Mentor: Adam Geballe
Title: HCMV -TRS1 Mutational Analysis
Abstract: Human cytomegalovirus (HCMV) affects about 50 percent to 80 percent of the population in the United States, but it is more prevalent in developing countries. This virus is critical for immunocompromised patients and unborn children because it can cause blindness, birth defects, pneumonia, coma and even death. This virus encodes for more than 150 proteins in which TRS1 and IRS1 are said to be in charge of preventing the shutoff of the synthesis of the proteins. The purpose of our experiment was to find the region that binds with the double stranded RNA during the process of synthesis. This was analyzed by using pEQ-999 which has similar genetic information as TRS1 and by creating mutations to see what kind of proteins were produced.
Mentor: Yansong Gu
Title: Study of the Origin of Chromosomal Translocations that Cause Leukemia
Abstract: Using the DNA of mice, their genotype and phenotype were determined. This data helped determine what type of cancer and other problems the mice would develop. PCR (polymerase chain reaction)-based genotyping methods were used to identify mice with mutations in one or two of these genes. Understanding the cause of the chromosomal translocations caused by drugs such as VP16 would aid in determining why the translocations occur and what other substances would cause the gene abnormalities and ultimately Leukemia.
Mentor: Jeffrey Schwartz
Title: Is High Radiation Sensitivity a Cause of Recurring Cancers?
Abstract: In our laboratory we are looking at whether patients who are sensitive to the effects of radiation are more prone to second cancers later on in their lives because of the radiation. We are testing our hypothesis using white blood cells lines from lymphoma patients who are treated with radiation to prepare them for a bone marrow transplant. My main project in the lab is performing experiments and gathering data to generate growth curves on these cell lines. This is one way of testing cells' radiation sensitivity. We studied 10 different cell lines from 10 different patients. There was no obvious relationship between final cell number divided by initial cell number (F/I) with any of the patient characteristics or D50 with any of the patients characteristics. We did see an apparent relationship between F/I and D50. Cell lines that grew faster were more sensitive to radiation. There are clearly differences in radiation sensitivity that can be detected in the lymphoblast cell lines. The relationship between radiation sensitivity and growth rate needs to be further examined because of the large interexperimental variability in the growth rates. If this hypothesis proves to be true, patients who are sensitive to radiation could be treated with lower doses of radiation or other types of treatments to reduce cancer risk.
Mentor: Karl Böhringer
Title: Micro Fluidic System for Brine Shrimp Hatching Study
Abstract: Artemia salina (also known as brine shrimp or sea monkeys) have been studied by aquacultural engineers for many years. Aquacultural engineers studied their biomass, extension, growth and many other features. These studies led us to build a micro fluidic channel that has the ability to study the hatching, allowing us to control and monitor the growth and behavior of the eggs. We designed and built acrylic micro fluidic channels and tested the micro fluidic channels' capability of transporting individual eggs through a network of channels to selected hatching locations.
Mentor: Stephen Hauschka
Title: The Effects of Wnt-3a and IGF-1 on Somite Myogenesis
Abstract: Somites are cells found along the neural tube of an embryo. Myogenesis spurs from somites, which are directed into myogenesis from path signalling proteins such as Wnt and Insulin like growth factor (IGF). Individually, the proteins can direct the somites into myogenesis, but it is unknown if, when combined, proteins such as Wnt and IGF will have a synergistic relation. Having a synergistic relation would increase the amount of Myosin positive heavy chain (MHC) cells, thus speeding up the process of muscle growth. To investigate the relation between the two proteins, dissection of chicken embryos and immunohistochemistry was conducted.
Mentor: Mary Lidstrom
Title: Identification of Active Populations of Microorganisms Involved in C1 Compounds Metabolism by Stable Isotope Probing of DNA
Abstract: Active populations of microorganisms involved in C1 compound metabolism were identified using stable isotope probing of DNA. Sediment from Lake Washington was incubated with 13C- and 12C-labeled Methanol and Methylamine and 13C- and 12C-labeled DNA were isolated from the sediment after centrifugation on CsCl gradients. To identify the active microbial community, 16SrDNA were amplified by PCR, cloned, screened by RFLP, and sequenced. The 16SrDNA from 12C and 13C Methanol experiments were closely related to Methylophilus, Pseudomonas, Janthinobacterium, Rhodoferax and Matsuebacter. Interestingly, sequences related to Rhodoferax and Matsuebacter (not described as C1-utilizers) were only identified in the 13C-labeled DNA fraction, suggesting their potential implication in the use of C1 compound in Lake Washington sediment. The future direction of this project is to continue identifying C1-utilizers with different C1 compound substrates and phylogenetic markers.
Mentor: Anton Krumm
Title: Constructing a Vector to Study Long Term Silencing
Abstract: My work over the summer was to create a vector, IRES-CD20 (internal ribosomal entry sites), to study the effects of long term silencing, which is what makes most gene therapies unsuccessful. To do so, I had to first create a map of the psbc-1 vector, so I would know where to excise the IRES-CD 20 fragments. The main problem was that some of the restriction sites (where enzymes cut) were unknown and were later discovered to be included in the fragments that were needed. We used a partial map, created by Wilhem Dirks, Manfred Wirth, and Hansjorg Hauser in Dicistronic Transcription Writs for Gene Expression in Mammalian Cells, and tested the provided sites. Then we tried other possible restriction sites, running digests, and measuring the sample against ladders to test our hypotheses. When we got the desired fragment, we excised it from the gel, and purified it. That is the point we reached this summer. Hopefully, this will clear up some of the unknown issues in boundary elements, making it possible not only to cure cancer, but many other diseases through gene therapy.
Mentor: Deirdre Meldrum
Title: Polymerase Chain Reaction
Abstract: Follicular lymphoma is characterized by the presence of a gene aberration in the patient genome. In this disease, a part of the chromosome 18, consisting of the bcl2 gene, is transferred to the 5' end of the chromosome 14, and it is fused with Jh gene. This translocation is defined as t (14; 18). A PCR method to detect this translocation for the high throughput analyzer is required. Here we describe a PCR method and it can work in two ways. After the PCR reaction, running the reaction mixtures on agarose gel can be run to identify the product. Alternatively, the generation of the specific product can be monitored in real time PCR. Our real time method consists of the key reagents, Taqman_MGB probe along with the primer for this translocation. The reaction is done in glass capillaries with 2 L reaction mixture. Forty-eight reactions can be done in one cassette on the MRD (minimal residual disease) analyzer. We have developed these methods up to the stage that the translocation can be detected in the patient DNA samples. Very stringent conditions are required to minimize the background reaction, and yet to allow the specific reaction to proceed to detect the presence of t (14; 18), in the bulk of the patient DNAs.
Mentor: Neil Dobson
Title: Transformation of DNA to RNA to Protein
Abstract: The aim of this project was to prepare 1URN, a modified version of a protein called U1A, a component of the spliceosome. The two proteins will be compared to see if the structures are similar. 1URN was created by Rosetta as a modified version of U1A with the same 3-D coordinates.
Mentor: Suzannah Rutherford
Title: Genetic Differences in Osmotic Stress Signaling and Response in Wild Yeast
Abstract: The idea of this research project was to understand the relationship between osmosensitivity and the strength of signaling through the osmotic stress pathway in wild yeast cells. We developed three assays to measure yeast osmosensitivity. KCl and sorbitol were used to cause osmotic stress. We found that a growth assay most clearly discriminates strain differences in response to salt. Wild yeast varied more in signaling outputs than in their response to salt, suggesting that variation in osmotic stress signaling is buffered downstream of the transcriptional control of osmotic stress responsive genes.
Mentor: Aimée Bakken
Title: DNA Fingerprinting: Finding Our Path Toward a Better Method
Abstract: Forensic DNA testing has been questionable to many people for a very long time. No one is certain about whether or not a certain analysis will give out accurate assumptions yet be quick and easy to carry out. Two methods of DNA profiling stood out in the research findings done throughout the 2004 GenOM summer program. These methods were the VNTR methods and the PCR methods. The two methods were put to test, research was done, and conclusions were derived as to which one was best in order to obtain data not only faster, but also achieve better results for DNA profiling.
Mentor: Ray Monnat
Title: What DNA Target Sites can Homing Endonucleases See?
Abstract: Homing endonucleases are rare cutting enzymes that make site-specific double strand breaks in the target DNA. Homing endonucleases also have long recognition sequences that span 12-40 basepairs (bp). In the Monnat Lab one of our goals is to evolve homing endonucleases to recognize new sequences of DNA. Previous evidence has shown that homing endonucleases are able to recognize sequences that are closely related to their native homing site. Homing endonucleases can be evolved to recognize new sequences by combining the domain of one homing endonuclease with the domain of another homing endonuclease. Why do we want to evolve homing endonucleases? Why do we want them to recognize new sequences? Many pathogens have genomes with sites that differ from homing endonuclease's homing site by a few bp. Being able to cut the essential gene necessary for the pathogen to survive, could kill the pathogen. Evolving homing endonucleases can also allow us to target specific human genes to either suppress or stimulate their expression; this can help cure certain diseases. This summer I have worked on two separate projects with homing endonucleases: 1. H-DreI and 2. I-CreI, each project trying to address some of the above questions.
Mentor: Aimée Bakken
Title: The Localization of Human Nucleoside Transporters in Transgenic Xenopus laevis Frogs
Abstract: The summer of 2004 I spent at the University of Washington in the Biology department under the guidance of Aimée Bakken studying the localization of human nucleoside transporters in transgenic Xenopus laevis frogs. The process of producing such frogs carrying a human gene seems virtually incomprehensible; however, with time I was able to grasp the concept with deep understanding. In the beginning the experiment proved to be more challenging than expected; since it is an extensive process it is hard to identify sources of errors. All solutions were made in the lab and many of the apparatuses used were manual. The results found were both expected and unexpected. However, substantial conclusions could be drawn from the results.
Mentor: Babak Parviz
Title: Self-Assembly as a Means for Nanofabrication
Abstract: A new method for fabricating nano-scaled machinery is described. This method is inspired by the many exemplary building techniques in biology and is called self assembly. Mimicking nature's ability to self-build and self-heal, self assembly allows tiny, man made particles to assemble into certain desired forms without actual manual contact or force. The work first involved creating silicon wafers with micro-sized "holes" called templates. These templates were filled with solder, and perforated in very intricately detailed patterns across the surface. Then, four different shapes that were complimentary to the many templates were introduced and scattered across the surface of the wafer; by doing this, the experiment would hopefully have each specific shape unite with its complement, and stay in place due to the interaction with the solder. However, the lack of capillary force exerted by the solder proved to be a limiting factor when hundreds of different shapes were randomly floating about, searching for a stopping point that would only luckily be the correct destination. There were results, but major scientific breakthroughs do not come overnight.
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Last Reviewed: March 9, 2012