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CLUSTER 7: BIOENGINEERING/MECHANICAL ENGINEERING: THE AMAZING RED BLOOD CELL The focus of Cluster 7 in the first two weeks of COSMOS 2015 is “Bioengineering; the Amazing Red Blood Cell”. The first week has been packed with hands-on laboratory work including learning how to use small volume transfer equipment (micropipettors), an indispensible tool commonly used in bioengineering research labs. Students immediately applied their newfound expertise in a lab that analyzed bovine blood cells under different experimental conditions. Blood cell morphology was analyzed using light microscopy to distinguish red blood cells (RBCs, erythrocytes), white blood cells (leukocytes) and platelets. Image J software (from the National Institutes of Health) was then used to quantify the morphology of RBCs under hypertonic, isotonic or hypotonic conditions. First week labs were very closely linked to the highly engaging mini lectures given by Dr. Carlos Vera on the molecular and cell biology of blood cells. Outside the lab students attended a presentation on the UCSD requirements for lab safety and a second presentation that focused on biosafety and other safety issues when working in the Bioengineering building. The head of the UCSD library system also presented a very nice summary of the electronic resources available to students to facilitate their COSMOS final projects. All COSMOS students attended the first of a series of Discovery lectures given by Professor Tom Bewley of the Mechanical/Aerospace Engineering Department who presented a highly engaging overview of various robots developed and commercialized at UCSD. In the science communication segment of cluster 7, students have begun to analyze the steps involved in generating and effectively analyzing scientific data. They have also begun to consider their final projects as well as the ethical considerations involved in mechanical or bioengineering research. Finally, students launched a biography presentation series this week in which the lives and contributions of prominent scientists are researched and summarized in an informal presentation made to all of Cluster 7. In summary, Cluster 7 students have shown a very high level of engagement in their first encounter with bioengineering research and are off to a great start in COSMOS UCSD! 10 CLUSTER 7: BIOENGINEERING/MECHANICAL ENGINEERING: THE AMAZING RED BLOOD CELL The focus of Cluster 7 during COSMOS 2015 week two were molecular and cell biology studies of red blood cells (RBCs). Purified RBC “ghost membranes” were analyzed in week two by the combined techniques of SDSPAGE (to separate the mixture of proteins contained in membranes) and western blotting (for protein identification). Students discovered the immense power of western blotting in the identification and quantification of the protein actin. In western blotting, RBC membrane proteins were separated by electrophoresis and then transferred to a paper matrix that was first mixed with an antibody that only binds to the protein actin and then visualized using and second antibody and chemiluminescence. High quality western blot results were obtained by all lab groups in Cluster 7! By the end of the week students used the polymerase chain reaction (PCR) technique to convert small amounts of DNA into very large quantities.. The PCRproduced DNA was then analyzed using agarose gel electrophoresis to confirm the huge capacity of PCR to amplify targeted DNA. Finally students learned about a powerful method of gene silencing known as a “gene knockout” (KO), a commonly used technique in bioengineering and biotechnology research labs. Students were able to analyze the presence or absence of a gene for the RBC membrane protein, ETmod from a KO mouse created in Dr. Vera’s research laboratory. Using PCR, students could genotype the KO mouse and determine whether the mouse was completely lacking the E-Tmod gene compared to positive control levels found in normal mice. Students also measured oxygen transport by red blood cells using the technique of pulse oximetry, a fingertip method for monitoring a patient's oxygen saturation level. Students also explored Electrocardiography (ECG or EKG) which is the recording of the electrical activity of the heart. An ECG is used to measure the heart’s electrical conduction system and displays the overall rhythm of the heart and weaknesses in differ- ent parts of the heart muscle. Students learned that a regular heart rate is between 60 and 100 beats per minute (bpm); less than 60 bpm is called bradycardia; more than 100 bpm is termed tachycardia. Students learned additional aspects of ECG including QRS patterns and P waves. In the science communication portion of cluster 7, students continued to work on their independent bioethics essay. Cluster 7 also had its first field trip to the J. Craig Venter Institute (JCVI), and got a behind-the-scenes look at a dynamic biomedical research laboratory. Students learned about various projects at JCVI including the use of algae as a new source of oil and the global sampling of sea water for the identification of new species, complete with their genomic DNA sequences. Having achieved a sound foundation in RBC molecular and cell biology over the last two weeks, Cluster 7 students are now well poised to build and analyze RBC models using mechanical engineering principles that should provide further insight into the structure and function of the amazing red blood cell. 10 CLUSTER 7: BIOENGINEERING/MECHANICAL ENGINEERING: THE AMAZING RED BLOOD CELL The second half of Cluster 7 began with the introduction of tensegrity structures by professor Mauricio de Oliveira and teaching assistant Tamoz Dunov. Tensegrity structures consist of elastic strings under tension that connect wooden sticks that are under floating compression in such a way that the sticks do not touch. The objective for week 3 was to develop an appreciation for tensegrity structures as models for the mechanical properties of red blood cells (RBCs). A tensegrity structure stabilizes itself mechanically based on the way tensional and compressive forces are distributed. The simplest tensegrity structures, called Snelson prisms, were constructed by students which led to the creation of some very interesting 3-D shapes (and fashion statements)! This was followed by mechanical engineering experiments to determine the forces associated with the tensegrity structures. Using Hooke’s law (F = -k ∆X), students first experimentally determined the stiffness (k) of various elastic materials (strings, bungee cords, etc) and then analyzed Force (F) versus Load Displacement (∆X) curves for a selected string. Students then used their knowledge of Hooke’s law to determine the pretension characteristics in a 6 string / 3 rod Snelson prism. From these experiments Cluster 7 students are now poised to connect the value of tensegrity structures as models for RBC membrane shape and function. With only one week to go in COSMOS 2015 students have been busy in developing their final projects but also in devising a novel approach to preventing/treating malaria in a class-wide collaborative essay. Cluster 7 final projects are somewhat unique in that students use their laboratory experience and data from weeks 1 and 2 to formulate a research proposal focusing on a novel hypothesis linked to red blood cells. Some of the tensegrity structures built during the last two weeks of COSMOS represent good models of normal versus atypical red blood cell shape and flexibility and as such are often included in Cluster 7 final project presentations that, amazingly, are just around the corner! 12 CLUSTER 7: BIOENGINEERING/MECHANICAL ENGINEERING: THE AMAZING RED BLOOD CELL The final week for cluster 7 was a busy one with students learning new engineering concepts that apply to tensegrity structures as well as completing all the preparations for the COSMOS final projects. Professor Mauricio de Oliveira continued to develop the concept of tensegrity as students began to explore the engineering principles of feedback and control using a DC motor equipped with a potentiometer and interfaced to a beaglebone computer running Python programming. Students learned how to add line by line Python3 code to implement numerous experiments to learn how a motor responds to variable voltages and how feedback is used to regulate voltage changes. These investigations were an excellent exposure to the types of engineering analyses that can be applied to tensegrity structures that can serve as models of red blood cell morphology and function. Cluster 7 students had their last field trip this week to Illumina, Inc., a leading local biotech company that develops and markets products for the analysis of genetic variation including DNA sequencing, genotyping, gene expression and DNA methylation. Students were also treated to an insightful overview of life at UCSD by former Cluster 7 student William Coulter, a 4th year UCSD bioengineering major. Students also got a close up look and some hands on experience with Professor Bewley’s MIP and Rover robots (featured during his week 1 Discovery Lecture) that was presented by Talesa Bleything, a Ph.D. student in Professor Bewley’s lab and former Cluster 7 TA. As we reach the conclusion of COSMOS 2015, Cluster 7 students wish to thank Dr. Mauricio de Oliveira and Dr. Carlos Vera, and Cluster 7 TA’s Anusha Pasumarthi, Sherry Zhang and Tamoz Dunov for all their efforts in guiding a detailed exploration of bioengineering and mechanical engineering principles and their application to studies of the amazing red blood cell. Thanks also to all COSMOS staff with a particularly big shout-out to cluster 7 RA’s Martha and Kevork. It was a truly memorable academic and residential experience at UCSD this summer for all Cluster 7 students! 10