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Carolyn Berthelot
Internship Report
12/1/11
Carolyn Berthelot
Texas Biomedical Research Institute
[email protected]
I picked the Texas Biomedical Research Institute as the place that I wanted to
do my internship because of the incredible resources available and my own
fascination with biomedical research. Before I settled on forensic anthropology as
my field of interest I was looking into virology and epidemiology as possible career
paths. The Hot Zone by Richard Preston is one of my all-time favorite books and
details a minor outbreak of Ebola that occurred on the East Coast in the early 1990s
after a facility received some infected primates from Africa. Texas Biomed has a
Level 4 Biosafety containment area where they do research on viruses such as AIDS
and Ebola, much like the one described in The Hot Zone. I was really excited to find
Texas Biomed because it gave me an opportunity to do an internship that combined
anthropology and microbiology.
The Texas Biomedical Research Institute is an independently run, non-profit
institution that was founded by Thomas B. Slick, Jr. in 1941. Slick imagined a “city of
science [that could be] a great center for human progress through scientific
research.” Texas Biomed was recently renamed; it used to be called the Southwest
Foundation for Biomedical Research. Texas Biomed is located in San Antonio, Texas
on a 200-acre campus. Texas Biomed has more than 400 employees and more than
200 ongoing research projects.
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The Institute has two departments: Genetics and Virology/Immunology.
One of the resources that makes this site unique is the Level 4 Biosafety Lab that the
Virology/Immunology Department uses, inside which diseases such as Ebola and
HIV are studied. However, the Genetics Department is the site of my internship, and
also boasts an extremely unique resource: the world’s largest colony of baboons for
use in biomedical research. Texas Boimed is home to about 3,000 nonhuman
primates, around 2,000 of which are baboons. Among the baboons, nearly 1,200 of
them are pedigreed; scientists have kept their genetics and family histories for
seven generations.
The genetics and physiology of nonhuman primates is so similar to humans
that it makes them very useful tools in studying different diseases, such as diabetes,
cardiovascular disease, osteoporosis, and various infectious diseases. Research on
primates has led to medical breakthroughs such as the polio vaccine, the hepatitis A
vaccine, and many of the drugs that are effective in treating AIDS, to name a few.
I work in Dr. Lorena Havill’s Osteolab. She is using baboon skeletal remains
to examine issues pertaining to osteoporosis and osteoarthritis, primarily. She has
currently published at least 25 articles in scientific journals and is working on
several more. One of the newest grants that the lab has received is for a study on
bone structural integrity (BSI). Her main goal for all of her research is to identify
factors (both genetic and environmental) that contribute to bone health in an
attempt to find ways to target those vulnerable to bone deterioration early on and
possibly find some preventative measures.
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Internship Report
12/1/11
The scientists that work under Dr. Havill in the lab are Jennifer Harris,
Shayna Levine, Heather Coan, and Ahsan Choudry. Ted Macrini is a professor at St.
Mary’s University in San Antonio who also works in the lab. He has two students
from St. Mary’s that work as interns in the lab as well. I mainly work with Jennifer
and Shayna. Heather and Ahsan deal primarily with tissue cultures, while Jennifer
and Shayna deal with bones. The atmosphere is very friendly, almost family-like,
and if you are willing to pay attention, work hard, and learn, they are willing to
teach you.
Jennifer is the lab manager, which means that she is in charge of making sure
that everything runs smoothly and takes care of problems as they arise. She also
has to know enough about the different projects everyone is working on so that she
can help out whenever it is needed. Without Jennifer it seems like the lab would
become a completely chaotic environment. Shayna is working on a project with Ted
dealing with osteoarthritis (OA) in the knees. Shayna is taking pictures and
measurements of hundreds of baboon knees so that she can map the affected areas
on the computer. Ted is helping with that, as well as using histology to examine the
level of OA that is present in the animal. Heather and Ahsan work in a separate
tissue culture room most of the time because the majority of their work involves
incubating and growing cells. They are attempting to grow stem cells from samples
taken from baboon knees.
My tasks varied depending on who needed help with a project, if people were
gone from work, and if any deadlines for any projects were approaching. The first
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thing I did every morning when I got to work was go to the lab to check on the
progress of the skulls that I was processing at that moment. Sometimes I would
need to drain the liquid and refill the Crock-pots if the liquid was dark in color or a
lot of the flesh had finally fallen off the bones, other times I would just need to top
off the liquid because some of it had evaporated off and the bones were exposed.
Processing skulls was one of my main projects at Texas Biomed. In the autoclave
room there is a freezer filled with baboon heads that Dr. Havill has received from
necropsies throughout the years. They are not being used for projects or
experiments and the freezer space is needed to store more long bone samples, so
one of my tasks was to process as many of the skulls as I could in order to free up
storage space. The processed heads go on shelves in the lab. There are just rows
and rows of baboon skulls lining the left wall of the lab.
I was actually extremely excited to get to process the skulls because
processing bones was one of the skills that I had hoped to learn while I was at Texas
Biomed. In fact, the first time Jennifer and Shayna taught me how to process
remains, they came up to me and said, “We have something really fun for you to do.”
And they were right, I was absolutely thrilled. Any time I had down time or there
was nothing else for me to do, I went to the head freezer and pulled one out to work
on. Sometimes I just reached in and pulled one out at random, other times I would
sift through and try to find one that I thought would be fairly quick to clean if I didn’t
have a ton of time. I could usually tell by feel if the head was male or female based
off of the morphology of the skull, and if I was short on time, I would attempt to find
a really small one or a male. The males were easier because generally their skulls
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were broader and did not have as many tight nooks and crannies (especially under
the cheekbones) that were hard to clean out.
It is important to note that any time I was working on projects in the lab, I
had to wear protective gear. I always had to wear long pants, close-toed shoes, and
a shirt with sleeves, and then in the lab, a lab coat, safety glasses, and gloves were
added. The first step in processing the skull was to defrost it as much as possible. I
would have to wear a lab coat, safety glasses, and cut-resistant gloves under latex
gloves whenever I worked with the heads. Then I would use a scalpel, forceps, and
tissue scrapers to clean as much soft tissue off of the skull as possible. There is no
right or wrong way to accomplish this part of the process. I would usually start at
one of the zygomatics (cheekbones) and keep my scalpel as close to the bone as I
could and try to take off as much off the tissue as I could in one big piece. The
hardest parts were cleaning out underneath the zygomatics and trying to detach the
mandible. The mandible was cleaned, but it was not processed. Instead, it was
wrapped in gauze and put back in the freezer for storage.
Once the majority of the soft tissue was removed, I disposed of the waste in
biohazard bags and placed the bones in a Crock-pot. I would then pour 10%
ammonia solution into the Crock-pot until the bones were covered, turn it on low,
and let the bones begin to process. The heat and ammonia would help the rest of
the soft tissue fall off the bones, and the number of times I had to drain and refill the
Crock-pot depended on how much tissue I was able to remove beforehand. It took
anywhere from 1 to 3 weeks for the soft tissue to completely detach from the bones,
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at which point I would remove the bones and place them in acetone for no more
than twenty-four hours. This is to help get rid of any remaining sticky residue and
discoloration from the bones.
Some of the teeth would fall out during the Crock-pot part of the process so
after the acetone soak I would use super glue to glue the teeth back into their
appropriate sockets. It was a little bit like a puzzle trying to figure out which tooth
went where before I glued them back in. I would let the teeth dry for a day, then I
would label them with the animal ID number. This involved painting a strip of clear
nail polish on the skull and any cervical vertebrates that had been processed with
the skull. After the clear polish dried, I would use a calligraphy pen and ink to write
the number, let that dry, and then add an additional layer of clear nail polish on top
of the ink. The first layer of polish is to prevent the bone from eventually absorbing
the ink (and then not being able to know what animal the sample is from) and the
top coat is to help prevent the ink from rubbing off. The lab has two Crock-pots, so I
was able to have two skulls processing at all times, along with other skulls in
varying states of acetone soaks and ready for labeling on the counter. Bone
processing was one of my favorite parts of the internship.
Every Tuesday I would attend weekly lab meetings. Dr. Havill held these so
that everyone could touch base and give updates on their projects. I found the
meetings very interesting because she would also use them for people to practice
any presentations they may be giving at schools or conferences at a later date, so I
learned a lot about everyone’s different projects. On a normal day after I checked on
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the skulls, I would then either wrap bones for Shayna and Ted if they were taking
pictures of long bones or work on my pathology report project. Shayna and Ted
would take pictures of long bones from freezer storage, which then needed to be
wrapped back up in two layers of gauze soaked in an 85% saline solution before
they were packaged up for return to the freezer in order to help prevent freezer
burn.
My pathology report project was one that Dr. Havill came up with when I first
started at Texas Biomed. She thought that because of my interest in microbiology
and medicine that it would be interesting to me. They collect pathology reports for
every animal for which they have a sample stored in their freezers. These reports
were stored in about a dozen three-inch binders and dated back about six years. My
job was to create an Excel database that listed the animal ID number, date of birth,
date of death, cause of death, gross medical conditions, and microscopic medical
conditions. The purpose of this is so that when samples are being picked for use in
projects, the researcher can just search for the animal ID number and then make
sure that the animal did not suffer from any medical conditions that would interfere
with the study. It took me about a month to transcribe all of the past reports, and
then every few weeks after that I would update it with the new pathology reports
that Jennifer received. I really enjoyed this project as well because I learned a lot
about different medical conditions. It was interesting to see that when an animal
had a certain condition, that also meant it had three or four other conditions that
went along with it. I could also tell what kind of experiments were being done at
certain times throughout the years based off of the causes of death. Some days it
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took me longer than others because I would type a medical condition into the
database, then go type it into Google to read about it. My typing speed drastically
increased as a result of this project.
My afternoons alternated between working on the pathology reports and
helping Jennifer with inventory. Jennifer has an inventory that lists all the samples
that lab has, as well as which freezer they are located in and where in the freezer
(left, middle, right and front or back) they are located in. However, because so many
different people had been using the samples and putting them back, they had
recently been finding out that a lot of samples were not where they were supposed
to be and they were also finding a lot of samples that were not listed in the
inventory. In order to be able to progress with the projects efficiently, an accurate
inventory was needed and most of the projects were in a holding pattern when I
first got to Texas Biomed until the inventory was completed. I would pull all of the
bones out of the freezer, and then read off the animal ID number and the location I
was putting it and Jennifer would record it. We also had to separate out genotyped
and non-genotyped long bones, as well as pull out any bones that were not listed at
all in the previous inventory. The mystery bones were set aside and we would go
through them at a later date to see what was in the packages and add them to the
inventory. We did this to about twelve freezers, each of which had five shelves.
Once inventory had been completed for the most part, my daily routine
varied greatly. After getting tested for tuberculosis, I was able to observe any
necropsies that our lab was getting samples from. I didn’t get to touch anything, but
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those were basically one giant gross anatomy lesson. I had never studied baboon
anatomy before, and this was a great learning opportunity. I also made more of our
reagents on a regular basis: 85% saline solution, 70% ethanol, and 10% ammonia
solution. This was definitely where my chemistry lab skills came in handy, as far as
measuring and preparing chemicals.
Another one of my tasks involved creating more freezer space. The lab
freezers have long bones (usually the right humerus and left and right femurs),
heads, feet, hands, and vertebrates. When the vertebrates are send over from
necropsies, they are usually in a huge chunk and the pelvic bones are often still
attached. All that Dr. Havill needs is the vertebrate column and the entire chunk
took up about five times as much space as just the column would. So my job was to
clean the verts enough so that they could be sectioned and the extraneous material
could be thrown out. They needed to be cleaned in order to be able to see where
you need to section, and if a Stryker saw was necessary, it does not cut through soft
tissue. If the sample was a normal, healthy one, I could just use the scalpel to cut
through the disc and separate the column. If the bone was osteoporotic or
osteoarthritic, I had to use the Stryker saw to cut through the disc. This is always
done in the fume hood and surgical masks are worn to prevent inhalation of the
bone dust that is produced when the saw is used. I would try to do two to four of
these a day when there was time.
I will be continuing this internship next semester and several new projects
are in the works for me. I will be potentially figuring out how to articulate and wire
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Internship Report
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together a marmoset skeleton that is stored in the lab. I will also be learning
histology, which involves sectioning bones and creating microscope slides from the
sections. Jennifer started to teach me how to section bones last week using a
diamond saw. The saw has a pan of water that sits underneath it in order to keep
the wire from overheating and potentially damaging either the saw itself or
compromising the bone. A bottle of water is also kept nearby to continually wash
the sample off as the wire cuts through it. The saw works off of gravity and when
you release a button, it slides forward and begins to cut through the bone sample
being held by clamps. Before you actually begin taking sections, you have to “face”
the bone. This means that you have to cut off a piece of the bone to ensure that you
are working with a flat, smooth surface. Then you take five to six different sections.
The thickness of the sections depends on the project you are working on. Next
semester I will hopefully learn how to stain the sections and create slides from
them.
One of the coolest things that I got to do at Texas Biomed allowed me to use
what I learned in my Paleopathology course I took at Texas State University last
semester. After one of the skulls I had been processing had been in the Crock-pot
for a few days, I noticed something strange. The frontal, parietal, and nasal bones
had become extremely porous and appeared to be disintegrating. I had processed
seven or eight skulls at this point, using the exact same methods and chemicals, and
this had never happened before. The bone had appeared normal when I first put it
in the Crock-pot, but it had also still been covered by a fair amount of tissue. I also
noticed that the left supraorbital margin (eyebrow) was much larger than the right
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and the cranial vault was about twice as thick as in a normal baboon skull, resulting
in a grossly misshapen skull. Jennifer, Shayna, and a few people from other labs
came to look at the skull and none of them had ever seen anything like that happen
during processing before. I went ahead and finished it up in the Crock-pot to
remove all of the soft tissue. I had to be extremely careful removing it because it
was so porous that it was just falling apart in my hands and shedding pieces of
porous bone.
The animal ID number that had been on the bag that skull had been in and on
the tag inside the bag had read 6910. However, when Jennifer looked up the
pathology report for animal 6910, it was supposedly an animal from 2004 that had
no medical conditions that would explain the pathology we were observing.
Jennifer said that Dr. Havill had not even been collecting samples in 2004, so it was
impossible for us to have a sample from that year. It was decided that whoever
labeled the skull must have written down the wrong number, which was not helpful
to us.
Jennifer borrowed several pathology books from Dr. Havill and we looked
through them, trying to find a condition that could potentially explain what we were
observing. We were very curious at this point, and it had become a puzzle. In
Paleopathology, one of the things we learned was how to do a differential diagnosis.
A differential diagnosis is where you find several conditions that could explain the
observed pathology and then narrow it down by looking at all the symptoms that go
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with each condition. My first thoughts from just looking at the pathology were
tuberculosis, syphilis, some kind of tumor, or osteomyelitis.
I spent several lunch breaks poring over the pathology textbooks trying to
get a good idea of the manifestation of the different conditions. I used The
Cambridge Encyclopedia of Human Paleopathology and The Identification of of
Pathological Conditions in Human Skeletal Remains. The pathology of tuberculosis
includes osteomyelitis, but we ruled out tuberculosis because of the lack of large
holes on the skull that are often characteristic of tuberculosis. Dr. Havill also does
not accept samples from animals that suffered from infectious disease because we
just put the samples in the freezer and the soft tissue could still potentially contain
the disease. However, we did not rule that out solely on that because we have no
idea what animal the sample came from. We also ruled out syphilis because the
skull lacked the caries sicca, or holes that look like wormholes on the outside of the
skull (Ortner and Putschar 1981).
We looked long and hard through pages and pages of material on tumors, but
ultimately ruled out a tumor because of the extensive spread of the porosity and the
lack of similarity we found between our skull and the photos of skulls affected by
tumors (Aufderheide and Rodriguez-Martin 1998). Ultimately, we settled on
osteomyelitis as our tentative diagnosis. However, osteomyelitis is just a general
bone infection and can encompass a variety of medical conditions. Our next step
was to take the skull to the vet on staff, Dr. Dick.
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Dr. Dick was really excited to see the skull. It was really great being in an
environment full of people who get excited about things like that like I do. At first he
questioned us about the procedure we use to process the bones. He said his first
thought was that the porosity was caused by something in the processing
procedure, but ultimately what made him think that it was not caused by that was
the fact that one eyebrow was markedly larger than the other, indicating that
something funky had been going on inside the skull. We also brought him a normal
baboon skull later on to demonstrate to him how much thicker the cranial vault in
6910 was compared to the cranial vault of a normal baboon. He agreed with us that
some form of osteomyelitis was the most likely cause for the pathology.
Dr. Dick said his best guess was a bacterial infection and that he thought it
could be caused by the bacteria Actinomycosis. Actinomycosis causes lumpy jaw in
cattle, which is large swellings in the mandible and skull. The bacteria usually
enters through a penetrating wound in the mouth. Dr. Dick said that the large area
of porosity and misshapen skull were indicators of a large abscess consistent with
that of lumpy jaw in cattle. However, he also said that we will never be able to know
for sure what was wrong with the animal because there is no soft tissue left to send
off for testing. My mystery skull was one of the coolest parts of my internship, and
the puzzle solving is exactly why I love anthropology.
One of the mindsets that I came across during my internship, and found very
interesting and relevant, is how anthropologists view themselves or describe
themselves to others. Dr. Havill said that biologists and chemists describe
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themselves as just that: biologists or chemists. However, she has found that
anthropologists do not refer to themselves merely as anthropologists, but as
biologists, chemists, statisticians, sociologists, and even psychologists as well. She,
and other anthropologists that I met, said that anthropology only describes a part of
what is really involved in the field of anthropology. The consensus seemed to be
that anthropology is a mingling of a variety of fields, and in order to be successful
you need to realize that. They study bones and civilizations, but they also have to
use statistics to write research articles. They have to have an understanding of
chemistry to know what could potentially cause harm to remains that are found or
how not to damage artifacts. Biology is obviously a necessary tool in biological
anthropology. Dr. Havill has to use sociology when working on a lot of projects
because she has to look at the whys of the results she is getting, and how different
environments and lifestyles may be affecting her results.
An example of this concept is evident in the research that Ahsan and Heather
are working on at Texas Biomed. Ahsan spent some time one afternoon showing me
his project and explaining his research, and I found it so interesting that I went
home and looked up information on the topic. The main mission of the lab is to look
at osteoarthritis and osteoporosis in the baboon model in the hopes of being able to
better understand it in humans. The directions in which this main research is
branching off inside the lab is the perfect example of how many fields anthropology
really covers. Genes are being mapped, environmental and lifestyle factors are
being examined, morphology of the bones is being examined, outside medical
conditions are being taken into account, and menopause is even being incorporated
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into the general idea of discovering better treatments and ways to prevent
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osteoporosis and osteoarthritis. And now, Ahsan and Heather are working on stem
cell research in relation to osteoarthritis and osteoporosis.
Stem cells often get a bad rap because many people automatically think of the
stem cells always in the news: the ones being grown from fetuses. However, there
are actually many kinds of stem cells that are typically found in the bone marrow of
human adults. Stem cells start out as basic cells, but as they grow they are able to
morph into different types of tissue cells that include fat, bone, muscle, cartilage, and
tendon. The cells are grown up in culture and can then be sorted by exposing them
to signals through a flow cytometer (Murphy et al 2003). Ahsan explained to me
that a flow cytometer can be programmed with a specific antibody that exists in a
type (such as bone or fat) of stem cell. The flow cytometer shoots a laser at each
cell, and will either go through the cell or bounce off of it depending on whether or
not it contains the antibody in question. The flow cytometer sorts the cells based on
which ones the laser goes through and which ones the laser bounces off of. This can
be used simply as a sorting device, but it can also be used as a way to prove that a
cell is the type of stem cell that it morphologically appears to be.
Stem cells have the potential to advance research in the field of osteoarthritis
and osteoporosis because of their healing potential. Stem cells often move to areas
of the body that are in need of healing to help speed the process along (Pittenger et
al 1999). It has been hypothesized that stem cells exist in joints affected by
osteoarthritis because they are drawn there by the destruction of the bone.
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Pittenger et al believes that differentiated stem cells have the ability to be
cultured, grown, and used in therapeutic approaches for the restoration of damaged
or diseased tissue (Pittenger et al 2003). If this can be proven successful, it could be
a huge advance for the treatment of people suffering from osteoarthritis. Stem cells
could potentially be used to treat joints that have already been damaged by the
disease. Jorgensen et al agrees and has shown that damaged cartilage can be
regenerated. This could lead the way for the regeneration of much larger areas of
damaged cartilage, but Jorgensen et al caution that the complete healing of damaged
areas is still a long way away (Jorgensen et al 2001). It is not an impossible task, but
will require much further research.
If Ahsan and Heather are able to grow stem cells, this adds another avenue to
the Osteolab’s approach to the osteoarthritis and osteoporosis problem.
Anthropology is about the integration of multiple fields in order to see the big
picture of what is being examined. Before I started this internship, I would never
have thought that stem cell research could be tied into anthropology. My talk with
Ahsan completely opened up my view on the uses of anthropology in a way that I
never expected, and biomedical research has taken on an even more important role
in my eyes.
One of the many things that I love about this internship was the learning
potential. Not only did I learn a lot about osteology, paleopathology, and
osteoarthritis, but I learned about the many uses of the botulism toxin, how stem
cell research pertains to an anthropological outlook on osteoarthritis, never to
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consolidate my student loans, and many, many other things. I got to actually do a
differential diagnosis. I learned how a lab runs, and the many facets that go into
keeping it running smoothly. Time management, precise scheduling, and being on
time are important aspects in a lab where numerous projects are being
simultaneously run.
If you are considering an internship at Texas Biomed, I highly encourage it.
However, I strongly recommend that you have a good grasp of lab techniques
(biology and chemistry), as well as a foundation in osteology. One of the most
important parts of the internship is also the ability to show up on time and be there
when you say you are going to be there. Some projects are time sensitive or there
could be people waiting on you to start working or go somewhere. The one problem
I had was silly really, but it was with the gloves. I had never had a problem with
latex before, but after wearing the gloves so frequently and for so long, I began to
develop rashes and bumps on my hands. Apparently it is common to develop an
allergy to latex if you are in frequent contact with it, and you can just use non-latex
gloves if that occurs. Just watch out for that, because allergies can worsen with
prolonged exposure. You also need to have a strong stomach because you will
observe some graphic things since you are dealing with remains containing soft
tissue and may be observing necropsies.
I realized that you never stop learning, even once you are in the real world
with a real job, and Texas Biomed offers many opportunities to continue learning. I
was able to attend several talks on research projects going on in other parts of Texas
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Biomed and found out that they offer those talks to employees regularly, along with
a question and answer session afterwards. The room was always full when I went
to these talks, with researchers from all parts of Texas Biomed, which demonstrated
to me how passionate many of these people are about biomedical research in
general and that they do not only care about their own research. They want all of
the research to succeed and proceed at Texas Biomed.
I always came across Jennifer or Ahsan or another person in the Osteolab
looking up research articles pertaining to a project or a procedure so that they could
learn more about a topic or try to find a better way to tweak a procedure. They
recognize that science is always changing. I was given the opportunity to always ask
questions, and if they did not have the answers they were more than happy to help
me look up research. This is a great internship because I got so much great advice
from everyone. They didn’t just teach me about the projects in the lab, but they gave
me meaningful advice on job searches, resume creation, how to pay back student
loans, and how to get the most out of my education. That will really help me in my
endeavor for my Master’s and Ph.D in forensic anthropology, which is my next step
in my education and career goals. This internship really brought home what my
anthropology professors are always trying to nail home: anthropology is a multidisciplinary subject and requires constant learning and a good camaraderie with
others in the field in order to be successful.
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Internship Report
REFERENCES
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Aufderheide AC and Rodriguez-Martin, C. 1998. The Cambridge encyclopedia of
human paleopathology. Cambridge University Press.
Jorgensen C, Noel D, Apparailly F, Sany J. 2001. Stem cells for repair of cartilage and
bone: the next challenge in osteoarthritis and rheumatoid arthritis. Ann Rheum Dis
60:305-309.
Murphy JM, Fink DJ, Hunziker EB, Barry FP. 2003. Stem cell therapy in a caprine
model of osteoarthritis. Arthritis Rheum 48:3464-3474.
Ortner DJ, Putschar WG. 1981. Identification of pathological conditions in human
skeletal remains. Smithsonian Institution Press.
Pittenger MF et al. 1999. Multilineage potential of adult human mesenchymal stem
cells. Science 284:143-147.