As we finish up another very productive semester in the Bioscience Research class, this final report of the year will focus on a project we recently took on that will continue through the summer, into next year. This past week our CAPS Bioscience students joined forces with the Business students to hear from Dr. Barney Graham, the head virologist with the National Institutes of Health (NIH) and brother-in-law of one of the CAPS Business teachers, Mrs. Janet Graham. In addition to his administrative duties at the NIH, Dr. Graham conducts research into the development of vaccines. While he works on multiple viruses, one of his primary pursuits is to study the respiratory syncytial virus (RSV). Most every child becomes infected with RSV at least once by the time they are two years old, and symptoms can be quite severe at times, causing hospitalization in as many as 125,000 infants a year. In his effort to develop an effective vaccine against RSV, Dr. Graham and his colleagues have been studying the molecular structure of the virus, which was the focus of his talk this week here at CAPS.
After presenting to the students about RSV and the research into its structure, Dr. Graham proposed a project for our continuing Bioscience students. During the process of infection by RSV, the virus itself changes shape. One approach that is being used to develop a RSV vaccine is to impact certain aspects of this shape change. Currently, Dr. Graham and his collaborators have diagrams of the molecular structure of the virus at the beginning and ending stage of the shape change, but do not have information about the minute movements the molecule makes as it moves from one form to the next - which leads to the involvement of the CAPS students. In order to determine the full range of movements made by the virus as it changes shape, computer modeling programs will be required, with the final product being a short animation illustrating the overall molecular movement. This task will be undertaken by the CAPS Bioscience Research class. A group of students will be working on the preliminary aspects of the project this summer, with a completion target of early autumn. We will certainly be providing a project update early next semester.
This week we will revisit the work of Meryl Engle. As shared in the February 8 update, Meryl has spent the semester working the laboratory of Dr. Shrikant Anant, a cancer researcher at KU Medical Center. Dr. Anant and two of his staff scientists recently gave a talk at CAPS and they all gave rave reviews about Meryl’s performance. In the Feb. 8 update, Meryl discussed her developing skills in a particular protocol, western blotting. Her mentors shared with that by the end of the semester, Meryl’s skill in this procedure exceeded that of many second-year PhD students. They were amazed at the clarity of her final product. Dr. Anant was so pleased with Meryl’s work; he reached out to colleagues at Meryl’s college of choice, University of Arizona, to ensure that she had a laboratory in which to work as soon as she lands. In today’s competitive landscape, it is key for a developing scientist to gain laboratory experience before applying for graduate school. Meryl’s experiences at CAPS provided a firm research foundation and Dr. Anant’s recommendation will ensure she maintains her trajectory towards being the superstar scientist she is destined to be.
As the Research students wind down their projects for the semester, several of them are shifting their efforts towards this year’s iGEM competition. The iGEM (International Genetically Engineered Machine) competition began as a collegiate class at MIT in 2003 that focused on manipulation the genetic code of a microbe to perform some novel task. This year, there are teams from over 200 universities worldwide, each designing and constructing a molecular device that will address some problem. Projects range from addressing very important societal challenges such as detecting arsenic in drinking water to somewhat less serious projects such as developing biologically based lava light. In 2011, iGEM started a high school competition and last year, 2012, CAPS sent our first team. Those of you who were reading the CAPS weekly update at that time will recall last year’s team project was the “Arom-O-Clock”, a microbial alarm clock that emitted a soothing banana smell while you sleep at night, but switches to producing an invigorating wintergreen smell when the sun hits it in the morning.
This year’s CAPS iGEM team will be tackling the problem of providing sustainable fuel sources into the future. One current challenge facing production of biologically-produced liquid fuel (biofuel) is that it is necessary to input some type of energy rich feedstock to convert to usable fuel. The most common input currently is corn, which has an abundance of easily accessible energy-rich sugar. Corn, however, is also a major base of the human food chain in much of the world, and too much demand on its consumption ultimately causes food prices to raise – an undesirable result. The CAPS iGEM team is looking at utilizing the ability of a class of microbes called cyanobacteria to harness energy from the sun to produce easily accessible chemicals for use in biofuels. Below is the scientific explanation for the team’s project.
Alkanes are a primary component of diesel fuel and are one class of molecules that cyanobacteria can synthesize. Furthermore, alkanes are excreted from the cell and then float on the surface of water, making harvesting of alkanes energy efficient. Like other fatty acid derived products, acetyl-CoA is the initiation point for synthesis of alkanes. In a photosynthetic system such as cyanobacteria, acetyl-CoA is formed from pyruvate which is the end product of glycolysis. Since pyruvate kinase catalyzes the final step in glycolysis (the conversion of phosphoenolpyruvate (PEP) to pyruvate), this enzyme is a common regulatory point of glycolysis in most organisms. Because the production of pyruvate provides the initial carbon source for lipid and alkane synthesis, we hypothesize that increasing the enzymatic activity of pyruvate kinase will increase the cellular concentration of pyruvate and thus increase the production of alkanes by the cell.
This year’s team is also benefitting from the scientific mentorship of Dr. Aron Fenton at the University of Kansas Medical Center. One area of focus in Dr. Fenton’s lab is the biochemical analysis of pyruvate kinase and its biological function, which has made him an invaluable advisor to the team.
The competition is June 28 and 29, 2013, in Cambridge MA. We will certainly be reporting on the team’s success in this space in August.
This week we will check in with Tyler Hamedi concerning his work in the lab of Dr. Lisa Stehno-Bittel at the University of Kansas Medical Center. As discussed in the January 25 update, the primary research focus of the Stehno-Bittel lab is diabetes and potential therapies. Tyler’s primary role thus far has been to conduct an image-analysis of cells comprising key structures within the pancreas known as islets. As you will see in the following excerpt from his journal, Tyler is in the process of transitioning into a role of greater responsibility, as he will be continuing his work in the Stehno-Bittel lab this summer.
“This week in lab was a big week, on Monday I assisted in doing islet decomposition. Islet decomposition is the process in which we break down islets into single cells. After we do this there are a few things we can do. Either freeze them or turn them into what we call ‘kanslets’. On Tuesday I did my first solo Islet decomposition and cryopreservation. This is a process which I will be doing many more times as the year goes on. It is a great thing for the lab, because whenever they need the single cells they are frozen and ready to go. This is preferred to having to put in a request, waiting and then breaking them down once we get them. This is great in the sense this is my first real solo lab/bench work I have done, and I am thoroughly enjoying it. I also started to do my own media changing and taking care of all my own human cells. This is a big step for me, getting away from the analysis and into the real lab work. The islets that I am working with are only 50% pure human islets; we got these for me to practice with. Hopefully I will be working with highly pure islets in the near future.”
Normally we report on the work of an individual CAPS student in this weekly update, but the Bioscience Research program has also supported the work of several middle school and high school students over the last year. We would like to highlight the work of a few of these aspiring young scientists.
Alexis Vance (BVHS Freshman)
conducted her Honors Biology project here at CAPS this year. Her overall focus was on the concept of “iron fertilization”. The goal of iron fertilization is to create enormous blooms of algae growth in the open ocean to capture and sequester carbon dioxide from the atmosphere. Alexis modeled one aspect of this process in the labs of CAPS. In addition to providing an experimental home for her, CAPS also aided Alexis’ professional growth by helping her identify and seek guidance from experts in the field. Through her networking, Alexis was able to obtain the mentorship of a researcher at Woods Hole Oceanographic Institution in Massachusetts, Dr. Mak Saito.
Mimi Garimella (Lakewood 7th Grader)
performed her research for the Greater Kansas City Science Fair at CAPS. The title of her project was: Effect of Curcumin on Metal Ions that cause Plaques and Tangles in The Brain. Mimi developed her project after learning about current research into the biological basis of Alzheimer’s disease (AD). Although there is limited knowledge of the root causes of this disease, it is known that in AD patients, aggregations of proteins form plaques in the brain and that there is an association between the formation of these plaques and the presence of specific metal ions. Mimi was also aware that there has been some preliminary work done on the use of curcumin (a chemical found in turmeric, a staple spice in Indian cuisine) as a potential therapeutic. Like Alexis, CAPS aided Mimi in obtaining mentorship on her project. She was guided by Dr. James Chapman at Rockhurst University, who provided intellectual support, as well as the use of his mass spectrometer.
Shwetha Ramachandran (Overland Trail 7th Grader
) has been examining the use of the small flatworm, Caenorhabditis elegans (C. elegans) as a tool in genetic research. Specifically, Shwetha has been working on the Silencing Genomes project, sponsored by Cold Spring Harbor Laboratory in New York. This project affords students across the nation the opportunity to gain experience in genetic manipulations using a process called RNA interference (RNAi), in which researchers can disable the function of specific genes and observe the physical results. Many recent discoveries in the biomedical sphere are attributed to the use of RNAi in C. elegans, and Shwetha is positioning herself well to be at the forefront of this research in the coming years.
This week we will visit the project of Muriel Eaton. Muriel’s project is entirely of her design, but she has obtained guidance in its development from multiple professionals, including Dr. Liskin Swint-Kruse at KU Medical Center and Dr. Krzysztof Kuczera at KU Lawrence. Muriel has been interested in a class of molecules known as chaperones since she studied them last semester in CAPS Molecular Medicine and Bioengineering. Chaperones function to process proteins within the body, allowing them to function properly. Protein function depends, in part, on how it is folded upon itself, and several diseases have been linked to mis-folded proteins. Below, Muriel explains her project, which focuses on chaperone function and a particular malady.
“Alzheimer’s disease has been linked to the accumulations of a short peptide (protein fragment) known as beta amyloid (Aβ) in patients’ brain tissue. While exact mechanisms involved in the aggregation and accumulation of this peptide are currently unknown, there is a suspected association with an error in the folding and processing of the amyloid precursor protein (APP) that is cleaved to yield Aβ. A molecular mediator of Aβ processing is the chaperone, HSP70 (Heat Shock Protein 70). Studies have shown that an increase in HSP70 expression in experimental models alters Aβ aggregation. The goal of this project is to engineer modifications to the primary structure of HSP70 to increase its binding efficiency with Aβ.
“Modifications of HSP70 have already been identified in E. coli that affects the binding affinity with the Aβ. Since HSP70 is highly conserved, we will be using C. elegans as our model because of its RNA inhibition. The first phase of the project, which is currently underway, is to identify amino acids in C. elegans HSP70 that may affect Aβ binding. Once candidate mutations are identified, site-directed mutagenesis of HSP70 will be utilized to make the changes. Once the mutations have been confirmed via sequencing, the binding efficiency of the novel HSP70 to Aβ will be compared to that of the native HSP70 using a kit-based binding assay.”
This week we will highlight the work of Melissa Parcell. Melissa’s career plans are focused on veterinary medicine, and she will be attending Kansas State University in the fall as a Vet. Med. major. Melissa has engaged herself in multiple projects during her time here at CAPS, all of which support her professional interest in animal health.
One of Melissa’s activities is assisting in the office of Stilwell veterinarian, Dr. Kelly Hoyt. The following is an excerpt from Melissa’s journal:
“On Tuesday, there was a major surgery on a Great Dane, named Olive, for ACL repair. Dr. Hoyt began by shaving the front leg to put the I.V. in and put lubricant in her eyes because she cannot blink while unconscious which will cause her corneas to dry out. Next, she put a tube down her throat to aid her in breathing. After this, she shaved both sides of the injured leg where the torn anterior cruciate ligament (ACL) is. After sanitizing the leg with soap and alcohol, she removed her tools from an unopened package and covered her leg with blue paper, cutting a hole out where the incisions would occur. Next, she cut along the front of the knee, wiping away the blood with gauze, and continued to cut through several layers of skin. She then cut into the knee and removed the remnants from the torn cruciate ligament. She used scissors and a scalpel to make all of her incisions through the very thick connective tissue. Dr. Hoyt’s vet tech, Elyse was simultaneously checking Olive’s vitals, such as her breathing, pain scale, and heart rate. Dr. Hoyt then located the joint capsule which is a collection of different tendons. At this point, Olive began to show signs of pain because we were beginning to grind against her bone, so Elyse upped her anesthesia to 5%. I could now see the cartilage attached to the femur, which was very rough, rather than smooth due to months of wear after her ACL was torn, this caused severe inflammation. Dr. Hoyt began to put in a few internal stitches….”
Melissa has also been working at Cedar Cove Feline Conservatory and Education Center in Louisburg, KS. Here is some of Melissa’s description about the goings-on at Cedar Cove:
“I have been volunteering at Cedar Cove for four weeks now. My time is mainly spent on small chores such as carrying hay for the dens of the animals, but I also spend a fair amount of time shadowing the tour guides. There are 6 different species of tigers in the worlds, two of which are represented at Cedar Cove, the Bengal tiger and the Siberian tiger. During my time at Cedar Cove, I have learned much about Tigers in general, including their hunting techniques, poaching of wild tigers, and their specific characteristics, range in which each inhabit, breeding, and anatomy.
“Aside from the tigers, there are four Bobcats, three Leopards, three Cougars, one Caracal, two Servals, two Lions, two Leopard Cats, two Wolves, and two Coatimundis. I am getting to know all of the individual personalities of the animals, as well as developing a special connection with Bob, a previously abused Bobcat. I will be able to go into the enclosures with the smaller animals soon, including the Cougars, Caracals, Servals, and Coatimundis. I have also taken an interest in the two brother tigers who were born at the park, Mohan and Raja who are half Bengal, half Siberian Tiger. Hopefully in the future, I will be able to interact and feed the two brothers.”
This week we will highlight the work of Ariel Chou, who has been working in the lab of Dr. Simon Kaja at the UMKC School of Medicine Vision Research Center. Dr. Kaja utilizes molecular and cellular techniques to study neurobiology, with a particular focus on neurodegenerative diseases and visual disorders. Below are a few excerpts from Ariel’s journal that provides good insight into her work in Dr. Kaja’s lab.
“The lab is in the basement area of the vision research center. Dr. Kaja assists everyone with their projects at the lab. There are two research assistants, Mark and Bryan, who I’ve worked with during experiments. Medical students stop by and have their own experiments to assist them in getting their residency and also to get experience. I sometimes pair up with these medical students to work on projects.
“Today Dr. Kaja showed me the ropes on the confocal microscope. These microscopes are special (and really expensive) because they use a scanner to absorb the light instead of a light beam hitting the objective. The microscope can take multiple images and feed them into a computer to be assembled into a 3D image of the structure/cell you are examining. He put in a slide of a certain astrocyte that comes from the optical nerve. He used fluorescence microscopy to light up the nucleus in blue and a certain protein structure in green.
“I have also been working with proteins. I assisted a medical student in extracting proteins from rat brain (procedural details omitted by editor). We performed multiple tests on the protein extract. Dr. Kaja allowed me to perform my own dot blot, which indicates the presence of specific biomolecules. I also worked with three other medical students and assisted them as they conducted their western blot experiment. I got to talk with them and ask them some questions about medical school.
This week, we will highlight some of the experiences of Kylie Bold. Kylie will be heading off to college next year to study marine biology, but her work this semester will be more terrestrial-based. In general, Kylie is very interested in how animals interact with the world around them, and in particular how they function intellectually. She has been conducting an extensive literature review about canine cognition and has learned much about what is currently known about how this group of animals perceives, analyzes, and reacts to situations. One interesting characteristic of canine cognition is that domestication of dogs has actually yielded biological alterations to their genetic makeup in regards to their ability to process cues delivered by humans when compared to other canines such as wolves. At one time, the prevailing thought was that dogs and wolves had almost identical intellectual structures and the primary differences existed at the gross anatomy level. Evidence now points to differences in genes related to cognition.
In order to study dog cognition first-hand, Kylie is volunteering at Wayside Waifs, an animal rescue and rehabilitation operation located just over the state line in Missouri. Kylie’s primary role at the Wayside Waifs up to this point has been working with dogs and cats in an effort to improve their social interaction skills. Many of the animals brought to Wayside Waifs have come from abusive or neglectful homes and need to be retrained in order to promote their successful integration into human society. Several of the dogs that Kylie works with have been rescued from dog fighting operations or from homes of hoarders. In either case, much relearning needs to occur in order to prepare these animals for adoption by caring, responsible homes. This experience has provided Kylie with a laboratory of sorts to study canine cognition, as well as allowing her a mechanism to provide a great service to society.
This week we will check in with Meryl Engle’s progress. This semester, Meryl is spending four days a week in the lab of Dr. Shrikant Anant, one of the lead cancer researchers at KU Medical Center. Meryl keeps a very detailed journal, so we will look at a few excerpts from the past month.
“This week I perfected my Western Blotting skills. The scientists at my lab often refer to it as a ‘Western’ lab - they joke that it is all they do. I learned about the techniques for choosing which protein you want to highlight and how important exposure time is when developing Westerns. One of my main mentors Jessica Johnson said that “science is about proving your point in a bunch of different ways.” She meant that getting results one time, isn’t enough. You must repeat an experiment multiple times and then do different kind of experiment to get solid proof that what you’re saying is supported. In short, I have learned that science is often luck, but you have to prove that it isn’t.
“I was asked to perform a protein assay as part of an immunoprecipitation Jessica was working on. An Immunoprecipitation or IP is a method of pulling a protein antigen
out of solution using an antibody
that binds to that specific protein. The process takes a few days all together and each step requires precision. Our immunoprecipitation was checking for differences in cancer cell lines with varying resistance to an extremely harsh cancer treatment. Jessica chose to use a kit for this immunoprecipitation as her last two immunoprecipitation experiments that she made everything from scratch didn’t turn out as expected. She also decided to use a kit as it promises to compensate for human error. I used to think that using a kit was the easy way out, but I learned that sometimes a kit is the best way to run an experiment as companies have perfected each step and the kits optimize results.
“I started my very own project this week!!! I am the sole caretaker of two flasks of cells. This means that I am in charge of adding fresh media to the cells every day or two to maintain their health. I have learned from everyone in the lab little “tricks.” The cell line I am working with is named “HCT116.” This is a colon cancer cell line. I plated six plates of cells for my first experiment. I then let them grow for a weekend and added a treatment to the media in 5 of the plates. The treatment was developed in the lab. I took samples at different time intervals of 30 minutes, 1 hour, 4 hours, 8 hours and 24 hours. The plate without the treatment was used as my control and was allowed to grow for 24 hours. I plan to use the growth factor EFG to “exaggerate” my results or make them easier or clearer to understand. I will be running protein and RNA extractions next week.
We have, to this point, been sharing the work of our students’ whose projects would fall into the cellular/molecular biology category. However, we also have three students focusing on animal health related projects. Today, Rachel Chall will be sharing her experiences in the veterinary medicine profession. Below is an excerpt from her weekly journal.
“Tuesday, I started my day by going to a stable on a farm call with Dr. Palmer. He was called to the farm to remove the staples from a horse who had had a tie-back procedure. A tie-back procedure is to repair collapsed cartilage around the larynx which causes impaired breathing. The surgery leaves about a 12 inch long scar on the front of its neck. Dr. Palmer removed the staples and then we returned to the vet clinic. I then observed the vet tech remove stitches from a blue heeler’s stomach from a surgery. Dr. Palmer and I then went on another call to a different stable for two horses. The first horse simply needed a wound on its leg redressed and an antibiotic for an infection. The second horse had pigeon fever, a bacterial disease which causes a puss filled abscess. Dr. Palmer popped and drained the abscess, then rinsed it with sterile water and iodine.”
“On Wednesday, Dr. Palmer and I made one farm call that day to the Saddle and Sirloin club. The first horse he worked on he gave an arthritis injection right into the fetlock. Before that injection however the horse was given a sedative and a local anesthetic was injected into the area. The arthritis injection was then injected into the joint. This was a very sterile procedure compared with most in large animal field procedures. Sterile gloves and tools were used as well as cleaning the injection site on the horse. After that Dr. Palmer injected arthritis treatment injections into the vein of the neck on 11 horses. The last thing we did on the farm call was look at a horse whose eye was red and inflamed. The owner was not sure what was wrong with the horse and had already treated the horse for pink eye. Dr. Palmer injected a sedative then examined the eye. He discovered the eye had a small amount of bedding in his eye. He then used a dye test to make sure the ducts which connect the eyes to its nose passageways are open. The test was positive that they were open so he continued to flush the eyes with eye drops and to clean out the debris with cotton swabs. Dr. Palmer then prescribed a cortisone cream before leaving”
This week we will highlight the work of Tyler Hamedi. Tyler is working three days a week in the lab of Dr. Lisa Stehno-Bittel at the University of Kansas Medical Center. Dr. Stehno-Bittel’s work focuses on potential cures for diabetes. Her two main foci are the transplantation of pancreatic islet cells (the structures responsible for the production of insulin and other key hormones) and the generation of artificial islets. Here is a short description of Tyler’s work over the past two weeks in his own words:
“On Tuesday i was trained in how to conduct data analysis on our islet cells. We take pictures of the islets with a confocal microscope, and it shows a picture of the islets themselves and then it has another picture showing the apoptotic cells (experiencing self-imposed death) in the islet and, another picture showing the necrotic cells (dying due to external forces). We then upload the photos to Photoshop and get the number of pixels in the islet and then impose that outline on the apoptotic cells and necrotic cells to see what percent of the cell has died and how. The data I am collecting has to do with analyzing the percent of Insulin-producing (beta) cells, glucagon-producing (alpha) cells and somatostatin-producing (delta) cells. This is important because we can determine how severe the diabetes was in the subject, what type of diabetes they had, and how well the diabetes was regulated. With a rat islet, the insulin-producing cells are typically concentrated in the middle of the islet and there is a ring of glucagon cells surrounding the insulin cells.”
This week, we will be looking at the work of Dylan Geick. Dylan took the Molecular Medicine and Bioengineering class last semester and is going to focus this semester on mammalian cell culture. This area of research requires specialized skills and the ability to work with completely sterile technique. As such, a person who is skilled in cell culture is greatly advantaged when seeking out a student research position or as an actual member of the workforce.
Dylan has two project paths he is considering. His first idea is to screen specific consumer products with mammalian cells to determine some of the biological effects of these products. For example, several companies sell flaxseed oil as a nutritional supplement which supposedly has many health benefits. Dylan would like to determine what the actual effects are at the cellular level.
Dylan’s second project concept is to fuse pancreatic islet cells with tumor cells. Islet cells produce insulin, but are limited in the number of times they can divide. Tumor cells, by contrast, can potentially divide without limitation. Dylan would like to investigate utilizing fusion technology to inform potential diabetes treatments. We will be reporting on Dylan’s progress on these two fronts in the weeks to come.
This semester the Bioscience Research class has seven students enrolled, and we will be highlighting a different student’s work in this space once a week. Below are the students you will be hearing about, along with a short description of the work they will be doing.
will be working this semester at Wayside Waifs, gaining first-hand experience in animal rescue and the unique clinical needs of abandoned or abused animals.
will be working in a variety of veterinary medicine settings. She will be mentored by both small and large animal veterinarians. Rachel will also coordinate with professionals in the field to develop additional curriculum for use in the CAPS Animal Health and Environmental Science class.
will be further developing two projects she and her classmates began in their CAPS Molecular Medicine and Bioengineering class. One project involves investigating the molecular structure of a particular class of proteins known as chaperonins and the other focuses on genetically engineering a novel protein to be utilized in biofuel production.
will be working in the lab of Dr. Shrikant Anant at the University of Kansas Cancer Center at KU Medical Center. Meryl has already begun her experiments which involve a novel approach to working with cancer cells. Instead of growing the cells in a two-dimensional layer as done traditionally, researchers in the Anant lab have developed an approach which allows the generation of a three-dimensional tumor for use in experimentation.
will be venturing into the world of mammalian cell culture. The ability to work aseptically and successfully propagate mammalian cells is one of key skills required of the biomedical investigator. Dylan will be mentored by Dr. Diane Wyatt, who runs a business focused on providing cell cultures and growth media to the biotech industry.
will be working under the mentorship of Dr. Lisa A. Stehno-Bittel at the University of Kansas Medical Center. Tyler will be supporting an ongoing project of the lab which focuses on the development of pancreatic islet cells and their relationship to the development of diabetes.
will be working in the laboratory of Dr. Simon Kaja at the University of Missouri, Kansas City. Dr. Kaja is a neurobiologist who focuses on neurodegenerative diseases and visual disorders. Ariel will gain experience in a variety of research techniques, including confocal microscopy.
will also be working with a variety of veterinary medicine and animal rescue organizations. Melissa’s main interest is the rehabilitation of exotic animals that have been unsuccessfully maintained by their original owners.