Middle School Students: Science Outreach, Math Anxiety, and Resiliency

When students reach Middle School level academics, it is observed that their interest in STEM decreases. There are many theories that have been tested to discover why this shift occurs, however, it is thought that Math anxiety is the main contributor to this decline. Furthermore, there have been indications suggesting that Math anxiety is closely related to Resiliency. In this study, we are interested in looking at the relationship between Math anxiety and Resiliency in Middle School students. In doing so, a science outreach day was designed to both increase Middle school student\u27s interest and attitudes interest towards STEM. The students who attended self-selected into this science day and were surveyed on current levels of Math Anxiety and Resilience. This experiment allowed students to learn and explore science in their own creative way from a physics-based approach; and is an example of baseline student assessment that teachers can conduct in a classroom. Nevertheless, the same size was too small to confirm significance and it is encouraged that more research is conducted on the matter

Rev1 Protein Purification

1 in every 15-30 million nucleotides can be considered a mutation in healthy individuals. Replication of damaged DNA leads to genetic mutations. Genetic mutations lead to disorders and cancer. Rev1, a Y family polymerase, prevents minor mutations, such as abasic sites and exocyclic guanines, in the template strand from shutting down the process of replication. Our mutant Rev1, R324G/L325G, has replaced both the arginine located on nucleotide base number 324 and the leucine on nucleotide base number 325 with glycine. The arginine and leucine have more complex side chains groups with specific hydrophobic/hydrophilic properties. By replacing them with glycine, the side chains are now simplified to hydrogen. Our hypothesis is that Rev1 evicts the nucleotide from the active site and replaces it with an arginine while the leucine stabilizes the template base outside of the active site. We hypothesis that arginine and leucine side chains provide the mechanism for Rev1 to be a functional polymerase. This mutated Rev1 should be unable to perform this mechanism. Based on protocol provided by Dr. Bret Freudenthal and his associates at the University of Kansas Medical Center and the support of the Phoebe Laser Research Group led by Dr. Carlson and Dr. Grace, and the Chemistry Department at Northwestern, we have grown E. coli with wild type and mutant Rev1 and are in the process of purifying the Rev1 protein for crystallography

Science Interest and Confidence in Middle School Aged Students

In the middle school science classroom, students begin to decide whether or not they like science. This decision has long term impacts on their interests, future studies, and ultimately career goals. Further, the impact of this decision can be felt by the STEM field when fewer and fewer students are interested in pursuing jobs within the field. To explore the attitudes and confidence of these students towards science and math, the CURE survey and Math Anxiety Scale were adapted to gather data from a group of middle school students after attending a Middle School Science Day event. Through the research, we wanted to get a look at why some students lose interest in science around the time they are in middle school. At the event, students worked in groups to complete an engineering challenge and had the opportunity to see various science demonstrations. After the day’s activities, students were asked to complete the surveys. Surprisingly, our surveys displayed a lack of connection between math anxiety and science interest at the middle school level. This research will be useful to teachers at the middle school level as well as above and below, as they work to engage students in science class and make the content interesting and relevant, in addition to encouraging their students to be curious about science. Further, the research has laid groundwork for using an adapted form of the CURE survey at the middle school level

Progress in Developing Laser Tweezers and Control Systems

Optical tweezers are a Nobel Prize-winning technology capable of trapping microscopic and sub-microscopic particles using a laser beam. They can be used heavily in many different capacities within our organization and the research collaboration of ISLAND CURE. Some possible uses would be making measurements on DNA that we have synthesized. While that one of goals, another main reason for completing this would be to make this technology available at other smaller research institutions that cannot afford prebought systems. This would allow for more undergraduate research and opportunities all around the states. While executing our plan for developing our system while handling the natural complications that come with doing research, we have developed progress in our beam setup, temperature control system, and the current driver. The construction of the laser diode module and current driver been the focus of this year. We continue to develop closer to our end goals by combining our homebuilt inverted microscope with our beam setup. This will allow us to begin collecting data and optimizing our system from what it is now into a system that would be widely applicable for many other research purposes

Undergraduate Studies to Design and Build DNA Structure to be Used by Optical Tweezer

Our research team, ISLAND CURE, is the team to design and build a biological instrument, optical tweezer (OT), with a limited budget. The optical tweezer is an apparatus that moves micro-objects by using laser light. It allows the user to create and control the pico-newton, which is an essential force to move micro-objects. Our research is to design a target DNA sequence (Fig 4.), which our optical tweezer will control. To apply optical tweezer technology to living organisms, DNA is the essential first step. In this research, our team focus is to calculate the necessary forces to unzip DNA with optical tweezers. Thus, we researched and developed a simple DNA sequence that would not interfere with the force relationship between DNA and laser light. Our DNA sequence is structured by four types of the oligonucleotide, lambda DNA, biotin, and digoxigenin

Designing and Building an Inverted Microscope

Iowa Stonybrook Lasers And DNA Course Embedded Research (ISLAND CURE) is a new research collaboration group that is focused on undergraduate research for both the students and the professors. The goal of this research collaboration was to create physics apparatuses to make biochemical measurements. One of the tools we are developing is an infrared optical tweezing system. This requires an inverted microscope to facilitate the trap. To observe one of these measurements, an inverted microscope is required to observe the sample. Inverted microscopes can be expensive, and our budget is limited. To overcome this issue, our research group decided to create our own inverted microscope with the minimal budget we had. This microscope can now be used for optical tweezing and observation of a live sample

Slide Preparation for DNA Attachment for use in Optical Tweezers

Our research team, ISLAND CURE, is a multidisciplinary team of professors and undergraduate students with the goal to design and build instruments to make biological measurements on a limited budget. One of the apparatuses we are designing, is optical tweezers, which are a Nobel Prize-winning technology capable of trapping microscopic and sub-microscopic particles using a laser beam. Using a 1064 nm beam, we will trap a single strand of DNA using beads and this will enable us to exert minute forces upon the DNA. This experiment will give us a better understanding of the forces on damaged DNA; specifically, the damages that lead to mutations and cancer. With this knowledge our goal is to be able to provide insight into mutagenesis and cancer development, and ideally how to treat and prevent them. Our job was to find a way to prepare a slide in which a single piece of DNA can attach to be used in the inverted microscope setup

Utilization of Escherichia Coli for the growth of Y Family DNA Polymerase Rev1 and GSTrap column for purification​

Rev1 is a Y family DNA polymerase that specializes in translesion DNA synthesis. Rev1 is unique in that it preferentially incorporates dCTP in the growing DNA strand, regardless of the templating base. This is because the template base is evicted from the active site and a template amino acid, arginine 324 (R324) acts as the template for the incoming dCTP. We hypothesize that arginine 324 and the neighboring leucine (L325) facilitate the eviction of the DNA template from the active site. To test this hypothesis, we worked to purify R324G/L325G Rev1 double mutant for the purpose of X-ray crystallographic examination of the protein-DNA-dNTP ternary complex. We transformed Escherichia coli (E. coli) and induced expression of both wild type Rev1 and R324G/L325G Rev1. The bacterial cells were lysed by sonification, and the lysate was purified with a GSTrap column. We were able to successfully isolate the Rev1 enzyme. Further purification and crystallization will be necessary to explore the x-ray crystal structure of R324G/L325G Rev1 protein

Laser Beam Profiling and Crystallographic Analysis

Lasers and x-rays are widely used in the modern world for studying biomolecules. For the purposes of the physics department, future research requires certainty that lasers have Gaussian profiles, though the lasers used often deviate from this ideal. In this project, we investigate methods to measure and analyze laser beam profiles. We first reviewed the theory of Gaussian beams and their properties. We then measured our laser’s profile using two techniques: a knife-edge method and a cell phone photography method. The first involved moving a razor edge across the beam to measure transmitted light, while the second involved visualizing the profile through photographs. The second part of the project involved x-ray crystallography, a powerful technique for determining the three-dimensional structure of molecules. Crystallography analysis involves growing crystals of the molecule of interest and exposing them to x-rays. By analyzing the diffraction pattern, it is possible to reconstruct the molecule’s electron density and determine its precise atomic coordinates. However, crystallography analysis can be challenging due to the data processing and modeling required to interpret the diffraction data. We compared open-source crystallography software and practiced data analysis using publicly available sample diffraction patterns. In summary, we investigated methods to measure and analyze laser beam profiles, including hands-on techniques and imaging. We also discussed x-ray crystallography, a key technique in studying molecular structures. Our work provides the foundation for future optics and crystallography projects