bowen wished Obsidian “have a good day!” Put it down, tipped his hat, and went on his way And thought to himself how wonderful it must be To be as patient as a flow with high viscosity.

Elements Elements Magazine Magazine

They Said WHAT?

10.

11.

13.

Little known sayings from widely known scientists by

K ira Thurman

and

D avid S antill an

Albert Einstein

Carl Sagan

Richard Dawkins

Erwin Schrodinger

Charles Darwin

Isaac Newton

Sigmund Freud

Louis Pasteur

J. Robert Oppenheimer

10.

Marie Curie

11.

Jane Goodall

12.

Rosalind Franklin

13. Barbara McClintock

Scoring One point for each correct answer

Photos by Wikimedia Commons and Wikipedia (#12.)

12.

A. “A man who dares to waste one hour of time has not discovered the value of life.” B. “Certainly, if you look at human behavior around the world, you have to admit that we can be very aggressive.” C. “Chance favors the prepared mind.” D. “Insanity: doing the same thing over and over again and expecting different results.” E. “Every time I walk on grass, I feel sorry because I know the grass is screaming at me.” F. “By all means let’s be open-minded, but not so open-minded that our brains drop out.” G. “Time spent with cats is never wasted.” H. “The scientist only imposes two things, namely truth and sincerity, imposes them upon himself and upon other scientists.” I. “Science and everyday life cannot and should not be separated .” J. “I am become death, the destroyer of worlds.” K. “If I have seen further than others, it is by standing upon the shoulders of giants.” L. “I was taught that the way of progress was neither swift nor easy.” M. “If you wish to make an apple pie from scratch, you must first invent the universe.”

Undergrad: 1-2 points. Try again in a couple of years. Graduate student: 3-5 points. You still have much to learn. PhD student: 6-9 points You think you know everything, but you do not. Professor: 10-13 points Congradulations, you know everything!

Answers: 1-D 2-M 3-F 4-H 5-A 6-K 7-G 8-C 9-J 10-L 11-B 12-I 13-E

University of Puget Sound

Elements Magazine

CITATIONS NAKED MOLE-RATS BARE IT ALL

1. Borst, D., and Deyo, C. The Naked Mole Rat. N.p., 4 Dec. 2006. Web. 18 Apr. 2013. 2. Kutsukake N., Inada M., Sakamoto S.H., Okanoya K. A Distinct Role of the Queen in Coordinated Workload and Soil Distribution in Eusocial Naked MoleRats. PLoS ONE. 2012: 7(9), e44584. 3. Kutsukake N., Inada M., Sakamoto S.H., Okanoya K. A Distinct Role of the Queen in Coordinated Workload and Soil Distribution in Eusocial Naked MoleRats. PLoS ONE. 2012: 7(9), e44584. 4. Doug, Borst, and Deyo Christine. “The Naked Mole Rat.” Last modified December 04, 2006. Accessed April 18, 2013. 5. Larson J, Park TJ. Extreme hypoxia tolerance of naked mole-rat brain. Neuroreport. 2009: 20(18), 1634-7. 6. Kim EB, Fang X, Fushan AA, Huang Z, Lobanov AV, Han L, Marino SM, Sun X, Turanov AA, Yang P, Yim SH, Zhao X, Kasaikina MV, Stoletzki N, Peng C, Polak P, Xiong Z, Kiezun A, Zhu Y, Chen Y, Kryukov GV, Zhang Q, Peshkin L, Yang L, Bronson RT, Buffenstein R, Wang B, Han C, Li Q, Chen L, Zhao W, Sunyaev SR, Park TJ, Zhang G, Wang J, Gladyshev VN. Genome sequencing reveals insights into physiology and longevity of the naked mole rat. Nature. 2011: 479(7372), 223-7. 7. Azpurura, J., Seluanov, A. “Long-lived cancer-resistant rodents as new model species for cancer research” Frontiers in Genetics. 2013: 3, 319 8. Seluanov, A., Hine, C., Azpurura, J., Feigenson, M., Bozzella, M., Mao, Z., Catania, K.C., Gorbunova, V., “Hypersensitivity to contact inhibition provides a clue to cancer resistance of naked mole-rat” PNAS. 2009: 106(46), 19,352-19,357.

MY LOVE AFFAIR WITH THE EASTERN NEWT

1. Hammerson, G. Notophthalmus viridescens. IUCN Red List of Threatened Species, version 2012.2. 2004 2. Riemland, S. “Notophthalmus viridescens.” Animal Diversity Web. 2000. <http://animaldiversity.ummz.umich.edu/>

M MISSION TO MARS Science Laboratory [Internet]. Washington DC: NASA; 2012. Mars SciA 1.enceMarsLaboratory; [cited 2012 Oct. 01]; . Available from: http://mars.jpl.nasa. gov/programmissions/missions/present/msl/. Mars Science Laboratory [Internet]. Washington DC: NASA; 2012. Entry, DeG 2.scent, and Landing; [cited 2012 Oct. 01]; Available from: http://mars.jpl.nasa. A gov/msl/mission/timeline/edl/. 3. Mars Science Laboratory [Internet]. Washington DC: NASA. Sky Crane [cited 2012 Oct. 01]; . Available from: http://mars.jpl.nasa.gov/msl/mission/technolZ ogy/insituexploration/edl/skycrane/. 4. Mars Science Laboratory [Internet]. Washington DC: NASA; c2012. Launch [cited 2012 Oct. 01]; . Available from: http://mars.jpl.nasa.gov/msl/ I Windows; mission/timeline/launch/launchwindow/ 5. Webster, Guy and Dwayne Brown. Mars Science Laboratory [Internet]. WashN ington DC: NASA; c2012. Mars Rock Touched by NASA Curiosity Has Surprises; [Cited 2012 Oct. 20]; Available from: http://mars.jpl.nasa.gov/msl/news/ E whatsnew/index.cfm?FuseAction=ShowNews&NewsID=1375 6. Webster, Guy and Dwayne Brown. Mars Science Laboratory [Internet]. WashF L I P

ington DC: NASA; c2013. NASA Rover Confirms First Drilled Mars Rock Sample; [Cited 2013 Mar. 20]; Available from: http://mars.jpl.nasa.gov/msl/news/ whatsnew/index.cfm?FuseAction=ShowNews&NewsID=1427 7. Webster, Guy, Dwayne Brown, and Rachel Hoover. Mars Science Laboratory [Internet]. Washington DC: NASA; c2012. NASA Rover’s First Soil Studies Help Fingerprint Martian Minerals; [Cited 2012 Nov 3]; Available from: http://mars.jpl. nasa.gov/msl/news/whatsnew/index.cfm?FuseAction=ShowNews&NewsID=1385 8. Agle, DC. NASA Jet Propulsion Laboratory [Internet]. Pasadena, CA: NASA; c2013. Curiosity Rover’s Recovery Moving Forward; [Cited 2013 Mar. 20]; Available from: http://www.jpl.nasa.gov/news/news.php?release=2013-091 9. Webster, Guy and Dwayne Brown. Mars Science Laboratory [Internet].The Woodlands, TX: NASA; c2013. Curiosity Mars Rover Sees Trend in Water Presence; [Cited 2013 Mar. 20]; Available from: http://mars.jpl.nasa.gov/msl/news/ whatsnew/index.cfm?FuseAction=ShowNews&NewsID=1446 10. NASA. 2012. Jet Propulsion Laboratory [Internet]. Washington DC: Discovery Guide: Mars Rover Curiosity [Cited 2012 Oct. 01]; Available from: http://www. jpl.nasa.gov/education/marsrover.cfm

DEFINING SCIENCE

1. 2013 Feb 27 [Cited 2013 Apr 7]. What is the difference between an astroid, comet, meteoroid, meteor and meteorite? AeroSpaceGuide [Internet]. Available from <http://www.aerospaceguide.net/whatisanastroid.htm>

FRIENDS WITH BENIFITS

1. Smith S.E., Read D.J. Mycorrhizal Symbiosis. New York:academic. 3rd ed. 2008. 2. Bonfante, P., Anca, I., Plants, Mycorrhizal Fungi, and Bacteria: A Network of Interactions. Annual Review of Microbiology. 2009: 63, 363-383.

PHYSICS AND THE FRETBOARD

1. Rossing, T. D., Moore, F. R., and Wheeler, P. A. The Science of Sound: Third Edition. San Francisco. Addison Wesley. 2002. 2. McNab, R. J., Smith, L. A., Witten, I. H., Henderson, C. L., & Cunningham, S. J. Towards the digital music library: tune retrieval from acoustic input. 1996. In DL’96. Retrieved from http://dl.acm.org/citation.cfm?id=226934 3. Duffin, R. W. How Equal Temperament Ruined Harmony (and Why You Should Care). New York. W. W. Norton & Company. 2007. 4. Davis, M. “Guitar strings as standing waves: a demonstration.” Journal of Chemical Educa ion, 2007: 84(8), 1287-1289.

DELAYED EFFECTS ON STRESS

1. Kristoffersen, E.S., Grande, R.B., Aaseth, K., Lundqvist, C., Russel, M.B., Management of primary chronic headache in the general population: the Akershus study of chronic headache. The Journal of Headache Pain. 2012: 13(2), 113120. 2. Goadsby, P.J. Headaches. Bonica’s Management of Pain. Philadelphia: Lippincott Williams Wilkins. 2010. 3. Rasmussen, B.K. Migraine and tension-type headache in general population: precipitating factors, female hormones, sleep pattern and relation to lifestyle. Pain 1993: 53(1), 65-72. 4. Nash, J.M. and Thebarge, R.W. Understanding Pyschological Stress, Its Bio-

logical Processes, and Impact on Primary Headache. Headache: The Journal of Head and Face Pain. 2006: 46(9), 1377-1386. 5. D’Amico, D., Libro, G., Prudenzano, M.P., Peccarisi, C., Guazzelli, M., Relija, G., Puca, F., Genco, S., Meggioni, F., et al. Stress and chronic headache. The Journal of Headache and Pain. 2000: 1(1), S49-S52. 6. Nadoaka, T., Kanda, H., Oiji, A., Morioka, Y., Kashiwakura, M., Totsuka, S. Headache and Stress in a Group of Nurses and Government Administrators in Japan. Headache: The ournal of Head and Face Pain. 1997: 37(6), 386-391. 7. Sexton-Radek, K. The nature of recurrent tension-type headache and stress experiences. Psychotherapy in Private Practice. 1994: 13(3), 63-72. 8. White, K.S., Farrell, A.D. Anxiety and Psychosocial Stress as Predictors of Headache and Abdominal Pain in Urban Early Adolescents. Journal of Pediatric Psychology. 2006: 31(6), 582-596. 9. Houle, T., Nash, J.M. Stress and Headache Chronification. Headache: The Journal of Head and Face Pain. 2008: 48(1), 40-44. 10. Allen R.J., Hulten J.M., Roelofson M.J., Martin T.G., McCormack S.A. Delayed pain reactions due to stress in patients with complex regional pain syndrome. Physiother. 2007: 93, S293. 11. Harlow, L.M., Kumiji, K.T., Allen, T.L., Allen, R.J. Effect of perceived psychogenic stress on pain intensity and timing of increased pain episodes in patients with fibromyalgia syndrome. J Orthop Sport Phys. 2005: 35(1), A17. 12. Hulten, J.M., Martin, T.G., McCormick, S.M., Roelofsen, M.J., Allen, R.J. Influence of perceived stress on delayed onset pain episodes and related functional changes in complex regional pain syndrome patients. Neurol Rep. 2002: 26(4), 190-191. 13. Allen. R.J., McCann, C.J., Higa K.G. Relationship between delayed episodic pain flares and release of stress-related thryoxine in a patient with complex regional pain syndrome- a case report. J. Phys Ther. 2011: 32-42. 14. Pyle, C.W., Moe, A.S., Terao, M.M., Luppino, E.R., Athing, C.R., Allen, R.J. Stress-related latency in sensory and affective dimensions of reported pain in patients with fibromyalgia syndrome. Eur J Pain. 2009: 13, S147. 15. Seyle, H. Stress in health and disease. Boston, MA: Butterworths; 1976. 16. Guyton, A.C., Hall, J.E. Textbook of medical physiology. 10th ed. Philadelphia, PA: Saunders. 2000.

PB & A

1. Johnson, A.E. “Antibiotics”. The American Journal of Nursing. Vol. 50, No. 11 (1950), pp. 688-690 2. Dye, C. and Marcos, A. “Will Tuberculosis Become Resistant to All Antibiotics?” Espinal Proceedings: Biological Sciences, Vol. 268, No. 1462 (2001), pp. 45-52. 3. Lipsitch, M., Bergstrom, C. T. and Levin, B. R. “The Epidemiology of Antibiotic Resistance in Hospitals: Paradoxes and Prescriptions.” Proceedings of the National Academy of Sciences of the United States of America. Vol. 97, No. 4 (2000), pp. 1938-1943 4. Trehan, I. et al. “Antibiotics as Part of the Management of Severe Acute Malnutrition”. New England Journal of Medicine, 2013: 368, 425-435

GARDEN GOSSIP

1. Dicke, M., Baldwin, I. The evolutionary context for herbivore induced plant volatiles: beyond the cry for help. Trends in Plant Science. 2012. 2. Harvala C., Menounos P., Argyriadou N. “Essential Oil from Origanum dictamnus”. Planta Med. 1987: 53(1), 107–9’ 3.Ghelardini C., Galeotti N., Di Cesare Mannelli L., Mazzanti G., Bartolini A. “Local anaesthetic activity of beta-caryophyllene”. Farmaco. 2001: 56(5–7), 387–9. 4.Zheljazkov V.D., Cantrell C.L., Tekwani B., Khan S.I. “Content, composition, and bioactivity of the essential oils of three basil genotypes as a function of harvesting”. J. Agric. Food Chem. 2008: 56(2), 380–5. 5.Wang G., Tian L., Aziz N., et al. “Terpene Biosynthesis in Glandular Trichomes of Hop”. Plant Physiol. 2008: 148(3), 1254–66. 6.Gertsch J, Leonti M, Raduner S, et al. “Beta-caryophyllene is a dietary cannabinoid”. Proceedings of the National Academy of Sciences of the United States of America. 2008: 105(26), 9099–104 7. Farmer, E., Ryan, C., Interplant communication: airborne methyl jasmonate induces synthesis of proteinase inhibitors in plant leaves. PNAS. 1990: 87, 7713-7716. 8. Jurgens, A., Witt, T., Gottsberger, G. Flower scent composition in Dianthus and Saponaria species (Caryophyllaceae) and its relevance for pollination biology and taxonomy. Biochemical Systematics and Ecology 2003: 31, 345-357 9. Wenke, K., Kai, M., Piechulla, B. Belowground volatiles facilitate interactions between plant roots and soil organisms. Planata. 2010: 231, 499-506

BACK FROM THE BRINK

1. Jönsson, K.I., Rabbow, E., Schill, R.O., Harms-Ringdahl, M., and Rettberg, P.. Tardigrades survive exposure to space in low Earth orbit. Current Biology. 2008: 18, R729-R731. 2. Rebecchi, L., Guidetti, R., Borsari, S., Altiero, T., and Bertolani, R. Dynamics of long-term anhydrobiotic survival of lichen-dwelling tardigrades. Hydrobiologia. 2006: 558, 23-30. 3. Garcia, A.H. Anhydrobiosis in bacteria: from physiology to applications. J. Biosci. 2011: 36, 939-950. 4. Pereira, T.C. and Lopes-Cendes, I.Cryptic anhydrobiotic potential in man: implications in medicine. Medical Hypotheses. 2009: 73, 506-507. 5. Yamaguchi, A, Tanaka, S., Yamaguchi, S., Kuwahara, H., Takamura, C., ImajohOhmi, S., Horikawa, D.D., Toyoda, A., Katayama, T., Arakawa, K., Fujiyama, A., Kubo, T., and Kunieda, T. Two novel heat-soluble protein families abundantly expressed in an anhydrobiotic tardigrade. PLoS ONE. 2012: 7,e44209.

THEY SAID WHAT?

1. 2013 [Cited 2013 Apr 7]. Barbara McClintock Quotes. Today in Science History [Internet]. Available from <http://todayinsci.com/M/McClintock_Barbara/ McClintockBarbara-Quotations.htm> 2. 2013 [Cited 2013 Apr 7]. BrainyQuote [Internt]. Available from <http://www. brainyquotes.com/> 3. 2013 [Cited 2013 Apr 7]. Rosalind Franklin Quotes. Good Reads [Internet]. Available from <http://www.goodreads.com/author/quotes/232917.Rosalind_Franklin>

ODE TO THE IMAGE IN SCINECE

1. Tercedor-Sanchez, MI. 2005 The Role of Images in the Translation of Technical and Scientific Texts. URI http://www.erudit.org/apropos/utilisation.html

University of Puget Sound

P I L F E N I Z A G A M

Ode to the Images in Science

By Claire Simon

The Photo:

cientists will spend the majority of their lives in search of that perfect image, which depending on the goal, can vary. The right image can illuminate the beauty of an object and inspire public awareness and involvement or it can shed light on a life process. Through submitted photos and illustrations in Elements, we bring attention to the importance of an image in science. The lengths that the passionate will go to get accuracy, beauty, symmetry, and perfection can take hours or a lifetime. Here is an ode to the photographer...

In the mid-late 1880’s, Wilson Bentley began his life-long endeavor to photograph snowflakes. Since his subject melted upon contact with Karl Blossfeldt was another scientist photographer from skin or the slightest blip of heat, he had to move quickly, catching the Germany who took close-up photos of plants and seedlings. snow flakes on black velvet with thick gloves. While not breathing, he His images portrayed the beauty and intricacy of plant life arranged the snowflake under a microscope as well as provided sciAsk Yourself: Particularly in a scientific context, that was jerry-rigged with a film camera ence with information without breaking them. His patience and is photo manipulation justified to achieve a desired on their processes and careful technique paid off; to reveal the purpose, or does that lead to misguided inferences growth development. first stunning images of this crystallization and decrease the image integrity? process.

The Figure:

igures must communicate a concept from the depths of one mind to another. In order to promote growth of knowledge and establish theories, one person’s understanding must be accessible and translatable to a variety of logical minds. A figure must face the challenge of appealing to a specific audience while remaining true to its original concept. As a soon-to-be graduated molecular biologist I immersed myself in the study of cells, bacteria, and molecules, aka the realm of figurative images and invisible subjects. In molecular research, the subject of study (usually proteins and DNA) are invisible until the scientist has used creative techniques just so an image can be taken. The only way we can “see” these molecules is by staining them with dye or linking them to a glowing molecule ( Fig 1. Protein B). From there, we get images in lab that look like dark gray bars or glowing green dots and nothing like our text books. Of these microscopic entities, some are blue circles in one text book ( Fig 1. Protein C), squiggles in another (Fig 1. Protein A), or glowing green dots in the figure of a research article. In this discipline, it wouldn’t be surprising if a student didn’t really know what a protein was until their senior year of college even after succeeding on multiple exams and passing several science classes (I may or may not have been one of those students...).

It is the duty and a challenge of the scientist to convert those pretty green dots into a conceptual understanding of molecular structure, chemical behavior, and role in cellular operations.

Elements Magazine

Protein A is quantum mechanically calcualated by a computer to show atomic accuracy and detail. The different colors correspond to different subunits of the protein, the round bulges are atomic masses, and the colored space in between them represent electron charge distribution. Protein(s) B are fluorescently “tagged” proteins extracted from a cell that glow from a special molecule attached to the amino acid chain. In each lane of this “gel”, smaller proteins are dragged farther down this porous gel by an electric current. When compared to a standard, the size and identify of a protein can be determined. Protein C is simplified to a blue oval “enzyme” with shapes cut out of it to depict a structure that specifically binds to the other “substrate” protein drawn as basic orange shapes.

Images from Wikimedia Commons

Figure 1. Confunding Figures, 3 Depictions of a Protein

Honorable Mention: Staff Favorites We were impresssed with the great response to this contest with over 35 submissions from several University of Puget Sound students. We wanted to publish them all-this is our attempt. Keep taking photos and keep Elements in the loop because we want to publish them! Sincerely, Elements Staff

Top: Bryce Bunn Left: Abby Mattson

Top: Lexy Woods

Left: Martyn Reif Titled â&#x20AC;&#x153;Stay Awhileâ&#x20AC;? Taken in the Enchantments, Alpine Lake Wilderness, WA

University of Puget Sound University of Puget Sound

29 29

Photo Contest Winners:

2nd Place

Touching on Sensitivity |

By Kathryn Papoulias

Elements,

Most Creative Interpretations of the Theme Feeling Out of Our Element | By Shana Murraywolf

The Golden Orb spider, Nephila clavipes, use their legs to pluck their asymmetrical webs and feel everywhere in the web for prey. This is the largest (female) neotropical orbweaving species of spider. Kathrynâ&#x20AC;&#x2122;s image captures a spiderâ&#x20AC;&#x2122;s delicate touch. We love this depition of a sensational element.

Two girls on a bridge in Amsterdam. This photo is unique r for this theme and an abstract representation of a common human experience.

Elements Magazine

however you interpret it...

3rd Place Elements to me mean the natural things in life, materials we see everyday but end up taking for granted or forgetting | By Diedre McNally This was taken last summer on my birthday in Portland, Oregon. We love this perspective of appreciating the small things around you.

University of Puget Sound

Element of Fear | By Erin Jamroz Climbing Mt. Rainier and walking across an icy chasm. We love the immediate gut reaction of fear to this photo. Taken from the photographerâ&#x20AC;&#x2122;s perspective, you are put in his shoes (or wooden planks?) to imagine the experience of crossing a deep, icy chasm. What happens if you fall? His gear is also in focus, which adds another dimension to the experiemce.

Elements The Scientific Magazine of the University of Puget Sound

Photo Contest Winner!

more contest winners inside...

Element/Earth|By Sharon Styer

“This photo was taken last Fall at Terry’s Berries in Puyallup. Bee, whose feet these are, had just returned from a workshop on making outdoor ovens. She learned how to use her feet to mix mud with straw and create building material for the ovens. Combining the mud, straw, and other organic matter actually takes quite a bit of physical strength and energy to bring the mix to the right consistency.” Not only was this photo artistic, but we also immediately thought of Elements Magazine and how many ways it fit the contest theme, “your interpretation of elements”. The feet are squished in the earth that is squirming with organic matter, microbes, roots, and the life-supporting nutrients. It invokes a feeling of human connection with earth and all its wonderful elements.

Elements Magazine 32 13, FLIP SIDE, Spring 2013 Issue