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2009 Science Horizons Projects

Stoyana Alexandrova

(Mentor: Dr. Usheva-Simidjiyska, Beth Israel Deaconess Medical Center)

Research Summary:  This summer’s research comprised of work on several very exciting projects. I had the opportunity to do cutting-edge research on reproductive endocrinology, DNA melting, DNA methylation, chaotic magnetic field effects on growth rate, and gravitational effects on cellular growth. Besides skills acquired through experiments, I also received training in writing research articles and the process of submission for publication. I worked with a multinational team of post-docs, as well as M.D. doctors and surgeons who spent half their time researching in the lab, during which I worked with them, and the other half of their time with patients. I really enjoyed working with and becoming friend with these high-rank specialists. It was fascinating to learn about their research and career decisions. I also organized, guided, and assigned work to three high-school students who participated in my work, and whom I helped with their own individual projects. On all my work, I was closely mentored and monitored by my program’s initiator. It was most exciting to visit the Boston IVF Hospital to isolate women’s follicular fluid. There I worked with live samples from patients, isolating their serum layer and follicular fluid in a timely fashion. I also really enjoyed learning about the different phases of the Moon, and performing tightly-timed cell culturing and harvesting procedures in correspondence to full and new moon stages, as well as apogee and perigee stages.
 
I received experimental training for basic laboratory maintenance and organization. I learned to prepare many different solutions, and I mastered pipetting. I learned to do HeLa cell splitting, culturing and strictly timed harvesting; protein assay; NanoDrop Machine operation; DNA UV spectrometer operation with controlled temperature, DNA sample preparation with different salt concentrations, and DNA-denaturation output UV-data analysis; Thin-Layer Chromatography; gel retardation assay; Real-Time PCR; ELISA; and Western Blot technique. I explored many different theoretical topics that were currently significant for the laboratory, such as DNA dynamics, and the importance of transcription factors for the gene expression. Another project I worked on in support of the thin-layer chromatography experiment was with restriction enzymes for methylation sensitivity. I really enjoyed researching the different types of Dam, Dcm, and CpG restriction enzymes, designing an experiment with specific REs, and producing the photographs of migration.
 
My experience in this internship has made a huge impact on my life. I am very appreciative of the skills I acquired and the friends I have made. It provided a window for me to see and to experience what it is like to be a researcher in a professional laboratory, as well as how a medical career will benefit scientific exploration. Everything I learned this summer contributed to my decision to have a career as a medical researcher.

 

 

 

Regina Kukola

(Mentor: Dr. Melissa Murphy, University of Wyoming)

Research Summary:  Determination of an individuals’ sex from skeletal remains has applications in both archaeological research to better understand population dynamics and forensic investigations to identify deceased individuals (Frutos, 2004). While the most accurate method of sex determination is visual assessment of non-metric sexually dimorphic traits of the crania and pelvis (Buikstra & Ubelaker, 1994), frequently, preservation of skeletal materials impedes the practical application of such methods (van Vark & Schaafsma, 1992).  When the pelvis and/or crania are unavailable, postcranial metrics of long bones can be used to determine sex when regression equations have been previously calculated (Vark & Schaafsma). Osteometric variability of populations from different geographical locations (Iscan et al, 1998) and time periods (Buikstra & Ubelaker, 1994), necessitates unique values and equations for each population under study.

    I spent this past summer in Peru analyzing the skeletal remains of costal archaeological Peruvian populations. My mentor, Dr. Melissa Murphy, has provided me access to data she, along with other student researchers, collected from 1999-2006 as part of the Purucho-Huaquerones Bioarchaoelogical Project. Using this data, I was able to run statistical analyses that allowed me to create equations for estimating sex. I found that the equations that I created were more accurate in assigning sex in the Purucho-Huaquerones population than equations that were derived from Modern Thai, Chinese, Japanese, European, African, and Guatemalan populations.

    It is interesting to note that the rural Guatemalan population has a much less skewed predictive power compared to the predictive power of other populations’ formulae. Due to the fact that the Guatemalan population is the closest geographically, one could suggest that possible gene flow between past populations could be responsible for this similarity in sexual dimorphism. However, the difference could also be attributed to the rural nature of the Guatemalan population that could place health or nutritional constraints, that aren’t present in populations residing more developed areas. Further investigation would be required to determine the roles of genetics and the environment as they relate to the similarity of sexual dimorphism in modern rural Guatemalan and archaeological costal Peruvian populations.  

    In addition to analyzing the Purucho-Huaquerones data, this summer I was also able to collect data of my own from another contemporaneous Peruvian costal population, and a colonial Peruvian costal population. The next steps in my research will to be to test the accuracy of the formulas developed from the Purucho-Huaquerones cemetery on these populations. High levels of accuracy across these populations will suggest a broad applicability of the sex determination formula I initially developed. Varying degrees of accuracy will open up new channels of cultural and scientific inquiry as to why varying degrees of sexual dimorphism may exist across geographic locations in time in past Peruvian populations.

 

Madison Schaffer

(Mentor: Dr. James S. Diana, University of Michigan)

Research Summary:  When looking at a species' range, populations of animals are often divided into "core" and "peripheral" sections. Although these groups are members of the same species, they may face very different environments, leading to different selective pressures. Therefore, core and peripheral populations may show differences in life history strategy, morphology, and genetics.

Because populations of spotted gar (Lepisosteus oculatus) in Michigan are peripheral, our lab group is working to understand differences between local gar populations and those in Louisiana, at the core of the spotted gar's range. We focused our analysis this summer on capturing, measuring, and tagging Michigan gar in local lakes and on a "common garden" experiment to compare growth rates in LA and MI juveniles.
Since relatively few studies have been done on spotted gar in Michigan, we worked to document basic information about population sizes, age distribution, sexual dimorphism, and habitat preference. We collected gar via "boom shocking," an electrofishing technique wherein current was passed through the water to gently stun fish, which we could then net. We also used this technique to survey the overall fish community in Michigan lakes. This capturing technique allowed us to analyze fish per unit effort (gar/second), which gave us a general idea of abundance, both in individual lakes and in specific habitats. We discovered that gar show a strong preference for heavily vegetated areas, presumably because gar use submerged aquatic vegetation throughout their lives. We tagged and released most of the gar we collected, vouchering five from each lake for breeding and eventual dissection. By dissecting fish, we were able to confirm sex and age, leading to a clearer picture of age distributions in the overall population. Analysis of data pointed to clear differences in size/weight ratio and size distributions between Michigan and Louisiana fish. Because of these differences in life history strategy, genetic variation between the two populations is likely to exist.
            For our common garden experiment, we obtained juveniles from Louisiana and compared them to Michigan juveniles bred from vouchered adults. Our lab set up consisted of twenty gallon aquaria which we divided into three equal compartments. A two-month old gar was placed into each compartment. We offered juveniles an unlimited ration of local minnows, then measured them weekly to compare growth rates. Michigan juveniles must reach a certain size to survive their first winter, leaving them with a much shorter growing season than Louisiana fish. Because of the strong selective pressure for fast growth to survive the winter, we hypothesized that Michigan fish would grow more rapidly than those from Louisiana. Initial results were inconclusive, but as the experiment progresses, more data will become available.
            As an apex predator, spotted gar play an important role in the fish community of Michigan lakes by helping to regulate prey fish populations. Additionally, our study suggests that conservation of these fish is important from a biodiversity perspective; since Michigan gar are genetically different than Louisiana fish, preserving Michigan populations is important for overall genetic diversity of the species. Although conservation and management of these fish may prove challenging due to angler attitudes and habitat loss, there are several important steps to be taken to maintain gar populations. Since there is an obvious link between habitat quality and the presence of gar, preserving aquatic vegetation is vital for the survival of gar in Michigan lakes. By managing habitat and educating anglers and the public about the role of gar in the ecosystem, we can help ensure this fish will always be present in Michigan lakes and rivers. 

 

Lisa Lamprou

(Mentor: Dr. Deborah Kim; University of Pennsylvania)

Research Summary:The summer of '09 was not simply memorable, but a season of great personal growth for me.  It was the quintessential intern experience.  Having the opportunity to work behind-the-scenes in a major world-class hospital, I believe I developed a profound understanding of the medical profession, how medical research is conducted at the clinical level, and at the same time, picked up valuable tips in the art of science writing.  Equally important, I also learned a great deal about myself. I went into this fellowship with the hope that it would enhance my resume for medical school admission should I chose to pursue a career in medicine. Now, ten weeks later, I realize that being a physician may not be for me; not because I am intellectually or physically unable to take on the rigors of medical school, but because I may not have the emotional discipline that in my view is required.
 
I was very fortunate in this fellowship because my mentor, Dr. Deborah Kim, has proved to be one of the most competent and professionally impressive persons I have come to know. With her selfless guidance, support and direction, I was able to learn and grow throughout the past two months.  Dr. Kim helped me to learn about myself through the projects she assigned me and by allowing me to follow her in her daily routine in the University of Pennsylvania Hospital where she is an attending psychiatrist.
 
I would arrive at the hospital between 0845 and 0915 daily.  The first order of the day was rounds during which Dr. Kim and the other attending psychiatrists, fellows, residents and medical students met to discuss each patient that required a consultation that day. Once the patients needing attention were identified, the physicians and other support persons were grouped into teams and assigned to particular patients.  We would set off walking from one wing of the hospital to the other visiting the patients. These morning sessions gave me a valuable insight into what it was like to work in a hospital. Many of the patients were distressed, and for some, it was clear that they were not going to get better.  For me, this was the hardest part of the whole experience. What I learned from those morning rounds was that in order to cope with the emotional burden of being a physician, one must be able to separate her personal life from what she witnesses and has to deal with at the hospital. This proved difficult for me. I discovered that I was unable to erase from my mind many of the patient faces I saw during my workday once I left the hospital. I worried about the patients we visited and could not help thinking about their likely fates.
 
Morning rounds took place daily except for Wednesdays, the day of the week that Dr. Kim had clinical consultations from 0900 – 1200. These consultation sessions were my favorites. The were held in the 'Maternal Fetal Medicine' section of the hospital. The majority of patients there were either pregnant women, women who had given birth in the past six months, or women who wanted to become pregnant. What these women all had in common was that they suffered from mood disorders – primarily anxiety and depression. Dr. Kim allowed me to sit in on these sessions and I observed how capably she interacted with these patients, effortlessly putting them at ease by addressing their concerns and prescribing treatments where necessary. She firmly stands by the notion that a healthy mother -- not just physically but mentally as well -- is more likely to have a healthy baby. Dr. Kim strongly supports the idea that mothers that require medication to treat their mood disorders should not abandon such treatment once they became pregnant; unfortunately many do because they feel it may harm the fetus. A specialist in her field of high-risk pregnancy -- with the risk being mood disorders and their consequences – Dr. Kim encouraged patients to continue with treatment plans and in most cases, convinced them that the benefits by far exceeded the small risks involved.  This was a novel concept for me as I had the impression that all medications should be banned during pregnancy.  To observe a professional weighing the risks and recommending otherwise was an eye-opener.
 
In addition to the Wednesday morning clinic, Dr. Kim was also involved in a clinic she ran on Monday afternoons from 1300 – 1730. This clinic was very different from the first in that these patients were not always pregnant women, but people of both genders requiring psychiatric attention. At this clinic session, all patients were seen first by the residents.  Afterwards, the attending physician would come in to make sure that the session went well and that any changes in medication recommended by the residents were appropriate. During these clinics it was extremely interesting to observe the professional relationship that unfolded between the residents and the patient, the residents and Dr. Kim, and finally between Dr. Kim and the patients. I was given the opportunity to observe Dr. Kim guiding her residents to arrive at better treatments or solutions for each patient.  I watched as Dr. Kim mothered the patients that needed mothering, set boundaries for the patients that did not have any, and organized the thoughts of patients who came in providing mixed medical histories.  These sessions were clearly valuable for the future physicians.  I recall Dr. Kim discussing with one of the residents the issue of inadvertently coming across a patient outside the clinic.  The resident did not feel comfortable with the idea. I had never considered the possible problem that would arise after discussing with a patient his or her personal life in great detail and then meeting the patient outside of a medical setting.
 
 
Dr. Kim is currently investigating an exciting and novel research project dealing with the use of transcranial magnetic stimulation (TMS) to alleviate the symptoms of depression in pregnant women. If proven harmless for the fetus, it would provide an alternate treatment option for women, who are reluctant to take anti-depressant drugs for whatever reason. These women are currently not only unprotected from antenatal depression during pregnancy, but are also likely to develop postpartum depression, a condition that would make it more difficult to become effective mothers.  TMS is an FDA-approved somatic, non-pharmacological treatment for depression in adults.  It works and Dr. Kim's pilot study to test safety and efficacy during pregnancy could revolutionize the treatment of antenatal depression.

Many women are reluctant to undergo TMS because it is a relatively unknown treatment and fear that it could harm them. One of the tasks I was given by Dr. Kim was to survey prospective candidates and try to recruit them for treatment if they passed certain criteria for selection. I was given a project of scripting and directing a ten-minute video presentation for potential candidates educating them about TMS and what the treatment entailed. It involved a great deal of hard work but it paid great dividends in the satisfaction I felt after it was successfully completed.  It also made me feel as if I had made a positive contribution to the treatment of those unfortunate women who suffer from major depression during pregnancy and putting both themselves and their future children at risk.  

Another project I as given involved facilitating a blood draw from patients before and after they received transcranial magnetic stimulation. This blood sample would be used to assess their brain derived neurotropic factor levels (BDNF), what is believed to be an important factor in depression. With respect to BDNF I was also asked to write a scientific review on what is known about it thus far and what its potential link to antenatal depression could be. This scientific review will hopefully be published in a journal upon its completion. I am proud of the work I put in to all of my projects this summer and I feel as though I am ready now to make an informed decision about my future either as an M.D. or not.
 

Yang Gao

(Mentor: Dr. Georege Amato; American Museum of Natural History, New York)

Application of DNA Barcoding to the Monitoring of Bushmeat
Research Summary:  The hunting of wildlife in the tropics of Asia, Africa, and Americas has historically been conducted as means of subsistence and local commercial trade. Recently, however, the rate of bushmeat harvest has increased at an alarming rate due to population growth, increased access to remote forests, more advanced hunting methods, and an increased demand of international trade (Fa et al. 2005; Albrechtsen et al. 2007). The increase of bushmeat hunting has resulted the decrease of wildlife sustainability; overhunting of wildlife is considered a primary reason for loss of biodiversity in many tropical regions (Fa et al. 2005). Current regulations of wildlife trade depend on accurate identifications of distinct species or taxonomic groups. Species identifications traditionally rely on morphological characteristics, which can often be impaired due to the different types of products involved, such as processed leather products or butchered meats. Thus, the use of more accurate methods of species identification, such as DNA barcoding, is being more frequently used to improve the efforts to protect wildlife biodiversity.
 
DNA barcoding was proposed by Herbert et al in an effort to develop a database of gene fragment of the mitochondrial gene COX1 as standardized barcodes to classify the diversity of life (Herbert et al. 2003). The proposed DNA barcode is a 645 basepair fragment toward the 5’ end of the gene sequence. The effectiveness of COX1 as DNA barcode has been tested in birds, mammal, fish, and groups of arthropods; its efficacy in identifying endangered species collected from wildlife trades has also been demonstrated (Waugh 2007; Eaton et al. 2009).
 
Recent studies have also explored the potential of smaller barcodes to use on archival or heavily processed specimens that contained degraded DNA (Meunier 2008). A bioinformatics analysis done using available COX1 barcode sequences to calculate the probability of having species-specific barcodes for varies size fragments showed that barcodes as small as 100 bp can yield 90% success rate when performed a species identification test. 
 
My project is a continuation of a study performed by Mitchell Eaton from the American Museum of Natural History to test the applicability COX1 barcode as a practical metric for the detection of the origin of bushmeat species, with specific emphasis on 350 bp short fragment barcodes (Eaton et al 2009). The organisms included in this project included 79 crocodiles, 34 caimans, 17 ungulates, and 13 primates from Central Africa and South America that were either collected during field studies or requested through the tissue collections from the Yale Peabody Museum or the American Museum of Natural History. In addition, 16 processed leather products that were illegal imports confiscated by the US Fish and Wildlife Service (USWFS) were also included this study. DNA was extracted from all specimens; full length (650bp) and short fragment (350bp) barcodes were amplified by polymerase chain reaction (PCR) using universal COX1 primer “cocktails” as well as primers designed for this study (Ivanova et al. 2007). They were then sequenced, edited, and compared with voucher COX1 sequences on GenBank and Barcode of Life Database (BOLD).  
 
High quality short fragment target sequences were generated for majority of the tissue specimens (success rate of 99% for crocodiles, 89% for caimans, 94% for ungulates, and 92% for primates), and were comparable to that of 650 bp sequences (95%, 84%, 59%, and 85%, respectively). Only one out of 32 DNA extractions from leather products, however, was successfully sequenced for a short fragment barcode.
 
Successfully sequenced barcodes were compared to the voucher sequences on GenBank and BOLD. For species whose DNA have been extensively sequenced and published, both databases assigned their long and short barcodes with the closet matching species congruent with those identified using the morphological keys. For species whose DNA sequences have not yet been published, GenBank assigns the different length barcodes of the same specimen with different species, whereas BOLD clustered them with the most similar species regardless of the barcode query length. The leather product that was successfully sequenced was labeled as a Dwarf Crocodile Skin Purse (Osteolaemus sp.) by USFWS, but was assigned to be Niles crocodile (Crocodylus niloticus) by both databases.
 
In conclusion, this study showed that extraction, amplification, and sequencing of fresh tissue and recent museum samples are successful with both full length (650bp) and short fragment (350 bp) barcodes, while more challenging with processed leather specimens containing more degraded DNA. In addition, the short fragment barcodes yielded similar success rate in species identification, confirming the results of the study done by Meusnier et al. This provides potential for further truncating the DNA barcode length (to ~150bp) in order to increase the success rate of identifying species of unknown bushmeat samples that are traditionally difficult to identify. 

Brie Stark

(Mentor:  Dr. Paul Grobstein, Bryn Mawr College)

Research Summary: I interned in the summer institutes with K-12 teachers, sponsored by Howard Hughes Medical Institute.  The goal of my summer research was to participate in and facilitate discussion, form relationships and develop new ideas in relation to the brain, education, mental health and inquiry with K-12 teachers in both the Brain and Behavior Institute, lead by Paul Grobstein, and the Inquiry Institute, lead by Wilfred Franklin.  I will summarize these institutes and offer conclusions and points of discussion for the future.


I was both a facilitator and an active participant in discussion during these institutes.  I took part in the daily blogging, as well as in the discussion of curriculum projects and open-ended projects developed for both institutes.  I helped facilitate the use of Serendip as an educator about the usage of the website, the HTML and the formatting, as well as taught side-programs like Windows Movie Maker and Excel. I maintained an ongoing synopsis blog about my experiences throughout the entire internship, which can be found at http://serendip.brynmawr.edu/exchange/bstark.


The Brain and Behavior Institute focused on facilitating emergent-oriented discussion revolving around understanding the nervous system and the brain and how to apply that understanding to the process of education. I helped to create the afternoon schedule for the participants.  My partner and I researched articles and formulated tasks for small groups to undertake and discuss.  We emphasized a new topic daily, so as to increase the knowledge of the participants on relevant behavior or brain oriented subjects.  These topics included neurodiversity, implications of the web, emergent pedagogy and the importance of web creation for both teachers and students. The participants of the course were asked to complete an open-ended project on Serendip that explored a realm that they found interesting, shared several websites or sources for further information and explained the way their ideas about this subject had changed over the course of the institute.  I created a model for approaching this concept.


The Inquiry Institute offered an environment for teachers to discuss and experience the concept of inquiry-based education.  The concept of inquiry was not given a concrete definition, and therefore, the participants created their own definition and method of implementing inquiry in the classroom. Fellow teachers then presented an open-ended lesson to the participants, an example being a lesson on electricity using circuits and pre-made vehicles.  These lessons were then critically discussed and apt to be changed and implemented by the participants according to their grade-levels.  


While observing these institutes, I drew several conclusions.  
 

Globally, I saw a slow shift of interest start to generate itself as the two weeks of the Brain and Behavior Institute progressed: in the first week, there was a lot of emphasis on personal contributions (such as how teachers had implemented discussion topics in their respective classrooms and their own personal experiences).  However, as the second week arrived, emphasis on personal interest started to decrease and there was a lot more discussion about universal culture, learning styles of students and how to assess the student in order to encompass these ideas.  


I learned, through my observations and participation in discussions, that the greatest environment of learning spawns from a willingness to put oneself into discussion without qualms: to socially interact with the other participants in an emergent fashion, and essentially to feel uncomfortable though content to learn something new.  When there was a lack of participation in the discussion, the discussion often became one-sided, lacked depth and lost its appeal to participants.  Another key development made by the institute was the realization, by many participants, that discussion should foster development and learning and is not a word synonymous with inciting anger or hostility.  Questioning and discussing are parts of the learning process.
I, like many of the participants, came to the institute expecting a more concrete definition of what ‘inquiry’ entailed.  However, as the weeks progressed, we all found that ‘inquiry’ did not have the solid definition that we had been expecting.  Many were disconcerted with the idea while many took the idea as a comforting.  Nonetheless, we did settle into the tone that there was no concrete definition for inquiry: that inquiry could be guided or unguided; have or not have overarching principles and that the teachers all had very subjective experiences with implementing these ideas in the classroom.  I personally found that the definition of inquiry is subjective to the teacher and to the student and must be explored on many levels. Inquiry has an entirely different meaning to the teacher because the teacher often has a pre-developed idea that they would like to explore.  The student is focused on the discovery of ideas that interest them on a personal level.


I would offer these following suggestions in order to further explore the above conclusions for future institutes:
I would like to incorporate more administrative figures into these institutes, as teachers mentioned problems with curriculum and school policy.  This way, we incorporate more of the whole system.  

It would, perhaps, be a valuable contribution to spend more time on deciphering the usage of the Web in education, as there were mixed opinions on the subject concerning such things as privacy, necessity and textbooks.  


I felt that a common sentiment from the institutes, and one that I adhere to, is that learning does not end when formal schooling ends, but rather, that education is a lifelong process.  I questioned, what exactly is the role of the teacher in this lifelong learning concept?  Should they prepare the student for what they will probably experience or teach them to question and take advantage of more opportunities?  


In all, I felt that this internship has given me a more global viewpoint of education and its many approaches, as well as connections with diverse behavior and learning styles.  I learned to express myself well through blogs and in person on a variety of subjects.  This opportunity helped me formulate several career paths of interest through exploration with many professionals in the field of education, biology and psychology.
 

Emily Lovejoy

(Mentor: Dr. Paul Grobstein, Bryn Mawr College)

Research Summary: This summer, I participated in the summer institutes for K-12 teachers.  The summer institutes bring together precollege and college educators to discuss ways to enhance science and mathematics education.  The summer institutes teach educators how to make use of classroom diversity, how to explore the idea of a discovery-based approach to education, and they facilitate collaborations between K-12 teachers and university educators.  The institutes aid educators in making science accessible to everyone.  Additionally, they help educators create a style of teaching that encourages students to understand material in a context that relates it to their personal interests and uses hands-on activities to allow for further exploration. Throughout the institutes, participants were required to actively participate in the discussions, and additionally post their thoughts on an online forum (http://serendip.brynmawr.edu/exchange/).  Lastly, they were to develop an open-ended transactional educational experience to share with the group.

I explored the relationships among mental health, science education, and the brain by pursuing long-standing interests of my own in the mental health area and connecting them to contemporary thinking about the brain and about education.  I expected these interactions would help me to develop new ways to think about the intersections of research on the brain, education, and mental health.

During the summer institutes, I facilitated discussions and developed new relationships and ideas with teachers.  The institutes gave me a broader perspective and viewpoint on education.  I learned a lot about different learning styles and human neurodiversity.  I blogged regularly about my experiences this summer, which can be found at http://serendip.brynmawr.edu/exchange/node/4481.  After my experience this summer, I have thought more about what I want to do in the future and am interested in exploring careers that combine education and psychology.

In the future, the inquiry science and brain and behavior institutes may be combined into one, 3 week institute.  I think the team teaching aspect will strengthen the program by providing different viewpoints and teaching styles that will create an even more dynamic discussion.

The summer institutes allowed educators to share their perspectives on how to enhance math and science education.  The participants received a stipend and development grant at the end of the institutes to further their classroom curricula.  I found the institutes to be extremely helpful in providing new perspectives for all participants.  Without the support of the Howard Hughes Medical Institute, none of this would have been possible.

 

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