Uts vol2

Proceedings of the Biological Sciences Student Research Showcase 2011

LETTER FROM THE EDITOR

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ast year, the students of The Saltman Quarterly did something extraordinary. They combined visual arts with biology in order to create a publication that not only represented the amazing undergraduate research done at UCSD but also conveyed science in an entertaining and aesthetically-pleasing way.

The new publication presented science in a way that was friendly to lay audiences, and enabled them to learn about the great work undergraduates do at the university. Out of the combined efforts of dedicated Saltman Quarterly editors, faculty advisors, and student artists, a new vessel for scientific communication was created: Under the Scope.

Born from The Saltman Quarterly program, Under the Scope is true to the dream of keeping the legacy of Paul Saltman alive. Dr. Saltman believed that knowledge and education set you free, and that is precisely what this publication aims to accomplish. A collaboration of student writers and artists, this volume of Under the Scope educates in a unique way. Just as biology encompasses all aspects of life, the journal encompasses an interdisciplinary approach to teach

both science and non-science communities about the mechanisms governing our everyday lives. Building upon the publication’s mission to promote student talent, this year’s Under the Scope includes a Perspective section, giving students a chance to write opinionated pieces on their favorites topics in the scientific world.

It is my pleasure this year to present to you the second volume of Under the Scope. Highlighting research presented at the 2011 UCSD Biological Sciences Research Showcase, this volume takes readers “under the scope” of the exciting biological research being done by our very own undergraduate student body.

It carries on the tradition of exemplary science and talent that is the very foundation of UCSD, and more importantly, inspires future innovation and excellence.

Nishita Shah, Executive Editor, Under the Scope

EDITORIAL BOARD

STAFF ADVISORS

FACULTY ADVISORY BOARD

WRITERS

ILLUSTRATOR

Executive Editor Nishita Shah

Associate Dean of Education Gabriele Wienhausen, Ph.D.

Brain, Mind, & Neurological Diseases Jill Leutgeb, Ph.D.

Nicole Oliver

Production Editor Shawn Shah

Media Specialist Katie Frehafer

Cell Growth, Development, & Control Jim Wilhelm, Ph.D.

Technical Editor-Graphics Erica Couzens Sabrina Trinh

Undergraduate Adviser Hermila Torres

Body’s Defenses Steven Wasserman, Ph.D.

Diana Ponce-Morado Adrian Van-Sickel Aditi Abraham Namrata Vora Zac Hodosevich Kritika Reddy Jessica Lau Matthew Mayeda Yasaman Pirahanchi

Technical Editor-Contents Esther Oh Annie Wang

Conservation & Ecology Teri Markow, Ph.D. Physiology & Metabolism Kathleen French, Ph.D.

TABLE OF CONTENTS 16

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4 If Only Money Grew on Trees

The need for public support in increasing scientific funding: a student’s perspective

8 Navigating Through Our Complex Nervous Systems Researchers use model organisms and new technologies to fill in the gaps in our intricate neuronal networks

12 From a Single Cell

By discovering new ways to regulate stem cell differentiation, researchers are expanding the therapeutic potential of stem cell research

14 Building Up Our Superhero Strength

As they delve deeper into the immune system and the pathogens it encounters, students are attempting to find novel ways to help strength our defenses

18 Uprooting the Mysterious Side of Plants

Student researchers find ways to maximize the benefits we get from plants

22 Can You Count the Beat?

By understanding the physiology behind diseases such as COPD and high blood pressure, students are opening new doors for effective diagnostic tests and therapies

26 Biological Sciences Research Showcase 2011 Abstract List

A STUDENT’S PERSPECTIVE

If only money grew on trees the need for public support in increasing scientific funding

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he eradication of smallpox, the flu vaccine, penicillin – all these life-changing events were brought to us by dedicated scientists. While the existence of these panaceas proves that scientists are powerful people, their intellectual power is constantly being checked by society.

Imagine having an idea that could revolutionize the way that

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scientists conduct science. Now imagine the idea not coming into fruition for a very sobering reason – you ran out of funding.

This is exactly what happened to Dr. Doug Prasher. His idea?

The ability to tag proteins with another smaller fluorescent protein, the Nobel-prize winning green fluorescent protein (GFP). However, the widespread utility that we now attribute to GFP was not recognized when Prasher was interested

PERSPECTIVES

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in it. His initial grant proposal to the National Institutes of Health (NIH) to study the protein was rejected by a panel of scientists. Though he was later able to receive funding from the American Cancer Society, Prasher was unable to fully explore GFP’s potential because this grant only lasted for two years.

process. Typically a grant is reviewed by what is called a study section, composed of certain scientists who are familiar with the field of research discussed in the grant. They consider many factors, such as the significance or potential impact of the proposed work, whether the investigator has the expertise to conduct the project, how the project will be carried out, and if all necessary Prasher’s story is not unique. Today, many outstanding resources are present to allow for successful completion of the scientists struggle to receive funding. With a funding rate project. When all these factors are accounted for, a percentile of barely 10%, many have their grants rejected as well, but is assigned to the grant. A low percentile is desired and means not necessarily because the proposed science is unsound. that there are few other grant applications that are considered to have a greater priority score from the study section. However, the The 2011 budget for the NIH, one of the largest distributers of value of a percentile seems to have diminished. Today two grants research grants, was around with similar impact $30 billion. Additional “Taking into account that not all investigators scores can be given a funding agencies include receive the same amount of funding, nor do all percentile of either 5% the American Heart investigators receive grant approvals every year, or 20%, the deciding Association, the National factor between the many will find themselves in a Prasher-like situation: Science Foundation, and two seeming arbitrary. great ideas, but without funds to explore them.” the American Cancer Society. Assuming that If there are specific investigators across the nation, numbering approximately 350,000, rubrics by which a reviewer should approve a grant, why are get an even share of the pie, that leaves around $200,000 per those rubrics ignored when making the final decision? The investigator. This might seem like a reasonable figure. Now consider answer again boils down to a shortage of funding. With limited that such a grant must pay an overhead to the university (55% for funding to allocate, reviewers are often forced to fund those UC San Diego) and provide salaries and fellowships for post-docs, projects that both Congress and, ultimately, the taxpayer find technicians, and graduate students. After such considerations have most useful – such as those relating to cancer or heart disease. been made, the funds available for reagents and equipment become sparse. Taking into account that not all investigators receive the While cancer and heart disease are enormously worthy causes, same amount of funding, nor do all investigators receive grant the strides made with regards to those ailments have not been approvals every year, many will find themselves in a Prasher- made without sufficient investments in basic research. It might like situation: great ideas, but without funds to explore them. be obvious to biology students why studying the regulation of the cell cycle is essential to understanding cancer, or that This problem could be solved by increasing the initial amount understanding how muscles contract and relax could provide of funding available. Before additional funding is approved, grant insight into heart disease, but to the average taxpayer they are not. reviewers have to apply several criteria to the grant approval

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drug could go a long way in earning taxpayer appreciation.

Considering the breakthroughs that have been made in recent years with regards to science and the pervasive way in which they affect humanity, it hardly makes sense to reduce funding for something that can continue to impact our lives so positively. Many have already attested to this fact on a petition at the Change.org website to increase NIH funding and have left comments such as “research saved my life.” While changing the way that prescriptions are labeled to better educate the public can take time, the fastest way to contribute to the cause is right here. Dr. Kerri Mowen of The Scripps Research Institute has started a petition to do just that.

photo courtesy of http://report.nih.gov

The success rate of awards granted to grant applicants have steadily declined over the years.

Perhaps it is worthwhile for us as part of the scientific community to better communicate to other taxpayers the benefits of science. Let’s start with the numbers that make one of the stronger arguments. For every dollar allocated to funding for the NIH, slightly over 2 dollars are put back into the economy. That is over a 100% return on an investment! For instance, that return could be used to create new jobs within the U.S. and possibly act as a stimulus for economic growth. Why should talent be driven abroad if the U.S. can provide the adequate resources for scientific innovation? It makes economic sense to vigorously fund research.

how can you get involved?

Go to: http://www.change.org/petitions/congress-increasefederal-research-funding-for-the-national-institutes-of-health.

By signing the above petition you would not only help increase funding for research but also help to fuel an attitude of enthusiasm for the process of learning, something we as college students have all experienced and would be amiss without.

ACKNOWLEDGEMENTS Special thanks to Dr. Kerri Mowen for giving her time to be interviewed, her insights into the grant funding process, and ideas on reaching out to the taxpayer.

Equally important is helping the taxpayer understand what research entails. Though pain relievers and antibiotics are readily available over the counter, the years of effort that WRITTEN BY KRITIKA REDDY. Kritika Reddy is a Biochemistry & Cell Biology went into ensuring their efficacy are not always apparent. A major from Revelle College. She will be graduating in 2012. simple label stating the number of years and the amount of funding that went into the discovery and development of the PERSPECTIVES

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Navigating through our complex nervous systems Undergraduates researchers here at UCSD are using model organisms and the technology available to them in order to help fill the gaps in the human neuronal networks. By doing so, they open new doors into disease treatments and potential cures...

BRAIN, MIND, AND NEUROLOGICAL DISEASES

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uman ingenuity and knowledge are both byproducts of our imagination; we use it to examine, reason, and solve problems. But when we look at the nervous system, an intricate network resembling a convoluted subway map, we are limited by the physical characteristics of the naked eye and can only perceive body movements as a response of neuron communication. The only way we can endeavor to better understand our own highly complicated neuronal maps, which are both mysterious and complex, is to perfect our ability to develop and compare biological models across a group of different organisms.

systems within the organism being examined. By answering these questions, especially within the scope of organisms with simpler nervous systems, great progress can be made in understanding the function of nerves more broadly, which itself is an important step in developing cures for neurodegenerative diseases. This was the objective of the research of Vaibhav Konanur, who, under the supervision of principal investigator Dr. Kathleen French, examined nervous inhibition in Hirudo verbana leeches. Leeches are excellent subjects for this kind of work because although they are generally simple in build, they exhibit remarkably complex behavior usually attributed to more sophisticated nervous Last year’s student research showcase offered fascinating systems, such as that of humans. Unlike in humans, it is relatively insights into the work being done to better understand the nature easier to identify the neural circuitry in leeches and determine of the human nervous system and neuroscience in general. the contribution of that circuitry to more complex behavior.

As neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease have come to the The particular phenomenon examined was the “local bend.” forefront of the public’s attention due to increased prevalence During this observed mechanism, leeches reacted to a point across the nation, it has also become clear that significant stimulus, such as a needle prick, with the stimulated area contracting progress has been made to in what is apparently an aversive understand the nervous “Whether they’re transfecting hippocampal reaction. By studying this systems of humans and other cultures of rats or zapping individual nerve cells local bend behavior and the organisms. Unfortunately, inhibitory neurons associated in leeches, student researchers at UCSD have a precise knowledge of the with it, as well as identifying problems that afflict people lot to bring to the table, not only to the showcase, GABAergic neurons, the – particularly that which but to the realms of both neurobiological neurons that produce the can be used to impede and and acid biomedical research in general. “ gamma-aminobutyric even reverse the progress of (GABA) neurotransmitter, those afflictions – continues to elude the scientific community. Konanur was able to characterize what he calls Cell 116, a The research presented at the 2011 Biological Sciences Student previously unidentified neuron. Through an electrophysiology Research Showcase showed us the many avenues through which study and a dot blot analysis to identify GABA while studying students are contributing to further advances in neurodegenerative individual neurons and neurotransmitters, the French lab was disease research as well as neurobiological research. able to identify which neuron was responsible for eliciting the aversive behavior characterized by the “local bend” effect.

There are many unanswered fundamental questions about how neuronal circuits interact with each other and with other Leeches and humans seem to have fairly little in common, but

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when asked about what significance this research bears for the understanding of the human nervous system, Konanur explained some of the things which we do have in common with leeches. For example, GABAergic signaling is important for deep brain activity in humans. The neurotransmitter GABA is important for neuronal communication underlying everyday functions such as memory and motor control. Furthermore, inhibitory neurotransmitters like GABA are key players in human frontal lobe activity, which is responsible for voluntary movement and sensations such as motivation. As it turns out, these neurotransmitters can be targeted by psychoactive drugs to prevent certain behaviors from being exhibited in a person’s immediate temperament. Thus, understanding GABA regulation in “simple” nervous systems gives us the potential to uncover fundamental principles and mechanisms common to all nervous systems, including our own.

When performing research pertaining specifically to neurological diseases in humans, rats are often the physiological model of study. Therefore, it was the subject of choice for Vishnu Parthasarathy and his principal investigator, Dr. Shelley Halpain. At the center of his work was the amyloid-β protein, which is associated with the underlying course of neuron cell death that is characteristic of Alzheimer’s disease.

The natural accumulation of the amyloid-β protein from the neuron synapses is hypothesized to lead to neuron death. In order to explore the mechanism by which nerve cells are eventually disabled, Parthasarathy studied the surfaces of dendrites of adult rat hippocampal neurons. His research showed that dendritic spines, the sites for communication between neurons, physically change in response to amyloid-β. Moreover, it is possible that finding a way to prevent these changes will shed more light on a method to slow, stop, or reverse the progression of Alzheimer’s. Further research regarding amyloid-β and synaptic plasticity, or the potential for synapses to change in a way that

affects memory and behavior, can help to find ways to impede the progression of memory loss, and eventually to find a cure.

The research being done on Alzheimer’s disease is becoming increasingly extensive, for good reason. According to data from 2011, Alzheimer’s afflicts approximately 5.4 million Americans, is the fifth leading cause of death in the U.S., and will increasingly affect more people in the coming years. It is important to understand that Alzheimer’s is not a regular part of aging, even though it has become the most common form of dementia.

Presently the only option for Alzheimer’s patients is treatment to relieve symptoms until they are no longer treatable, but work like that of the Halpain lab is being done all over the world in an effort to expand our understanding of the disease and stimulate future research directed toward new therapeutic strategies.

Whether they are transfecting hippocampal cultures of rats or zapping individual nerve cells in leeches, student researchers at UCSD have a lot to bring to the table, not only to the showcase, but to the realms of both neurobiological and biomedical research in general. The endeavor to understand the complicated, often frustrating nervous system continues, and hopefully it will produce findings to change, save, and enlighten the lives of people who deal, in one way or another, with matters of the nerve every day.

WRITTEN BY DIANA PONCE-MORADO & ADRIAN VAN-SICKEL. Diana Ponce-Morado is a General Biology major from Thurgood Marshall College. She will be graduating in 2012. Adrian Van-sickely is a Mathematics major from Revelle College. He will be graduating in 2013.

BRAIN, MIND, AND NEUROLOGICAL DISEASES

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from a single cell

by discovering new ways to regulate stem cell differentiation, UCSD researchers are expanding the therapeutic potential of stem cell research.

The National Institutes of Health (NIH) defines stem cells as “cells with the ability to divide for indefinite periods in culture and give rise to specialized cells.” For many years now, stem cell research has been deemed an extremely promising avenue for researching attempts to cure a variety of diseases. If research is able to successfully differentiate stem cell differentiation, it will be possible to use stem cells for organ repair and to achieve a deeper understanding of pathogenesis and human disease.

Undergraduate researchers at University of California, San Diego, such as Alexander Vu, who works in the Yu lab, are developing new tools to regulate stem cell differentiation. Vu’s research is focused on the effects of adenovirus infection on stem cell fate. Adenoviruses are small viruses capable of infecting many different species of animals. When infecting humans, they cause respiratory diseases such as pneumonia. Normally, adenoviruses infect and eventually kill cells through the expression of the lethal protein E1A. E1A is an oncoprotein, a Our bodies originated from protein that causes dangerous changes “if we could direct stem cells in the regulation of regular cell growth a single cell which divided into the many different types of cells to form the types of cells and that are likely to lead to cancer. E1A that are necessary to carry out the tissues we need, we would is a critical protein in viral infection different functions that make life because it is necessary for the viral have a new and powerful tool genes to be expressed. It facilitates possible. The neurons that allow for making progress towards increased replication of the adenovirus thought and feeling, the muscle cells that allow us to move, and curing many different diseases.” by causing changes in regular gene the immune cells that allow us expression in the cell. These changes to fight off a cold all originated cause the cell to speed through the cell from a single, undifferentiated cell. Stem cells play an important cycle unregulated, bypassing normal checkpoints. This causes the role in forming all of the different cell types because they are cell to divide more often and results in an increased number of pluripotent, which means they have the ability to divide into and infected cells as well as an increased number of copies of the virus. specialize as any type of cell, and do so based on environmental signals. Thus, stem cells are the raw source material for all of the The Yu lab exposed mouse embryonic stem cells to an cells in the human body. If we could direct stem cells to form adenovirus. This introduction of adenovirus into stem cells the types of cells and tissues we need, we would have a new and was a novel idea in research because it normally causes cancer powerful tool to progress towards curing many different diseases.

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and has a lethal effect on cells. The Yu lab avoided this problem by using a modified adenovirus which contained a non-lethal version of E1A. Because E1A has oncogenic properties of reducing cell cycle regulation and increasing gene expression, Dr. Yu hypothesized that stem cells exposed to E1A would have increased potential in expressing the various genes characteristic of different cell types while remaining pluripotent.

If, for some reason, the infection did cause differentiation, it was unknown into what cell type the stem cells would differentiate.

In order to test their hypothesis, they transduced, or infected, the mouse stem cells with the adenovirus and studied the effects for 72 hours using a real-time microscope to determine whether the cells were differentiating or remaining pluripotent.

Vu explained that pluripotent stem cells in culture will remain

clustered together. On the other hand, stem cells in the process of differentiation will migrate away from this main cluster, giving them more space to divide and create specialized tissues.

Since the cells were expected to remain pluripotent, they were expected to remain clustered together, but the results were surprising. Instead of clustering, the cells spread out.

After realizing that the adenovirus had signaled the stem cells to differentiate, researchers then tried to pinpoint the types of cells that the sample had specialized into. Specialized cells express certain proteins characteristic of their cell type. Therefore, by looking at the types of proteins expressed in a cell, they could deduce the cell type through quantitative PCR. Using this technique, the researchers found that the differentiated cells had high levels of certain protein transcription factors such as Brachyury-T, Goosecoid, and EVX-1. These proteins characterized the differentiated cells as primitive streak mesodermal cells and most probably cardiac cells. Further research showed that E1A exerted its effects by binding to the proteins p300, pRb, and CBP, proteins that are critical for both human and mouse development. Further studies are necessary to confirm that these cells are cardiac cells. If so, the research could have an extensive impact, giving researchers the beginnings of a procedure to regenerate functional heart cells.

Describing the future implications of his research, Vu stated, “Although most modern medicine is palliative, aiming only to simply treat the symptoms of disease, stem cell research can allow us to create therapies with the potential to actually cure disease.�

photo courtesy of http://www.chxa.com/what-are-stem-cells/

Stem cells are found in all multicellular organisms, and divide in order to differentiate into many specialized cell types, including blood cells and muscle cells.

WRITTEN BY ADITI ABRAHAM. Aditi Abraham is a Human Biology major from Sixth College. She will be graduating in 2012.

CELL GROWTH, DEVELOPMENT, AND CONTROL

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building up our Superhero Strength Literature is full of battles between good and evil. These battles can be found in novels, folklores, and comic books. Villains like the Joker and Green Goblin dominate the comic world, waiting in dark corners to attack the favored superhero. The battle of good and evil is not limited to childhood works of fiction. The battles exist underneath our skin and muscles. More specifically, the battle of good versus evil is comparable to the battle between invading pathogens and our body’s line of immune defenses. While the pathogens that invade our body may not include characters with lethal weapons, the pathogens have potential to be just as deadly to the human body.

THE BODY’S DEFENSES

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ome of the body’s biggest villains are infectious bacteria. us more information to classify the bacteriophage within a family The body’s defenses are not strong enough to deal with of bacteriophage with a similar genome. Once we understand deadly bacteria. For example, Mycobacterium tuberculosis the structure of bacteriophages, we can use them as allies to is the germ responsible for tuberculosis, a disease that killed defeat villainous bacteria in a process known as phage therapy. over 1.5 million people worldwide in 2010 alone. Fortunately Phage therapy has been used in Eastern Europe for the past one for us, bacteria have one unique weakness: attack from the hundred years. It is used to kill harmful bacteria, including those resistant to antibiotics, without bacteriophage.

Bacteriophages are viruses that specifically attack “About 1.5 million people die each harming the patient. Pneumonia, staph, and strep throat, bacteria. Vicky Hwang, a student year of tuberculosis and as much as along with tuberculosis, are in the Phage Genomics Research Initiative, a Howard Hughes one third of the world may be infected. examples of common illnesses Medical Institute sponsored Phages like Fionnbharth infect bacteria that phage therapy can treat.

The human immune system program taught by Professors and not humans, allowing for the Joseph and Kit Pogliano, is studying possibility of using viruses to treat has an intricate mechanism to bacteriophage reproduction bacterial infections like tuberculosis...” recognize and combat foreign cells. These defenses are mechanisms. “Bacteriophages latch onto their host and inject their genetic material […] Eventually absolutely crucial in keeping out unwanted organisms. However the host cell will be lysed and copies of the virus will be released,” these defenses also present a problem during transplant surgeries.

Hwang explained. Over the course of their research, Hwang and The body’s immune system will recognize foreign cells and her colleagues isolated and characterized a new bacteriophage – create antibodies that attack and destroy transplant tissue. This Fionnbharth. After sequencing Fionnbharth’s genome, Hwang ultimately results in the body killing its own transplant tissue. and her colleagues compared it to previously known genes This is evidenced by the 50 percent lung transplant rejection rate.

Knowing the genome of a bacteriophage helps us understand However, research being done at UC San Diego aims to lower how the bacteriophage works. Knowing the genome also grants this rejection percentage. Aditi Abraham, an undergraduate student at UCSD, studies lung transplant rejection in Dr. Patricia Finn’s Depiction of the typical structure of a lab. Abraham and her colleagues hypothesize that differences in bacteriophage. The the microbiotas of the lungs explain why transplant rejection pathogen’s structure occurs. Microbiota, the harmless microbes living in the human allows it to “inject” its body, differs from person to person. Therefore, when a patient own genetic material into goes through an organ transplant surgery, the patient receives a the host cell. The genetic material it injects can stranger’s microbiota. While the donor’s microorganisms may be be either DNA or RNA, harmless in their own body, they are foreign in the recipient’s body. depending on the type of This can cause organ rejection. Abraham explains, “Depending phage. on whether the bacteria are commensal or pathogenic, this causes photo courtesy of http://pudsandlosers.blogspot.com

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a corresponding immune reaction. Therefore certain profiles of bacteria may be more likely to cause rejection than others by causing an unfavorable immune response and rejection of the lung.” In other words, if two people have different microbiota in their lungs, the chance of a successful lung transplant is reduced.

research shows a significant difference between the expression of the 16S bacterial gene in transplanted lungs and the lungs of patients with COPD. This implies a difference in the quantity of bacteria . However, it remains to be seen whether this increase in bacteria is due to the disease itself , or due to the differences in microbes of the patient’s body and the body from which the transplanted lungs were taken. Like viral infections, transplant rejections must first be understood before they can be fought.

Abraham’s work involves analyzing the differences between the lung microbiota in patients with transplanted lungs and the patients with Chronic Obstructive Pulmonary Disease (COPD).

As of now, lung transplantation is the only viable treatment for The bacterial battles in the human body are reminiscent COPD, the fourth leading cause of death in America . Abraham’s of the battles of good versus evil in comic books. In order to prevent our bodies from invasion by evil pathogens, it is crucial to continue research on them. The sequencing and understanding of pathogens’ genomes illuminates the pathogens’ vulnerabilities. It is the illumination of these vulnerabilities that will help us with the fight towards healthier lives. The fight towards healthier lives is a fight towards building our superhero tolerance against the villains.

photo courtesy of http://www.austincc.edu

Antibodies have the structure pictured above. Each antibody is specific to a particular antigen and this specificity is accomplished by the vast diversity of variable regions, shown as the “V” regions above. Many transplant surgeries fail to be successful because the host’s immune system alerts the body of a foreign organ in the body, creating antibodies against the new transplant organ.

WRITTEN BY ZAC HODOSEVICH & NAMRATA VORA. Zac Hodosevich is a Human Biology major from Thurgood Marshall College. He will be graduating in 2013. Namrata Vora is a Human Biology major from Revelle College. She will be graduating in 2013.

THE BODY’S DEFENSES

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uprooting the mysterious side of plants We are constantly finding ways to alter plants in order to benefit ourselves by maximizing food production and agricultutal profits.

But little do we know that all these self-serving benefits may actually be helping plants even more than they are helping us.

UCSD researchers are turning the leaf over on the mysterious lives of plants...

ECOLOGY AND CONSERVATION

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ave you ever gazed at that shiny red apple in the cafeteria lunch line and craved to bite into it? Or longed for a bouquet of exquisite flowers from a loved one just because flowers are pretty? Plants are integrated into every aspect of our lives, and for thousands of years we’ve always thought that we control them – but what if they have been influencing us for their own purposes? From dispersing their progeny with exploding seeds to secreting chemical substances to sabotage the success of unwanted plant neighbors, the reproductive success of plants is easily seen in their nearly universal presence. Like all living organisms, plants’ ultimate goal is to spread their progeny, and they have evolved countless cunning methods of doing so.

Whether it is by harnessing a ride while snagged to the fur of a bear or giving its seeds aerodynamic qualities, plants are capable of traveling – and surviving – in a wide range of climates. Such

photo courtesy of the Yanofsky lab

A diagram of the Arabidopsis fruit opening; the Yanofsky lab focuses on flower development genes governing processes such as the one pictured above.

hardiness in plants has prompted humans to attempt to harness that evolutionary prowess for their own benefits – from hybridizing only the hardiest of potatoes to importing foreign plants to their hometown. Though we may believe we are in control of such a relationship, perhaps this is simply a failure to realize the larger implications of our actions: are we using plants, or are they using us?

Throughout history, humans have attempted to breed plants that produce higher crop yields, are resistant to pests and drought, or are otherwise beneficial to humans. Scientists of old may have relied on crossing different species to see which ones produced the best results, but today’s researchers photo courtesy of http://tl.wikipedia.org/wiki/Talaksan:Rice_Plants rely on increasingly more advanced technology to help them By genetically modifiying staple crops such as rich with essential learn about plants. Two such modern investigators are Lindsey nutrients, scientists are trying to help reduce vitamin deficiences Bailey and Scott Wu of the Yanofsky lab, who are investigating in several Asian countries whose diets consist heavily of rice. the mechanisms underlying fruit development. Understanding

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which factors influence fruit development may lead to the increasingly desirable, prompting their distribution worldwide. production of a crop that can be harvested at more opportune Not only are these plants able to reach regions that would be times to avoid threatening climate shocks or destructive pests. impossible without human transportation systems, the new alterations are beneficial to the plants themselves. By bolstering In particular, Bailey’s and Wu’s research focuses on the role their genetic armories to enhance pest defense and survival in of microRNAs (miRNAs), which are short RNA segments even the most infertile of habitats, we help plants propagate their capable of binding to complementary sites on mRNA. In doing future progeny more efficiently than ever. Simply by altering their so, miRNAs are able to inhibit characteristics to be most useful to translation and play a critical “By bolstering their genetic armories humans, plants have successfully role in silencing genes. Two to enhance pest defense and survival tricked us into helping them skip such miRNAs are miR-127 and in even the most infertile of habitats, millions of years of evolution, miR-156, which are capable of and become more reproductively we help plants propagate their future regulating flower development successful than ever before. progeny more efficiently than ever.“ and fruit maturation. Bailey and Wu have shown that the Popular belief views plants expression of these miRNAs plays a role in silencing genes that as passive organisms that we control. But a deeper look contribute to flower development. More specifically, studies into this relationship reveals a symbiotic one: plants’ ability have shown that overexpression of miR-127 causes premature to be modified and cultivated in many environments has flowering whereas overexpression of miR-156 delays flowering. provided us and our ancestors with sustenance. Likewise, The presence of control elements can also influence the levels of our attachment to plants have prompted us to spread them, miRNAs, allowing biologists to manipulate flower development allowing plants to enter new areas that would otherwise be with a particular phenotype in mind. Such manipulations can unreachable. Perhaps we are not as in control as we think. be potentially beneficial for global farmers who have difficulty achieving desired crop yields due to destructive pests and unforeseen weather conditions. If scientists can engineer crops that are able to flower off-season, pest or weather damage can be reduced, allowing farmers to reap the maximum benefits from their crops.

These scientific advances already have been utilized across the globe. In Asia, farmers have begun using a strain of rice engineered to be more vitamin-rich, thereby preventing common vitamin deficiency related maladies, namely night blindness caused by vitamin A deficiencies. Other crops, including zucchini and cotton, have been altered to be more resistant to pests and viruses. Such modifications have made particular plants

WRITTEN BY JESSICA LAU & KRITIKA REDDY. Jessica Lau is a Human Biology major from Eleanor Roosevelt College. She will be graduating in 2012. Kritika Reddy is a Biochemistry & Cell Biology major from Revelle College. She will be graduating in 2012.

ECOLOGY AND CONSERVATION

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can you count

ccording to U.S. News, the most visited city in the world is none other than Paris, France. Filled with spectacular sites like the Eiffel Tower and first-rate culinary experiences, it is no wonder that the City of Love tops many people’s vacation lists. Located less than nine miles away from the world famous Louvre museum in the city of Sérve, there is another very important building known as the International Bureau of Weights and Measurements. Locally know as the Bureau International des Poids et Mesures, this institution ensures a “world-wide uniformity of measurements” through the Metric Convention and safekeeping of the international prototype kilogram. Without the Bureau and its standard measurements, science progress would be painfully slow as it would be nearly impossible for scientists to understand each other’s work. While the Bureau International des Poids et Mesures does an excellent job standardizing many types of units, there are many specialized forms of measurements that still need some uniformity.

who were on blood pressure medications and those who were not, but failed to differentiate between the two populations. As a result, variations in some subjects’ blood pressure could have been altered by their medications, whereas there would be no such effect in the drug-free patients. That is, the experimental design did not allow for proper comparison between these patients.

In the past, researchers have tried one of two approaches to control any variability caused by the study of subjects’ medications. The most commonly used method is called the “sixth addition.” In this approach, 10 mmHg is added to the systolic pressure, and 5 mmHg is added to the diastolic pressure of any subject who is taking hypertension medications. The procedure is intended to compensate if the medication has altered the patient’s blood pressure and to estimate his or her “true” blood pressure (what it would be without medication).

However, the same factor is added to all subjects’ blood pressure readings regardless of what drugs the patient has been taking UCSD undergraduate Anish Dhamija, collaborating with Dr. or the number of different hypertension medications the patient Brinda K. Rana, decided to take on one of these issues in the is on. In an alternative method, called a “step addition,” a fixed world of medicine by delving into genetic computation through value is added to the patient’s blood pressure for each of drugs his project, which analyzes the correlations between blood the patient is taking. Although this method acknowledges pressure (BP), genetics, and body mass index (BMI). Previous the importance of multiple medications, it fails to take into studies investigating hypertension subjects included both people account differences in the effects of different types of drugs.

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the beat?

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To address the weaknesses in these two common approaches, classes of drugs in one formulation. In these cases, the model Dhamija integrated the sixth addition method with the step included data about the separate drugs and their unique addition method of evaluation to create a new, innovative approach effects, rather than compressing the data into just one drug. that could account for both the type of drug classes A novel – and valuable and the number of drugs – aspect of Dhamija’s study “Dhamija hopes that his new holistic being used. Additionally, was that it controlled for approach of analyzing blood pressure will his method of analysis heritability by analyzing be integrated into planning therapeutic took into consideration the data from middle-aged interventions with hypertensive (ranging from ages 40 to previous observation that medications and evaluating their effects.” as more hypertension drugs 60) cohorts of male twins are taken, adding more from around the United drugs to the mix produces less and less improvement. States. Each pair of twins was compared after their “true” BP was calculated by the model. Because the new model allowed Dhamija found that including in the analysis more specific for a strict comparison of genetics and accounted for other information about the effects of all medications that a patient external variables, researchers were then able to compare blood is taking, as well as other factors, increases the accuracy of the pressure changes between twins, and they discovered that estimated “real” BP; as a result, Dhamija’s approach provided genetic background contributed less to whether an individual a superior basis for comparison. In addition to including the will develop hypertension than had previously been thought. number and types of drugs a patient was taking, his model compensated for ethnicity. Previously such a model could Dhamija hopes that his new holistic approach of analyzing include data for only up to 3 drugs; his model expanded the blood pressure will be integrated into planning therapeutic capability so that up to 6 drugs could be included. In some interventions with hypertensive medications and evaluating their medications, a single pill or capsule incorporates two different effects. When computing an adjusted BP using more precise PHYSIOLOGY AND METABOLISM

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variables, the apparent relationship between genetics and BP shrinks, indicating that external factors may play significant roles in the BP of the patients. Also, the more medications the patients were taking, the smaller overall effect each drug had, suggesting that boosting the number of drugs a patient is taking may be illadvised. Furthermore, Dhamija hopes that more people will adopt the “Adjustment by Drug Class” method that he used because it provides a more accurate prediction of BP for future research.

Another undergraduate student, George Murano, performed breakthrough research in collaboration with Dr. Ellen C. Breen.

He sought the correlation between patients with COPD and the debilitating muscle dystrophy that is eventually seen in many patients with the disease. COPD begins in the lungs, and Murano investigated a current hypothesis that COPD causes muscle dystrophy by affecting the delivery of blood to the muscles.

He conducted a series of electrophysiological experiments in which he recorded muscle contractions in live mice. He stimulated the gastric muscle with an electrode, recorded the force produced in response to the stimulus until the muscle reached its maximum, then recorded the time it took for the muscle to decline from its maximum force to when the muscle contracted at just half of its maximum force value. This protocol allowed him to find the muscle exercise capacity of each mouse.

These experiments were done on 50 to 60 mice that each overexpressed the TNF-α gene in the lungs. TNF-α induces COPD in the mice and subsequently causes muscle dystrophy by travelling through the blood stream. Murano also found that male mice were more affected by COPD than the female mice were.

This research was unique in that it measured the response of the muscles while they are still in live mice instead of dissecting the muscle out of the mouse before recording the response. Therefore, it takes into account the impact of

circulatory and respiratory function. Murano hopes to expand on this project by measuring blood flow while he stimulates the muscle to see if the circulatory system truly mediates the impact of TNF-α on exercise – a new concept. These newly discovered interactions deepen our understanding of COPD and how blood flow to other systems can further impact a patient.

Looking at the International Bureau of Weights and Measurements, it makes one wonder how such important strides in measuring data have been made. No doubt, it took the combined efforts of many citizens to get such amazing standardizations. Thanks to the efforts of these research projects, great improvements in the areas of their respective studies have been made. In the case of Murano’s study, further efforts to understand interactions of TNF-α will allow for continued observation of its impact on COPD patients. Murano also hopes to further investigate pathways of interaction causing muscular dystrophy. Dhamija’s method will greatly impact blood pressure research, assisting in creating more accurate interpretations of what collected data really means. With their combined efforts, they have made contributions to their fields that will manifest themselves in their own kind of “Poids et Mesures”.

WRITTEN BY MATTHEW MAYEDA & YASAMAN PIRAHANCHI. Matthew Mayeda is a Biochemistry & Cell Biology major from Warren College. He will be graduating in 2012. Yasaman Pirahanchi is a Biochemistry and Cell Biology major from Revelle College. She will be graduating in 2015.

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2011 Biological Sciences Research Showcase abstract list 26

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Cell Growth, Development, & Control (Cancer, Cell Signaling, Stem Cells) Poster #1 Role of integrin alpha-4 in Neuroblastoma Maria Bahramzi Dr. Dwayne Stupack Poster # 7 Identification of CikA Localization Partners in Synechococcus elongatus Michelle Hoang Dr. Susan Golden Poster # 8 Transport Proteins Encoded within the Genome of Myxococcus xanthus Soheil Karbassi Dr. Milto Saier Poster # 10 Characteristics of Golgi Morphology Under the Condition of DNA Damage John Tat Dr. Seth J. Field

Poster # 12 Understanding Stem Cell Differentiation through Adenovirus E1A Oncoprotein Alexander Vu Dr. Benjamin Yu Poster # 13 Characterizing a novel isoform of caspase- 8 Robert Yuan Dr. Dwayne Stupack Poster # 17 The Role of Doa4 in Peroxisome Degradation in Saccharomyces cerevisiae Ishita Desai Dr. Suresh Subramani Poster # 18 The Transcription Factor RUNX1 and its Role in Hematopoiesis Randal Du Dr. Dong-Er Zhang Poster # 19 Interaction of Argonaute with tRNAs in Caenorhabditis elegans Aleksandr Gorin Dr. Amy Pasquinelli Poster # 20 Requirement of Cysteine Residues for the Function of the Peroxisomal Targeting Signal Receptor, Pex5 Danielle Hagtrom Dr. Suresh Subramani

Poster # 23 The recognition of substrate by Ire1 is determined by a variable loop site in the ribonuclease domain Shiqian Li Dr. Maho Niwa Poster # 24 Elucidation of the Mechanism of hDcp2 Stabilization

by Hedls Jeffrey Maloy Dr. Jens Lykke-Andersen Poster # 25 Bioinformatic Analysis of Bacterial Mercury Ion Transporters Timothy Mok Dr. Milton Saier Poster # 31 Seeing Through Skin: Evolving a Near Infrared Fluorescent Protein for Live Animal Imaging Geraldine Tran Dr. Roger Y. Tsien Poster # 33 Faithful Expression of Canonical NFkB Inhibitor IkBa and Single Cell Level Analysis of the NFkB/RelB Activation Kinetics Tony Yu Dr. Alexander Hoffmann Poster # 34 c-MYC Specific Defects of TGFβ1/Smad Signaling in Human Cancer Cells Nathan Zemke

Dr. Beverly Emerson Poster # 43 Bnip3 Interacts with LC3 to Induce Selective Removal of Endoplasmic Reticulum and Mitochondria via Autophagy Rita Hanna Dr. Ă…sa B. Gustafsson Poster # 45 STAT3 Suppress Invasion of Intestinal Tumor via Downregulation of SNAI Chang Kyung Kim Dr. Eyal Raz Poster # 48 The mechanism of AE9a regulation of ALOX5 Benjamin Lewin Dr. Dong-Er Zhang Poster # 49 Comparative binding of RXXPDG sequences to pentavalent ANK repeats in tankyrase Sunny Lu Dr. Nai-Wen Chi Poster # 54 Mechanism of E-cadherin mediated stem cell differentiation Michael Pham Dr. Colin Jamora Poster # 57 Defining Microenvironment Cues that Regulate Stem Cell Gene ABSTRACT LIST

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Expression Tyler Sloan Dr. Karl Willert Poster # 61 Evolutionary Relationships of ATP Binding Cassette Uptake Porters Weihao Zheng Dr. Milton Saier

Ecology & Conservation (climate, environmental changes, plant maturation) Poster #2 Role of Ubiquitination and the Proteasome in Arabadopsis Innate Immunity Kyle Begovich Dr. Steve Briggs Poster # 4 Plant Immune Signaling through NDR1 Kimberly Chia Dr. Steve Briggs Poster # 5 Using cyanobacteria to drive down cost of Algal biofuel production

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Keval Desai Dr. Susan Golden Poster # 9 Genetic Screening for Arabidopsis Mutants that Suppress the Phenotypes of npy1 cuc1 Double Mutant Zixuan Shao Dr. Yunde Zhao Poster # 11 Investigating the Metabolic Evolution of Chalcone Isomerase (CHI) with highthroughput protein-ligand screens Allison Van Vooren Dr. Ryan Philippe Poster # 14 Effects of Rainfall on Soil Moisture Conditions and Phenology in Coastal Sage Scrub and Chaparral Species Tina Beveridge Dr. Elsa Cleland Poster # 15 Hummingbird color preference within a natural hybrid population of Bush Monkeyflower Corinne Handelman Dr. Josh Kohn Poster # 16 Understanding the mating system of a rapidly invading Drosophilid, Zaprionus indianus Giovanni Hanna Dr. Therese Markow

Poster #17 Community Outreach Methods in Clinical Research, Clinical & Translational Research Institute Bryan Lam Dr. Howard Taras Poster # 22 Role of Thioredoxins in Plant Immunity Yujung Lee Dr. Steven Briggs Poster # 29 Exploring Transcription Co-activator overexpression effects on the Circadian Clock Ying Sun Dr. Colleen Doherty Poster # 36 Regulating Heavy Metal Homeostasis in Arabidopsis: OPT3 Affects Metal Toxicity Responses and Cadmium Distribution Garo Akmakjian Dr. Julian Schroeder Poster # 37 Evaluating the Effects of Projected Precipitation Shifts on South Coastal Chaparral Communities Angelita Ashbacher Dr. Elsa Cleland Poster # 38 miRroring the importance of the post-

transcriptional regulation in Arabidopsis fruit Lindsay Bailey Dr. Marty Yanofsky Poster # 39 Sublethal doses of the pesticide imidacloprid alters honey bee (Apis mellifera) response threshold and communication, potentially affecting colony health Eiri Daren Dr. James Nieh Poster # 41 A GLOBAL ASSESSMENT OF CORAL REEF HERBIVORES: Evidence for Fishing Effects on the Biomass of Different Taxonomic and Functional Groups Clinton Edwards Dr. Jennifer Smith Poster # 55 Phosphoproteomics of Arabidopsis thaliana defense mechanism Cheryl Philipsen Dr. Chris van Schie Poster # 56 Unraveling the Fruit Development miRstery Wu Scott Dr. Martin Yanofksy Poster # 60 Positional Cloning and Characterization of the Rotten Ear (Rte)/Truncated Inflorescence

Development (Tid) Gene Tabi Zara Dr. Robert Schmidt

Physiology & Metabolism (blood pressure, muscles, bone formation) Poster #6 APJ directs venous differentiation of the coronary endothelium and is regulated by ERG Leila Haghighat Dr. Patricia Ann Thistlethwaite Poster # 26 Lung overexpression of TNF-a impairs locomotor skeletal muscle function George Murano Dr. Ellen C. Breen Poster #27 Apatite Mineral Formation in Humans Tonhu (Tiffany) Nguyen Dr. Paul A. Price Poster # 30 Hif-1a’s Effects on Metastatic Success Tin-Yun Tang

Dr. Randall Johnson Poster # 40 Does Accounting for Antihypertensive Medication Alter Genetic Association Studies on BP? Anish Dhamija Dr. Brinda K. Rana

Body’s Defenses (pathology, the immune system) Poster #3 Galacto-Oligosaccharides reduce Entamoeba Histolytica cytotoxicity in vitro with and without the presence of Lactose.

Laura Bliss Dr. Lars Bode Poster # 16 Microbiome: Relevance for the Understanding of Lung Transplant Rejection Aditi Abraham Dr. Patricia Finn Poster # 21 Structural Protein Identification and Analysis: A Parts List of a Novel Mycobacteriophage Aleksandar Jamborcic, Garrett Brooks, Alexandra Chen, Vicky Hwang, Sher Khan, John Magarian Dr. Joseph and Kit Pogliano ABSTRACT LIST

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Poster # 28 Application of Mass Spectrometry to Bacteriophage Genome Annotations Chiara Ricci-Tam, Eileen Shi, Joanna Coker, Yasaman Pirahanchi, Rebecca Mazahreh, Hedieh Matinrad, Sean Jones Dr. Kit Pogliano and Dr. Joe Pogliano Poster # 32 Genomic Organization and Comparisons of Cluster K Phage, Fionnbharth Kit Wu, Carolyn Zhang, Jeremy Chou, Adriee Wong, Daphne Chen, Dieter Lam, James Zhang Dr. Kit Pogliano and Dr. Joe Pogliano Poster # 35 Varun Cidambi, Ben Rich, Ander Beckham, Rose Hill, Colee Evangelista, Jim Mcburney-Lin, Christina Dimopoulos Dr. Kit and Joe Pogliano Poster # 44 Alternaria induces STAT-6 dependent acute airway eosinophilia and epithelial FIZZ1 expression that promotes airway fibrosis and epithelial thickness Naseem Khorram Dr. David Broide

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Poster # 46 ATG16L1 suppresses IL-1β signaling via downregulating p62 HyeRi Kim Dr. Eyal Raz Poster # 50 The Presence of TGFβ-Receptor III in Kawasaki Disease Jennifer Lundergan Dr. Jane C Burns Poster # 51 Dynamin in Disease: a Fly model for a Human Centronuclear Myopathy Jen Nguyen Dr. Amy Kiger Poster # 53 Activation of AMPActivated Protein Kinase (AMPK) inhibits Biomechanical InjuryInduced Catabolic Reponses of Articular Cartilage Chondrocyes Freyr Petursson Dr.Terketaub Poster # 58 The Calcification of Staphylococcus aureus Bacteria: A Potential Defense Mechanism Against Bacterial Infections Linh Truong Dr. Paul Price

Brain, Mind, & Neurological Diseases (Alzeihmer’s disease, neuronal processing) Poster # 42 Effects of Spinal TLR-3 Activation in Non-Neuronal Cells of Rats on Pain Processing Hamid Ehsani-Nia Dr. Tony L. Yaksh Poster # 47 Identifying and characterizing leech neurons labeling for GABA Vaibhav Konanur Dr. Kathleen French Poster # 52 The Role of Actin Dynamics in Soluble Amyloid-Ă&#x; Induced Glutamate Receptor Endocytosis Vishnu Parthasarathy Dr. Shelley Halpain Poster # 59 Loss of R-spondin2 leads to additional hair cell development in the mammalian cochlea Andrew Yatteau Dr. Alain Dabdoub

Up close and personal

This photo was taken of a single leaf using purely sunlight as the backlight. The light allows a clear representation of the veins and the amazing networks are formed.

photo taken by Russell DuBois

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Division of Biological Biological Sciences University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0376 (858) 534-5635

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