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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!
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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.
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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!
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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!
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