SRI Blogs

This summer I had the opportunity to work with Nathan Whitsett, a former Summit graduate who is now in the Physics Department at Washington University in St. Louis. Nathan is affiliated with the Pisgah Astronomical Research Institute (PARI) in North Carolina and was able to obtain permission for me to collect data remotely using one of their radio telescopes. At PARI, there are two telescopes, one twelve meters, which I used, and one twenty-six meters, which is used for more in-depth data.

These large Radio telescopes detect radio waves between 3 m and 30 m in size coming from celestial bodies. Radio waves are the longest wavelengths in the electromagnetic spectrum. Radio astronomy can be used to characterize galaxies, planets being born, supernovas and supernova remnants using neutral Hydrogen emissions.

I chose to analyze two different Supernovae Remnants (SNRs) in the Milky Way galaxy to gather data about how fast they are moving. SNR is the structure that results from the explosion of a star in a supernova. Studying SNR allow us to calculate their age and understand how they contribute to planet formation and distribution of heavy elements throughout the galaxy. The SNRs emit radio waves around a base frequency of 1420 MHz. By measuring how far away from that center frequency the SNR is, I can calculate how fast it’s moving, and if it is moving towards or away from us. The 12m telescope scans for radio waves in a small range around 1420 MHz, and the further away my value is from 1420 MHz, the faster the SNR is moving. There were thousands of data points and multiple scans of both objects, but each had a clear frequency peak near 1420 MHz, making it much easier to determine their velocities. Amazingly, I did all of this from the comfort of my room, as all the features of the telescope were accessible from my computer. While there were some unexpected changes in my plans this summer, I was still able to successfully complete research on exactly what I had wanted to explore.

Sean LaMacchia is a senior in The Summit Country Day School’s Science Research Institute.

This summer I was able to research antibiotic producing bacteria in native soil at the Schiff Family Science Research Institute with Dr. Replogle at The Summit Country Day School. Due to COVID-19 restrictions, I was not able to do research with Dr. Rhett Kovall at the University of Cincinnati’s College of Medicine, but I was able to do two weeks of research at school in cooperation with the Tiny Earth network of researchers. Although it was not my first choice, Tiny Earth allowed me to learn how to perform research, develop numerous microbiology and molecular biology skills and techniques which were connected to the basis of biochemistry that had made me interested in Dr. Kovall’s lab.

Tiny Earth uses soil to discover new antibiotics because there has been a dramatic decrease in the discovery of new antibiotics. We need new antibiotics because bacteria are constantly evolving, and some are becoming resistant to the common antibiotics that we use. Soil is smart place to look because soil is in high supply and is very rich with many different types of bacteria.

Tiny Earth provides a framework to isolate bacteria colonies that appeared to produce antibiotics. I used many different plating techniques to grow the initial master plate of thirty bacteria, select for antibiotic producers and isolate individual antibiotic producing bacteria to their own three-way streak plates. I was able to learn many new lab techniques as I did many biochemical tests to determine the characteristics of my three isolated bacteria. Then, I amplified the 16S rRNA gene using PCR. This PCR product was sequenced and revealed the genus of the antibiotic bacteria as Bacillus. Bacillus are known for their antibiotic production. My isolated bacteria will be sent to the Tiny Earth organization at the University of Wisconsin for further analysis to determine if the antibiotics are novel. I am so grateful for this experience and the opportunity that Tiny Earth provides to students around the world to contribute to solving the antibiotic crisis.

Sam Perez is a senior in The Summit Country Day School’s Science Research Institute.

I worked in the Miller laboratory at the University of Cincinnati College of Medicine on a remote project this summer. My mentor was Dr. Miller, who was the Principal investigator, or PI, for the laboratory. The overall objective of the Miller laboratory is to investigate the mechanisms by which microbial pathogens can manipulate transduction pathways in host cells.  I was interested in researching cytomegalovirus (CMV) Infections, which infect as much as 80% of the population worldwide. During initial CMV infections, viral replication at the portal of entry was disseminated via a low-level primary viremia to multiple internal organs. Robust replication in these organs and a secondary viremic phase disseminates virus throughout the host to tissues including the salivary glands. 

DM33 is a form of the virus with decreased expression of the M33 gene, a gene that codes for a protein that appears to constituitively activate the Gaq/Gall subfamily of heterotrimeric G proteins. Once the GCPR proteins are activated, high dose infection in NSG mice indicates that Delta M33 virus reaches the salivary gland. However, the Delta M33 virus fails to replicate efficiently once it is in the glands. By understanding which genes are suppressed in the DM33 virus, scientists can begin to understand which genes are necessary to suppress with medication in order to understand and prevent further dissemination of human CMV. 

For my project, we focused on how M33 gene product in DM33 murine CMV would affect the promoters of other genes and would affect the expression of other genes in the genome.  We also looked at differences in gene expression in wild type virus in vitro and in vivo environments to determine if there were significant differences in viral expression in the different environments. We found that viral gene expression overall is decreased in the DM33 virus compared to the wild type (WT) virus. There were certain clusters of genes including M72, M73, and m73.5 which code for N-proteins was significantly under expressed in the DM33 virus as opposed to the WT virus. I also found that in vivo gene expression is significantly higher than in vitro gene expression when expression was compared relative to the most highly expressed gene, m168, and when using raw read counts to determine the differences in gene expression.  Therefore, in vivo viral gene expression is much more complex than in vitro viral gene expression. 

Overall, I had an amazing experience working from home this summer, as I was able to contribute to the scientific community in ways in which I did not expect. I was excited to embark upon a new adventure, as I had never really known much about bioinformatics and the techniques I was using to determining how DM33 and WT MCMV viral gene expression differs. Dr. Miller gave me guidance as to how I should start my project, and I went through the read count data to determine which genes are most highly expressed in each of the eight samples with which I was presented. I was excited to find the differences between the number of hit counts, even though at first the data seemed a little overwhelming to interpret. After easing into the process, I was able to concentrate on determining percent expression compared to that of m168 in the WT and DM33 samples. Finding the in vivo and in vitro percent expression, was a little more difficult, as we had to use two different ways through which we could compare gene expression. The first was by comparing in vivo and in vitro gene expression to the most highly expressed gene in both viral genomes, m168, and calculating percent change between the percent expression in relation to m168. To prove that these findings were correct, I went back and determined the percent change of expression in viral genes by comparing raw read counts of in vivo and in vitro cells. I enjoyed learning how to work with bioinformatics data even though I originally hoped to do benchwork. I have learned how to come to meaningful conclusions and how to pinpoint which pieces of data are important to include in reports. I have grown as a scientist, as I have become more confident in my ability to analyze and determine how pieces of data fit into and contribute to a larger purpose. I have been able to determine how viral gene expression differs between different strains of viruses and different types of environments. I have now become more confident in my ability to work on projects concerning complex issues such as virology. 

Sophia Stanisic is a senior in The Summit Country Day School’s Science Research Institute.

Over the past summer, I have conducted a literature search on bio-inspired surfaces with four additional groupmates. The starting point of this research is based on biomimetics, the study of biology or living nature in order to design artificial materials that mimic useful natural properties. Natural materials and surfaces have evolved specialized functions over approximately 3.8 billion years. There are a variety of surfaces that exhibit unusual and exciting properties. For instance, the lotus leaf causes water droplets to bead up and bounce off its surface. Several animal and plant species, such as the Namib desert beetle or spider webs, can capture water from fog. Shark skin have evolved to reduce drag from the water and the gecko’s foot demonstrates reversible adhesion.

In the course of the research, we have identified the unique surface functionalities associated with a wide range of biological species, including lotus leaves, rose petals, water striders, and pitcher plant leaves, by exploring the roles of surface composition and surface texture. Subsequently, we have examined the fundamental concepts of surface and interfacial energies, contact angle, reentrant texture, and hierarchical structure, as well as the relationships of Cassie-Baxter state and Wenzel equation. Understanding the role each of these concepts for each unique surface is crucial to determine the materials that can be used to engineer the bio-inspired surfaces of the future.

The final stage of the literature review was writing a review paper with the help of our mentor, Dr. Anish Tuteja at the University of Michigan-Ann Arbor. The research paper is mainly focusing on bio-inspired surfaces for fouling resistance. Fouling is the build-up of unwanted material on a solid surface with damaging effects and is a major problem for many industries. We have specifically analyzed superhydrophobicity, superoleophobicity, icephobicity, as well as their applications on anti-fingerprint displays, drag reduction for ships, fog harvesting, and ice-shedding to summarize the current knowledge of these unique surfaces.

Benny Shen is a senior in The Summit Country Day School’s Science Research Institute.

This summer I worked in the Linder Research Center in the Medical Offices Building at The Christ Hospital. My mentor was Dr. Tim Henry, M.D., but I also had help from a second-year medical school student. The overall goal of the research I was helping with was to create and expand a multi-organizational database containing clinical data from patients who presented with STEMI’s (ST-elevated myocardial infarctions). STEMI’s are a type of heart attack resulting from total blockage of a major artery, and the patients who present with them are in critical condition and require quick medical interventions to survive. Despite the seriousness of the situation, there is not much patient data in the United States about those who present with STEMI’s. The data collection and input I assisted with will be a huge help in the future for cardiologists to learn from this specific patient information to better help patients.

In addition to assisting with the multi-organizational databases, we also gathered data from left-main STEMI patients in an attempt to see how different presentations of STEMI patients, those with a left-main (LM) culprit artery, affected in-hospital death rates. Left-main patients are a specific type of STEMI patient who have blockage of the left main artery in the heart, which causes an even greater restriction of blood flow to the heart and body, making LM STEMI’s incredibly dangerous. This summer, I went through patient information and helped find crucial clinical characteristics for numerous patients which will be used to create an updated data table representing the dangers of LM STEMI’s when compared to other heart attacks.

Even though I was not able to experience benchwork this summer due to COVID19 restrictions, this clinical research project was a great and exciting experience. I was taught all about the vessels of the heart, different medications that are common within hospitals, various cardiac problems that Americans face every day, and I was even able to see a live procedure on a heart-attack patient at the cardiac catheterization lab at The Christ Hospital. I am extremely grateful to the staff at The Christ Hospital who made this experience possible and supported me through the process.

Evan Lakhia is a senior in The Summit Country Day School’s Science Research Institute.

 

Monarch butterfly populations have been plummeting at an alarming rate since the 1980s due to logging and herbicide use. This summer, I worked at the Cincinnati Nature Center in Milford, OH to support the preservation of this species. The Rowe Woods location is a 1,016 acre park filled with natural beauty, conservation efforts, and some of the kindest people you will encounter. I was mentored by Mrs. Olivia Espinoza, who manages the CNC chapter of the nation-wide Monarch Larva Monitoring Project (MLMP), affiliated with the University of Minnesota. 

MLMP channels the extraordinary power of citizen science, or data collection by the public, to amass more information on monarch butterfly migration patterns than a few professional scientists could collect on their own. People like you and I count and record the number of eggs, larva, and adult monarchs in community milkweed patches (the invertebrate’s food source of choice) and send the data to scientists at the University of Minnesota. The overarching objective is to provide accurate population reports to sway decision makers who could prevent further habitat loss and alleviate the monarchs’ plight. Along with contributing to this project, I also sought to identify which milkweed characteristics attracted migrating females for egg laying. I found that monarchs prefer plants that are taller, in better health, and grow at the edge of a patch in addition to laying the most eggs in late July. 

My experience taught me that science is best conducted in collaboration, even amidst a pandemic. When I first imagined research, I thought of a lone scientist in oversized goggles and white coat, spending hours experimenting in isolation. This is not the case! My first day, I was assisted by an elderly gardening enthusiast with valuable knowledge about the plants around my site. My discussions with passing hikers gave me new perspectives on my monitoring methods and allowed me to talk about my research with strangers. When my parents kept me company on my excursions, they pointed out interesting observations that I would not have noticed on my own. I also learned the value of perseverance, especially as I struggled to stay positive during the early weeks, when finding a monarch was a rarity and most of the plants I examined were empty. 

The opportunity to help preserve the monarch populations that are part of Cincinnati’s natural beauty was exceptionally rewarding. If you need a fun summer activity, consider printing your own data tables and contributing to the conservation of these extraordinary creatures!

Melina Traiforos is a senior in The Summit Country Day School’s Science Research Institute.

Over the summer, I participated in a research project to address the world’s diminishing antibiotic supply at the Science Research Institute laboratory with Dr. Replogle at Summit Country Day. We participated in Tiny Earth Network research which examines bacteria obtained from soil for antibiotic production.

Using the soil from my backyard, I cultured bacteria on plates to determine their identity and experiment with their ability to produce antibiotics. I selected a variety of colonies to test based on their unique morphologies. In the lab, I used safe relatives of ESKAPE pathogens, the leading cause of nosocomial infections, to test whether the bacteria from my soil sample could produce and secrete compounds that inhibit the growth of the safe relatives. Two colonies were identified that produced antibiotic compounds and inhibited the growth of Pseudomonas putida. P. aeruginosa is the related ESKAPE pathogen; it is an opportunistic pathogen with a 40-60% mortality rate. P. aeruginosa has developed resistance to antibiotics, therefore, it is important to identify novel antibiotics that can treat P. aeruginosa.

I used biochemical characterization tests to dig deeper into the identity of these two bacteria colonies. Additionally, the bacteria’s 16s rRNA gene was amplified using PCR. The PCR products have been sent for DNA sequencing, however, sequencing results have been difficult to obtain. These bacteria will be sent to the Tiny Earth headquarters at the Wisconsin Institute for Discovery at the University of Wisconsin-Madison. Scientist at Tiny Earth will continue to investigate these strains to determine if the antibiotics they produce are novel and a potential treatment for pseudomonas infection.

Despite COVID-19, I truly enjoyed my research with the Tiny Earth Network. I learned various techniques including pouring agar plates and culturing bacteria on a variety of nutrient plates. Additionally, learning sterile technique and the science behind the biochemical tests opened my eyes to the science behind research protocols. My experience with Tiny Earth taught me to look for the positive in any situation and make the best of it!

 Mona Hajjar is a senior in The Summit Country Day School’s Science Research Institute.

In January, my tour of the Wright Patterson Air Force Base Biological Research Laboratory was extremely enlightening and reminded me of Honors Biology Class at Summit from freshman year.  Even though I was eager to start my research within the Materials and Manufacturing Directorate, I felt unprepared and almost wished I had taken AP Biology.

I felt even more lost after attending the Virtual Kick-Off to start our remote summer research. Thankfully, things went significantly better after that. One of the project mentors, Dr. Chia Hung, sent very encouraging emails with links to videos, Khan Academy tutorials, and YouTube videos about rare earth elements and molecular biology. All of my mentors believed in us and were very willing to make sure everyone understood what was going on.

My internship was a virtual collaboration with three other students. We worked on the design of a protein based rare earth element sensor.  Rare earth elements (REEs) are defined as the 15 lanthanides, located at the bottom of the periodic table, along with Scandium and Yttrium. The name is a bit deceptive because they are not really rare, but they are very difficult to extract and purify. REEs are involved in the production of nearly all electronics, from cell phones to aircraft technologies.

However, modern REE extraction methods are incredibly damaging to the environment. The process of separating them from the other metals they are typically found with can produce wastewater and ponds that leak acids, heavy metals and radioactive elements into the environment and groundwater. Our main research objective was to develop a more efficient and environmentally friendly way to extract (REEs) from the earth.

We designed a theoretical sensor construct which could be expressed in yeast cells and inserted into a slurry of metals in order to bioleach REEs. The theoretical sensor construct utilizes a protein called LanM, polyphosphate synthesis, and a genetic modification system, CRISPR/Cas9. Polyphosphate is vital to the design because it isolates the REE once it is leached into the yeast cell. The cells can later be isolated and an extraction method can get the REE. Polyphosphate kinase (PPK) is an enzyme which controls the production of polyphosphate. Since yeast already has a gene for PPK, our construct uses a genetic modification system, CRISPR/Cas9, to activate gene expression.

One problem we focused on was LanM, binding to other common metals. To prevent the system from activation by nonREEs, we observed LanM’s interactions with other metals. We used PyMol, a python based molecular modeling program and a Metal Ion Binding Prediction server to gather bonding data. The final construct was designed using a cloud-based, research software platform for biology called Benchling. Since all of our work was done in silico, our mentors and their Air Force research team will continue the project research with in vitro testing in an actual lab.

In addition to completing the project, our group was able to attend professional lab meetings, and we even had two opportunities to present in front of research professionals. Even though I anticipated a learning curve, this virtual research experience far exceeded my expectations. With self-discipline and time management, I was able to acclimate and enjoy my new work environment. The opportunity to complete this summer research was one of the biggest reasons why I chose to attend The Summit. For that, I am extremely grateful to Dr. Jessica Replogle, head of The Science Research Institute and Dr. Nancy Kelley-Loughnane, Biological Materials & Processing Research Team Lead, for their patience and guidance during this unique learning experience.  It has broadened my exposure to STEM, demonstrated the interconnectivity of the fields of biology, chemistry and engineering, and strengthened my pursuit of a career in engineering.  

Sam Vessel is a senior in The Summit Country Day School’s Science Research Institute.

This summer, I had the privilege of working in the Schiff Family Science Research Institute lab at the Summit Country Day School in Cincinnati, Ohio, in conjunction with the Tiny Earth program at the Wisconsin Institute for Discovery at The University of Wisconsin-Madison. My mentor for this project was Dr. Jessica B. Sakash Replogle, the Schiff Family Science Research Institute Head at The Summit. Dr. Replogle is trained as a Tiny Earth Partner Instructor which provides Summit Country Day the ability to collaborate with and deposit materials at the Wisconsin Institute for Discovery. My fellow classmates, Mona Hajjar and Sam Perez, were also researching their own projects with Tiny Earth.

The Tiny Earth program was designed for students to study natural producers of antibiotics. It aims to address the worldwide health threat of the diminishing supply of effective antibiotics. The program does so through the collective power of many student researchers who seek to identify bacteria that produce novel antibiotics. Through its database and network of students, Tiny Earth provides an excellent and engaging science education as researchers work to solve the antibiotic crisis. The program was created by Jo Handelsman who is the Director of the Discovery Center of Wisconsin at the University of Wisconsin-Madison, and it is a global network of tens of thousands of students and their instructors. My main goal this summer was to discover novel antibiotic producers from local Cincinnati soil; it has been 30 years since a new type of antibiotic was found! 

In this project, we isolated our bacteria from soil. The majority of antibiotics have come from soil bacteria, making it a prime source for potential producers for our research. I collected my soil bacteria from the river’s edge of the Little Miami River in Cincinnati, Ohio, near Bass Island Park.

Since a gram of soil can contain 1010 bacterial cells, I had to dilute my soil bacteria so that I could individually select colonies and not have to pick through a plate overflowing with different types of bacteria. Once I selected bacteria from the plates (differentiating the bacteria based on their appearance), I created a master plate of about 29 colonies. Here, I faced a few issues when a particularly filamentous bacteria spread and grew over other colonies! Then, I decided to challenge these colonies against safe relatives of known pathogens, specifically Acinetobacter baylyi, Escherichia coli, and Bacillus subtilis. I also tested certain strains of bacteria for antifungal properties against the fungi papiliotrema and aspergillus. After collecting all the results, I narrowed my selection down to five bacteria strains that appeared to be producing factors that had antibiotic or antifungal resistance.

The bacteria underwent a few different characterization tests to discover their biochemical properties. The other students working in the lab and I performed PCR of the 16S rRNA gene for our colonies of interest. This PCR product was sequenced for identification of our antibiotic producing bacteria. I also attempted a crude antibiotic extraction from my bacteria, but it did not work. This may be a result of using the wrong type of filter paper for the disc diffusion assay, not growing the plates for the correct length of time or just human error. Though the test did not work in this instance, there are ways that this method could remain useful and be improved in the future to produce a relevant result! Currently, I am collaborating with the Tiny Earth by depositing my data on my strains of interest into their database and waiting for the 16S rRNA sequence in order to identify my strains.

I learned so much and gained invaluable experience during my time in this lab. Dr. Replogle walked me through each new test, and I gained experience using sterile technique and learning how to use different equipment throughout the lab, like the PCR thermocycler. Though there were times when I messed up or had to repeat experiments, I always saw them as a learning experience; patience became key so many times when I had to wait for completely new plates to grow. My time in the lab encourages me now to look for answers in even the smallest of places and leaves me with skills that I know will be vital in future laboratory environments. Dr. Replogle was a wonderful mentor and her diligence and willingness to teach me and the other students in the lab made my experience incredibly positive and beneficial. I look forward to unearthing more about the bacteria I am researching and seeing what Tiny Earth discovers in the future! 

Erin Devine is a senior in The Summit Country Day School’s Science Research Institute.

 



 

 

Ellie Adam, created a sleep study survey to investigate the impact of remote learning on high school student sleep habits under the guidance of Dr. Jessica Sakash Replogle. 

Due to COVID-19 restrictions, I was unable to assist Dr. Dean Beebe of the Department of Behavioral Medicine and Clinical Psychology at Cincinnati Children’s Hospital Medical Center this past summer. The study that I was going to assist Dr. Beebe with was investigating if sleep extension interventions should consider circadian phase alignments. Even though I was unable to work with Dr. Beebe this summer, his work inspired me to create my own study that also focused on adolescent sleep behavior. 

The American Academy of Sleep Medicine recommends that teenagers should be getting 8-10 hours of sleep in a 24-hour period. However, the CDC analysis of the 2015 National Youth Risk Behavior Survey revealed that approximately 72% of teenagers who reported less than 8 hours a sleep a night were not getting enough sleep at night. Trends have shown a decrease in sleep duration in adolescents, approximately 1 hour less per night, between 1905 to 2008. During early to late adolescence, sleep duration increases on the weekends to make up for lost time on weekdays. Early start times of schools can inhibit the required sleep length for the maturing adolescent. School start times have been a matter of debate in recent years because sleep is a key component in the overall health of the individual. Students that get less than the recommended 8-10 hours of sleep a night are at a greater risk for obesity, diabetes, and poor mental health. Adolescence is also a time when chronotypes start to shift from an early chronotype (morning lark) to a later chronotype (night owl).

The Stay at Home Orders mandated by Governor Mike DeWine had high schools in the state of Ohio adopt either asynchronous remote learning or synchronous remote learning. Asynchronous learning is when students' complete assignments in a remote setting on their own time with little to no real-time interactions. Synchronous learning is when students learn in a remote setting in real-time following a traditional school day schedule. The overall objective of the study is to determine if there is a difference in the sleeping patterns of high school students when they are exposed to asynchronous and synchronous remote learning styles. The survey was distributed to students in high schools across Cincinnati, both private and public schools.

Students that participated in the survey had a variety of responses and reflections, but many aligned with what I hypothesized. Schools that participated in asynchronous learning had an overwhelming number of students self-report an improvement in the quality of their sleep. These students got more sleep and overall felt more rested. Even though the asynchronous learning students felt more rested and gained more sleep, many agreed with their synchronous learning peers that school start time should remain the same and that in-school learning is more effective.

This study is significant because it can help educators better understand the sleep patterns of high school students. Educators can use this information when making decisions regarding school start time, specifically the synchronous and asynchronous learning environments that may be selected during stay at home orders during national or state emergencies. In the future, schools could start later or provide accommodations for students based on their optimal chronotype.
 

Ellie Adam is a senior in The Summit Country Day School’s Science Research Institute.

In pediatric medicine, recording the weight of patients is a common and very essential practice. By measuring weight, medical professionals can determine if a pediatric patient is growing properly and determine the patient’s physical composition. Very often, however, many recorded weights are inaccurate, and this can lead to serious issues. Drug doses are weight based, and it is important to have accurate weight inputs because incorrect weight inputs can lead to the improper dosage of a patient. Incorrect weight inputs could also cause unnecessary panic from both patients and medical professionals if they see a weight worthy of being prescribed weight-loss medication. To combat this issue, the WEED (Weight Entry Error Detection) project was put in place to create and find an algorithm that best finds and reports these weight errors. The goal of the WEED (Weight Entry Error Detection) project is to find a method that can be consistently and successfully used throughout medical centers to help combat human error in weight chart input.

Over the Summer, I had the chance to work on this project in the innovative Clinical Data Capture and Use (iCDCU) Laboratory within the Department of Biomedical Informatics at the University of Cincinnati College of Medicine. The iCDCU Laboratory is a blended community of informatics researchers, data analysts, software designers, statisticians and trainees. My role in the WEED project was to work closely with both a graduate student and the Primary Investigator, Dr. Danny Wu, to document and create a script analyzing a regression model. In this model, variables such as age, date of measurement, previous weights, and time between measurements were used to identify whether or not new weight measurements contained errors. With help from the graduate student I was able to document this process and create a flowchart for it. My next task was to use an existing script performing statistical analysis on the regression method created by the student and add 3 more majors to it. The majors were precision, recall, and f-score. Recall is the amount of errors the method identified compared to the amount of errors there actually were. Precision is the amount of errors identified that were actually errors according to professionals. The f score is the harmonic mean of precision and recall. Finally, using knowledge I gained from the previous documentation, I documented the analysis script.

What I found from my analysis of the three majors is that the regression method is not a very effective method of detecting errors. When calculating precision, recall, and f-score, a value of 1 means that the method was perfect in identifying errors. The further below 1 the majors get, the less accurate the method is. It was found that the precision was about .45, recall was about .21, and the f score was approximately .29. These low numbers (closer to zero) show that the method was inaccurate in both identifying errors that were classified as errors and at finding the correct amount of errors.

Through my experience working on the WEED project, I have learned a lot about creating a technical documentation and also have gained a considerable amount of knowledge in the R programming language. Experience with these tools was a great way to combine my interest in the fields of biomedicine and computers and will greatly benefit me in a future career of data analysis and programming.

Drew Reder is a senior in The Summit Country Day School’s Science Research Institute.

Over the summer, I conducted research as an intern at a local company called BioWish. BioWish is a company that develops innovative biotechnology solutions for the aquaculture, agriculture, and environmental management industries. BioWish uses advanced bioaugmentation solutions for the natural treatment of waste and surface water. The bioaugmentation solutions use natural products to shift the microbiome and boost the populations of beneficial microbes in the target area.

I worked specifically with their product called BioWish Remediate and tested it on some landfill leachate all the way from Texas. BioWish is working to determine the path of nitrogen in this bioremediation treatment process. During the treatment process, nitrogen is converted from harmful and smelly ammonia to nitrite then to nitrate and finally into the safe, odorless form of diatomic nitrogen gas. It has been proposed that the microbes in the BioWish Remediate are performing a nitrifier denitrification pathway, and our group was performing a benchtop scale “mode of action” study to determine if this is the reaction path of nitrogen.

The BioWish location where I worked this summer is located right under Hyde Park Square. There, I worked with the senior scientist and R&D lab assistant. My other mentors, the Director of Research & Development and the Director of Commercial Water Treatment, gave remote guidance to coordinate the research as well as educate me on the basic lessons of wastewater treatment. We were all on the same research team, and we all pursued the same goal – a better and more sustainable way to treat wastewater.

I learned a lot about the lab equipment, tools and reagents that are needed for these experiments that utilized both microbes and chemicals. I learned about the safety rules and protocols for different parts of the labs. I used a walk-in fridge and worked hours in a microbial room. I have observed the process of APC (aerobic plate count) assays along many more specialized techniques. Unfortunately, my study had inconclusive results, but I hope to continue the study now that possible contamination was ruled out. I have gained so much experience and insight about the scientific research process and how it is used to develop a product. Water is one of our most important natural resources. With advancing methods and technology, we will make sure the water we use to fulfill our needs will run back to nature, clear and clean like it was.

Arthur Li is a senior in The Summit Country Day School’s Science Research Institute.

student at laboratory

This summer, I had the opportunity to intern in the Gastroenterology, Hepatology and Nutrition Division at Cincinnati Children’s Hospital Medical Center. I worked in the lab group of Dr. Lee Denson which investigates inflammatory bowel disease (IBD): specifically, Crohn's disease and ulcerative colitis. When choosing a research project for the summer, at first, I had no clue what department I wanted to intern in. Finally, after struggling to find one that really piqued my interest, I chose the Gastroenterology (GI) department because my family members have experienced GI disorders. I wasn’t sure what to expect, however, once I started my job, I knew that I had made the right decision. 

IBD is an inflammatory disease in the intestinal tract. Up to 80,000 children and 3 million adults are reported to have IBD in the U.S. It is caused by an overactive immune system. When homo sapiens first evolved, their diet had a lot of dirt and bacteria in it.  Because of this, an overactive immune system in the gut was necessary to keep the human alive. However, nowadays our diets are much cleaner. Most food is processed and or/cooked, which eliminates a lot of bacteria from our diets; therefore, we don’t need an overactive immune system anymore. When this occurs, it is a problem. An overactive immune system causes recruitment of immune cells into the gut leading to normal tissue damage which is painful, can block digestion and lead to numerous health problems. The Denson lab works on understanding the genetic pathways that cause this overactive immune system and one day hope to develop gene therapies to treat this. 

My favorite part of working at Children’s was all the people I met. The members of the Denson lab group were very patient with me. They also answered my questions, even if the answers seemed obvious to them. My mentor, Erin, is a senior research assistant and was especially helpful in showing me the ropes and directing me around the lab. I loved eating lunch with my lab group and members of the lab groups on our floor and hearing them talk about their own research and their own lives. Honestly, I think that if my lab group had been a different group of people, I would have had a much different experience. This group truly made me enjoy my job. 

Overall, I learned so much from this experience. Although parts of my project did not end with a perfect result, I still gained a lot of knowledge and acquired new technical skills during my time at Children’s Hospital. Working in a lab gave me the experience of a research career, but I also learned a lot about myself during this time. I’ve always been worried that one day I would enter the workforce, wouldn’t find a job that I love. and I’ll be forced to take a boring job that I hate. However, this internship showed me that there are jobs out there that I really do love, such as research.   

Connie Nelson is a senior in The Summit Country Day School’s Science Research Institute. 

student at laboratory

Two summers ago, I took an Introductory Psychology course taught by a professor of neuroscience. The professor, because of his educational background, mainly taught the class based on the brain’s role in psychology, and this spin on psychology was fascinating. How neurotransmitters work and the different functions for various regions of the brain were part of a whole new educational world for me. I loved it so much that neuroscience was my topic of choice when selecting what kind of research I wanted to do this summer. Neuroscience research is of the utmost importance right now because the details on how the brain works is still mainly unknown. 

This summer, I worked in the University of Cincinnati (UC) Psychiatry and Behavioral Neuroscience Department under the direction of an assistant professor and a graduate student. The study I assisted with dealt mainly with depressed patients at-risk for bipolar disorder. According to the National Institute of Mental Health, approximately 5.7 million adults are affected by bipolar disorder. In addition, according to the same organization, about 17.3 million adults have depression. These mental illnesses affect many people, so research trying to decrease them is vital. 

The study’s research objective was to determine whether N-acetylcysteine (NAC) is effective in treating depression in adolescents and young adults who are at-risk for bipolar disorder. Children of a parent with bipolar disorder are at a much higher risk of contracting the disorder than the general population. Scientists do not yet know how NAC affects the brains of people at-risk for bipolar disorder, and this study may lead to findings on that topic. I helped to evaluate the levels of glutamate, a metabolite in the brain that can cause nerve cell death when levels are excessive. It is known that glutamate is significantly increased in the left ventrolateral prefrontal cortex (LVLPFC) in the experimental group (youth at-risk for bipolar disorder) compared to the control group. The key finding from my analysis was that NAC significantly decreased glutamate levels in the LVLPFC within the experimental group. Additional studies will continue to evaluate the role of NAC in treating depression in adolescents and young adults at-risk for bipolar disorder. 

This experience opened my eyes to the process of research. It is not just performing experiments however way you want. There is a procedure for proposing an experiment, having it approved, and keeping it ethical. In addition, there are specific protocols that must be followed during research, especially if the research is clinical.  I learned that writing is a very important step in the research process because if a scientist does not communicate his or her findings through writing a grant proposal or paper, then no one knows what they did; therefore, science cannot advance without writing. This experience helped me grow tremendously in confidence because it was my first time in a truly professional setting. Knowing that I can go to a professional department, work there and have conversations with specialists will be an invaluable experience as I progress on through life. 

Ryan Burns is a senior in The Summit Country Day School’s Science Research Institute.

student at laboratory

This summer, I have been working in a clinical research group with an orthopedic doctor, a first-year medical student and an undergraduate student interested in attending medical school. The group is part of the University of Cincinnati Department of Orthopaedics and Sports Medicine. The project I am working on will be either a meta-analysis or a systematic review of the effects of vision training on sports-related concussions and mild traumatic brain injuries. In the U.S., approximately 1.6 to 3.8 million sports-related and recreation-related concussions occur each year. 

 

Vision training can be used as a tool to treat concussions, especially when symptoms are not going away. My main goal was to complete a thorough literature search for pieces of scientific literature that can be used in the study. I performed the literature search using Google Scholar and the set of search terms selected by the group. Once we had preliminary results from the search, we excluded articles if they included children, traumatic brain injuries, or other treatments combined with vision training. Currently, the articles are being evaluated for the data each contains prior to the meta-analysis. 

As I continue the internship, I’ll be doing more shadowing and finding data for the end of the research project. Meta-analyses have an important role in evidence-based medicine, therefore, it has been great to be part of the team evaluating the results of multiple studies with the goal of creating the best clinical practice to treat concussions. Overall, my experience has been very positive, and I’ve learned a lot about clinical research including what a career in orthopaedics and sports medicine could be like. 

Rebecca Smith is a senior in The Summit Country Day School’s Science Research Institute.