Wow, I did not think that I would enjoy myself in May Project as much as I currently am, and I am actually feeling pretty sad that I am leaving, so I might volunteer a few more hours before I start work this summer. The employees that work here have such a genuine love for what they do here, and I have a hilarious time conversing with them about the actions and mannerisms of various residents and helping them engage with and organize activities for some of the most elderly and impaired residents; on a similar note, my fellow volunteers and I have bonded so well in our work and our long lunch breaks, and I feel like I have made some friends (within mere weeks!) from other schools, Vianney and Ursuline, and gotten to know one of our own classmates, Corrine Condie, so much better, and I am always excited to talk about and participate in events with these people. The level at which several of the elderly folks here function has also frequently surprised and impressed me, as I have consistently had conversations with residents in their nineties and above, who remain sharp and thoughtful, even as their bodies degrade at a much higher rate than their minds, which, admittedly, is depressing to see, but also interesting and truly real and genuine to experience. For example, while many of the elderly have a natural tendency to become more self-focused and really selfish as their minds decline and they become less cognizant of the needs of those around them, so many of them when asked what how the facility could be improved (I surveyed residents the other day), would complain about the quality or number of staff or the quality or variety of food, there are a small number of more humble and keen and grounded residents who would reply something as enlightened as "It would be difficult for me to say how this facility could be improved, and whether it meets my standards for success. The only way for them to be able to improve is for them to look at themselves and determine whether they meet their own standards for success," or something like that. The ninety-eight year old man said it in much better terms though, in my opinion, and I left our meeting genuinely wishing for this man to be my teacher! I appreciate my experience so far here, and I feel that I will miss this place much more than I was expecting to when I leave (similar to JBS), as some of the people here are so inspiring and interesting and energized that I am truly excited to go to work and just talk and be there for so many interesting people, and get complimented a lot by old ladies, which always helps, but honestly, within just two weeks, I have gotten into a flow and rhythm, and I have spoken to several residents and made friends with some of my favorite residents, and worked in almost every part of the building--maintenance, nursing, activities--and I will miss it all.
- ya boy Zach S
Thursday, May 19, 2016
I love bugs!
I have been doing some more literature review about my subject recently, since I need to learn as much as I can about how different cells, specifically cancer cells, progress through the cell cycle. Many of the articles I read through are very mathematical--many researchers seem to be interested in applying mathematical models to cell proliferation and other aspects in biology (such as the way organisms move in media). These math-heavy articles are not useful for my task now, but I find them very interesting, since they use partial derivatives and a variety of probability distributions to model life. I think probability theory and applied math research are intriguing, although I don't have any research experience in those areas...possible college research topics?
Next week, I will be giving a presentation on what I have learned about other computer simulations of cells that have been done. This is important to know so that we are not reinventing the wheel by doing something that someone else has already done. The most relevant article I have encountered was published in 1990, so the programming language mentioned is outdated (Cellsim). The more recent articles do not explain the programming process as well, and many use very high-level programming languages specific to scientific statistical modeling, which is not helpful since I am working with Java. They also tend to not include examples of their code, so it is difficult for me to figure out how exactly they were able to implement their steps.
As for my program, I am trying to hurdle the obstacle of programming cell proliferation correctly. Currently, my program can only track the mitotic divisions of the original cells, and not the daughter cells. Since the daughter cells have a different start time from the original cells, I would need a separate time counter for each generation of cells, which I haven't figured out how to do yet. When I talked to my mentor, he said that each cell should be an index in an array. Originally, I just had an input and output--no arrays.
UPDATE: I recently met with my mentor, Dr. Shoghi, and he clarified the goal of this computer simulation: to determine the kinetic parameters (such as cycle/phase durations, proportion of cells in each phase initially) under which there is a correlation between number of total cells and number of cells in the Synthesis phase. The S phase is significant because this is when the cell duplicates its DNA to pass on to daughter cells. By decreasing the number of cells in S phase, the growth of cancerous tumors can be slowed, since the genetic material will not be able to be passed on. Another goal of the simulation is to determine when there is a correlation between the total cell number and the number of cells that are not in G0 phase (in other words, are in the growth stages). I will try to do this if I have time; I am currently still working on the first goal. As for the visual representation mentioned in my first post, I won't have the time to accomplish that within the May Project time frame.
Today, I basically scrapped my previous programming and rewrote it. Before, I was assuming that all cells started out in the same condition: in G1 phase. However, after reading more articles, I realized that one of the program inputs should be the number of cells in each phase at the beginning of the simulation. Thus, I had to account for the fact that not all cells will be the same at the start. As of now, my program is not working as it should be, but I'll keep working on it. I probably have something wrong in the many nested loops that I have. (I love bugs!) Once I can get the program to spit out the right numbers, I will graph them using Excel. Hopefully, I can get to that and obtain some findings that I can present.
Another issue that I have come across is the statistical knowledge that comes with programming this. I am not sure how to program certain probability distributions mentioned in various articles, such as the Gaussian distribution, so I am currently just assuming that all cells spend the same amount of time in each phase (which is not accurate, since there is a distribution of times).
At times, it is frustrating trying to program, since I feel that I am not adept enough at programming to accomplish these tasks. Many times, I have to look up methods and classes in Java just to see what I have to work with. I have also been trying to learn algorithms, though learning the relevant ones that I can apply to my work now seems to be impractical. Sometimes, when I don't know what I'm doing, I try to write out each of my steps in my notebook and then resume my attempts at translating them into code.
Working at my desk can be very tedious at times. I share my office space with a very nice man named Tim, who also works with Dr. Shoghi. He is currently working on building a device that can manipulate the growing conditions of a small area (e.g. pH, cell density) that cells can be grown in and studied in their 3D forms under the microscope. (I hope I explained that correctly.)
Also, here is a picture of a piece of Cellsim code from one of the papers I read. I am not sure how the TRAP (trapezoid) function is used for the distribution of the times in each cell cycle phase. Another article I read contains FORTRAN code, which is pretty outdated. But I am using some of their program ideas to help with mine.
Also, here is a picture of the general overview of the simulation. My mentor wrote this. This board is right across from my desk, so whenever I feel confused, I just swivel around and look at it.
Next week, I will be giving a presentation on what I have learned about other computer simulations of cells that have been done. This is important to know so that we are not reinventing the wheel by doing something that someone else has already done. The most relevant article I have encountered was published in 1990, so the programming language mentioned is outdated (Cellsim). The more recent articles do not explain the programming process as well, and many use very high-level programming languages specific to scientific statistical modeling, which is not helpful since I am working with Java. They also tend to not include examples of their code, so it is difficult for me to figure out how exactly they were able to implement their steps.
As for my program, I am trying to hurdle the obstacle of programming cell proliferation correctly. Currently, my program can only track the mitotic divisions of the original cells, and not the daughter cells. Since the daughter cells have a different start time from the original cells, I would need a separate time counter for each generation of cells, which I haven't figured out how to do yet. When I talked to my mentor, he said that each cell should be an index in an array. Originally, I just had an input and output--no arrays.
UPDATE: I recently met with my mentor, Dr. Shoghi, and he clarified the goal of this computer simulation: to determine the kinetic parameters (such as cycle/phase durations, proportion of cells in each phase initially) under which there is a correlation between number of total cells and number of cells in the Synthesis phase. The S phase is significant because this is when the cell duplicates its DNA to pass on to daughter cells. By decreasing the number of cells in S phase, the growth of cancerous tumors can be slowed, since the genetic material will not be able to be passed on. Another goal of the simulation is to determine when there is a correlation between the total cell number and the number of cells that are not in G0 phase (in other words, are in the growth stages). I will try to do this if I have time; I am currently still working on the first goal. As for the visual representation mentioned in my first post, I won't have the time to accomplish that within the May Project time frame.
Today, I basically scrapped my previous programming and rewrote it. Before, I was assuming that all cells started out in the same condition: in G1 phase. However, after reading more articles, I realized that one of the program inputs should be the number of cells in each phase at the beginning of the simulation. Thus, I had to account for the fact that not all cells will be the same at the start. As of now, my program is not working as it should be, but I'll keep working on it. I probably have something wrong in the many nested loops that I have. (I love bugs!) Once I can get the program to spit out the right numbers, I will graph them using Excel. Hopefully, I can get to that and obtain some findings that I can present.
Another issue that I have come across is the statistical knowledge that comes with programming this. I am not sure how to program certain probability distributions mentioned in various articles, such as the Gaussian distribution, so I am currently just assuming that all cells spend the same amount of time in each phase (which is not accurate, since there is a distribution of times).
At times, it is frustrating trying to program, since I feel that I am not adept enough at programming to accomplish these tasks. Many times, I have to look up methods and classes in Java just to see what I have to work with. I have also been trying to learn algorithms, though learning the relevant ones that I can apply to my work now seems to be impractical. Sometimes, when I don't know what I'm doing, I try to write out each of my steps in my notebook and then resume my attempts at translating them into code.
Working at my desk can be very tedious at times. I share my office space with a very nice man named Tim, who also works with Dr. Shoghi. He is currently working on building a device that can manipulate the growing conditions of a small area (e.g. pH, cell density) that cells can be grown in and studied in their 3D forms under the microscope. (I hope I explained that correctly.)
Also, here is a picture of a piece of Cellsim code from one of the papers I read. I am not sure how the TRAP (trapezoid) function is used for the distribution of the times in each cell cycle phase. Another article I read contains FORTRAN code, which is pretty outdated. But I am using some of their program ideas to help with mine.
Also, here is a picture of the general overview of the simulation. My mentor wrote this. This board is right across from my desk, so whenever I feel confused, I just swivel around and look at it.
Tuesday, May 17, 2016
First Week
My first week has been great.
I have learned the protocols for what I need to do to successfully determine if the organoids are growing properly. The organoids are stored in a huge freezer because they are cryogenically frozen in a gel that is a clear liquid at room temperature (this is super important). It is so cold that it has a little sign on the side of the door that says that you should not touch anything inside with unprotected hands. The shelf and containers used to keep the freezer organized is always covered in a layer of snow. I have to pull out a heavy metal container and hold it as close to the freezer as possible to prevent the contents from melting. After removing the appropriate box, I then quickly run over to the sectioning machine. The holding chamber is kept at -16 degrees Celsius. There are many different types of organoids. For example, some are electrocuted with a certain voltage a certain number of times. Each little cube also has organoids of a certain age. Some harvested from the culture at 28 days others are only harvested after 200 days or more (they are frozen after they are harvested).
First, I have to section the organoids into fine slices. This allows me to look at a very small layer of tissue. The holding chamber contains an apparatus that allows me to cut up to 1 micrometer slices. For the purposes of the experiment, I only need to slice with a width of 20 microns (micrometers). That is about as thick or even thinner than half the thickness of a piece of tissue. I turn a crank to move the block along the edge of a really fine blade (I have been told multiple times not to let my hands near it). The consistency of the block is about as think as slicing through butter. After I make a slice, I then transfer it onto a slide that has been kept at room temperature and is labeled appropriately. You may be asking how I transfer it over without tearing the sample. Remember I said that "they are cryogenically frozen in a gel that is a clear liquid at room temperature" was super important? That's right! We flip over the slide and hover it near the sample. The sample will catch onto the slide and melt right on (literally the coolest thing ever :) ). The gel is clear and dries because it is so thin. The dried gel traps the organoid slice onto the slide but allows for fluids and particles to act on the tissue. I then store the slides in the fridge overnight. After intense sectioning this Monday and Tuesday, I can finish one block in 45 minutes. This includes the time for cleaning the chamber, mounting the block onto a chuck, aligning the block against the blade so that the slices are even, slicing the blocks and mounting the slices onto the slides (10-12 per block). Each slide has around 4-8 samples. In total, for one block, I make at a minimum 40 slices. Usually, it is around 72 slices, though. I finished all of the sectionings that I can do with the organoids that they have today so I won't be sectioning anymore.
The next part is antibody staining. Although I understand it theoretically, I've only seen my supervisor perform it once so I don't know the specific protocol in-side-out. There are six different stains that they use. Off the top of my head (the lab notebook can't leave the lab so I don't have my notes in front of me), five are used to show that the cells are undergoing mitosis (division) and one is used to show that cells are differentiating. This proves that the cells are growing, dividing, and differentiating. The type of antibody stain is labeled after the protein that the first antibody (FA) attaches to. The FA is programmed to see a specific protein as a threat and attaches to it. In a normal immune system, once the antibody is attached to the substance, it would trigger more antibodies to bind and also signal a macrophage to come and eat itself along with the foreign object. Obviously, there are no macrophages so the FA is just stuck onto the protein. The goal of antibody staining is to attach a fluorescent protein onto cells with a specific protein available in the cell. The second antibody (SA) is the one that has the fluorescent protein attached. The SA sees the FA and deems that protein as a foreign object. Therefore, just like the antibodies in your body, it attaches to the FA. While this process can identify if a process in the cell is occurring, it can only produce qualitative data, not quantitative (what is more respected in the scientific community). I will be showing my supervisor the process so that she can check and make sure I am not missing anything.
I have learned the protocols for what I need to do to successfully determine if the organoids are growing properly. The organoids are stored in a huge freezer because they are cryogenically frozen in a gel that is a clear liquid at room temperature (this is super important). It is so cold that it has a little sign on the side of the door that says that you should not touch anything inside with unprotected hands. The shelf and containers used to keep the freezer organized is always covered in a layer of snow. I have to pull out a heavy metal container and hold it as close to the freezer as possible to prevent the contents from melting. After removing the appropriate box, I then quickly run over to the sectioning machine. The holding chamber is kept at -16 degrees Celsius. There are many different types of organoids. For example, some are electrocuted with a certain voltage a certain number of times. Each little cube also has organoids of a certain age. Some harvested from the culture at 28 days others are only harvested after 200 days or more (they are frozen after they are harvested).
First, I have to section the organoids into fine slices. This allows me to look at a very small layer of tissue. The holding chamber contains an apparatus that allows me to cut up to 1 micrometer slices. For the purposes of the experiment, I only need to slice with a width of 20 microns (micrometers). That is about as thick or even thinner than half the thickness of a piece of tissue. I turn a crank to move the block along the edge of a really fine blade (I have been told multiple times not to let my hands near it). The consistency of the block is about as think as slicing through butter. After I make a slice, I then transfer it onto a slide that has been kept at room temperature and is labeled appropriately. You may be asking how I transfer it over without tearing the sample. Remember I said that "they are cryogenically frozen in a gel that is a clear liquid at room temperature" was super important? That's right! We flip over the slide and hover it near the sample. The sample will catch onto the slide and melt right on (literally the coolest thing ever :) ). The gel is clear and dries because it is so thin. The dried gel traps the organoid slice onto the slide but allows for fluids and particles to act on the tissue. I then store the slides in the fridge overnight. After intense sectioning this Monday and Tuesday, I can finish one block in 45 minutes. This includes the time for cleaning the chamber, mounting the block onto a chuck, aligning the block against the blade so that the slices are even, slicing the blocks and mounting the slices onto the slides (10-12 per block). Each slide has around 4-8 samples. In total, for one block, I make at a minimum 40 slices. Usually, it is around 72 slices, though. I finished all of the sectionings that I can do with the organoids that they have today so I won't be sectioning anymore.
The next part is antibody staining. Although I understand it theoretically, I've only seen my supervisor perform it once so I don't know the specific protocol in-side-out. There are six different stains that they use. Off the top of my head (the lab notebook can't leave the lab so I don't have my notes in front of me), five are used to show that the cells are undergoing mitosis (division) and one is used to show that cells are differentiating. This proves that the cells are growing, dividing, and differentiating. The type of antibody stain is labeled after the protein that the first antibody (FA) attaches to. The FA is programmed to see a specific protein as a threat and attaches to it. In a normal immune system, once the antibody is attached to the substance, it would trigger more antibodies to bind and also signal a macrophage to come and eat itself along with the foreign object. Obviously, there are no macrophages so the FA is just stuck onto the protein. The goal of antibody staining is to attach a fluorescent protein onto cells with a specific protein available in the cell. The second antibody (SA) is the one that has the fluorescent protein attached. The SA sees the FA and deems that protein as a foreign object. Therefore, just like the antibodies in your body, it attaches to the FA. While this process can identify if a process in the cell is occurring, it can only produce qualitative data, not quantitative (what is more respected in the scientific community). I will be showing my supervisor the process so that she can check and make sure I am not missing anything.
Friday, May 13, 2016
Pope Francis Slay
For my May Project, I am working downtown at the Mayor’s
Office in City Hall with Erin and Adam. We’re working under Mary Ellen Ponder,
the Mayor’s Chief of Staff, and Nahuel Fefer, an Administrative Assistant to
the Mayor. I started work on Monday, and my first task was to look into the
Ready by 21 Program in St. Louis, which focuses on training community leaders
to help children prepare for college, work, and life by providing support in
education, healthcare, transportation, housing, mentorship, and finances. Ready
by 21 provides a holistic solution to these issues by emphasizing cross-sector
involvement among businesses, the government, nonprofits, and educational
institutions over single issue-focused solutions. Overall, this initiative seems
really interesting and promising and is certainly a worthwhile cause given that
(according to this program) only 2 out of 5 youth in the nation are
well-equipped for college, work, and life.
Nahuel also had me look into the recent lawsuit filed by St.
Louis Public Schools, which was also a really intriguing read. SLPS and the
NAACP, among other organizations, are suing the State of Missouri and the
Missouri Board of Education, claiming that since 2006, $42 million in sales
taxes that should have gone to SLPS were directed instead to charter schools in
the area. The current lawsuit stems from a lawsuit about segregation in St.
Louis public schools filed in 1972 by a number of parents, which led to a 1999
agreement on a 2/3 cent sales tax intended to fund desegregation in education.
Everything was going smoothly until the funding formula of money raised by this
tax was changed in 2006, diverting a significant portion of the money to
charter schools and away from SLPS. Now SLPS wants that money back, but
unfortunately, finding a spare $42 million will be pretty much impossible for
the charter schools and could bankrupt them, eliminating the choice in public education
that many families take advantage of. No matter what happens, it seems to me
like unless more funding is acquired for all public schools in the area, kids
are kind of being screwed over.
We also went to the World Trade Center in Clayton on Monday and
began a project involving Sister Cities, which we’ve been working on for the
bulk of this week. Essentially, we’ve been researching how other sister city
partnerships have utilized their traditionally historical and cultural ties for
increased economic development. Citing previous examples that have worked, we
are going to propose how St. Louis can use some of these same strategies with
their 15 sister cities in a presentation at the end of our May Project. We
spend our time in the windowless Youth Jobs office at the very back of the
Mayor’s Office and work from 9-5 every day. The commute is pretty rough, but we
get validated parking!
On Tuesday I sat in on a gathering with 30 visitors from
Russia that came to the United States to help foster better Russian/American
relations post-Cold War. Mayor Slay welcomed them to our city and Nahuel
detailed more specifically much of St. Louis’s history and the plans the
Mayor’s office has for St. Louis’s future. It was pretty interesting to hear
from both of them, and the Russians had very thought-provoking questions for
Nahuel as well.
Today we sat in on the Aldermanic Full Board Meeting. Erin’s
Alderwoman, Lyda Krewson, invited us in as her guests, so we were able to sit
in on the ground floor as opposed to the balcony covered in caution tape (?).
We were invited to speak with the President of the Board of Aldermen next
Friday as well about the legislative process, which will hopefully be exciting,
or at the very least will get us out of the dreary office we are confined to.
The primary issue discussed during the meeting was a bill proposed by
Alderwoman Krewson, among others. The bill involves creating a database for the
city of St. Louis to keep a comprehensive electronic record of drug
prescriptions to prevent the abuse of prescriptions and opiate overdosing.
Every state other than Missouri (along with DC and Puerto Rico) has a similar
monitoring database already in place, but unfortunately, each time this bill is
brought up on the state level in Missouri, it is blocked, so they’ve had to
resort to passing this legislature on a local level first.
May Project is going well overall, but it kind of seems like
Nahuel is running out of tasks to assign us, so we spend much of the day
pondering the passing of time. If you crane your neck into the hall, you can catch
a glimpse of the outdoors/a reminder that there is a world outside of this
12x15 foot room.
Thursday, May 12, 2016
Working with Seniors - Intro (Part 1 of 3)
I took down my previous journal entry from last night, because I was kind of in a bad mood when I wrote it and my work today was a lot more fun than it had been earlier in the week. I work at a senior and assisted living facility in Webster, called Bethesda Dilworth, where I fulfill a variety of tasks given by my instructor, Darla. During the first few days, she had me work mostly in maintenance, so I spent most of my time cleaning chairs, which I was very good at, as I took a lot of time and care to ensure that my job was done well, however, it was not entertaining or meaningful, so I kind of grew bored of it. Today, I delivered mail to the residents on all six floors of the building, which was a lot more rewarding, and put me outside of my comfort zone a little bit; I enjoyed the smiles that I would get from random residents, but I'm not a huge people person, so knocking on doors and announcing myself was unfamiliar and kind of awkward at first, especially when I accidentally walked in on someone bathing (!), though I am very quiet when approaching new people, so this fortunately went unnoticed. I have also proctored Bingo several times, and I did this again today before I left, which is actually very fun, because the employees who organize activities tell me that I'm very good at it, as I can talk loudly and enunciate clearly so that all of the residents can understand me. The most fun part of my day was speaking to a few of the seniors one-on-one, asking them questions about their lives and talking about mine, which I find very satisfying most of the time; however, it is always a bit sad to see that some of the residents have declined to such a point that it is difficult to communicate with them, not usually as a result of alzheimer's, but often because their sight and hearing has withered to the point where they cannot easily make out what I am saying without me yelling and they certainly so not pick up on subtle aspects of conversation, so one always has to be completely frank with them. Overall, I am enjoying my experience so far, though I am very excited and ready for graduation and college next year, which is a frequent topic of conversation with the residents as well as with my coworkers, many of whom I have quickly befriended, as they appreciate my willingness to volunteer, and I genuinely appreciate the impressive level of enthusiasm that they bring to work each day. Not going to lie, I sometimes feel burnt out and tired, as working in a new environment can be kind of draining, especially with track and my very physically involved occupation on the weekends, but today was a good day, and overall very enjoyable, and so I hope that I will recover soon from my self-induced exhaustion, and I am hopeful that the rest of my work will be just as fulfilling as today.
- Zach
- Zach
Tuesday, May 10, 2016
First Day
The first day was interesting and informative. I am working at a WashU lab in the Medical Campus. It is on Euclid Ave near Barnes Jewish hospital South building and Eric P. Neumann Education center. The lab PI is Dr. Corbo who specializes in neuronal research. His assistant is Connie. They both were very welcoming and showed me the ropes today. I even got a Washington University badge....woohoo! The lab also has a couple of MD, Ph.D. students. The campus is huge and I am getting my daily exercise walking from the parking lot to the lab.
I spent the day learning about what they have been doing in the lab since January. Today's entry will be about the lab in general and what I read today. In the beginning, it took me 30 minutes to get through 5 sentences and I was just reading the Abstract! As I spent more time reading the articles, I was able to better understand the project. Dr. Corbo has given me a lot of good articles to read. This should help me understand the basic science behind my project in his lab.
Humans don't want to conduct experiments on other human beings without testing first on cell culture and animal models. However, brain development studies are hitting a wall currently with using mice and other animals as models for the nervous system. Human brains are not fully represented by animal brains. Recently three separate groups of scientists have found a way to use pluripotent stem cells to create a cerebral organoid.
Pluripotent cells have been a huge breakthrough for many scientists interested in various fields. A term that you may be more familiar to is stem cells. While stem cells are actually taken from a fetus, pluripotent stem cells (the official name) are, most of the time, altered skin cells that have reverted back to a stem cell-like state. Scientists have then been able to change the pluripotent stem cell (abbreviated in scientific literature as PSC) into any cell in the body with the right chemical concoction added to the medium in which the PSC reside. The concoction is determined by trial and error.
There are a couple of problems the three groups had to address. First, this process has never been done before with the goal to create neuronal cells. Each group had a slightly different way of attacking the issue. Second, when the process worked, the cells obtained were not good enough to actually do any scientific work on. This was fixed by using a scaffolding material. The most successful choice was Matrigel. Matrigel is a hydrogel that contains extracellular proteins. The proteins act as an anchor to allow cells to grow and spread out more. Third, the normal method of creating these cells only created a flat sheet of tissue. While that is a little interesting, it's not very useful for the scientists who want to study a three-dimensional organ. So, they "agitate" the solution. That basically means that they gently and continuously swirl the solution of cells around. This creates a 3-D shape resembling a sphere (really just looks more like a blob). What's even more cool is the fact that cells on the inside are starting to die and leave cavities. That sentence sounds weird because scientists want live cells. Brain actually has cavities called ventricles that are extremely important to the structure and function of the brain. So, noticing that the core cells are dying is a really good sign that the process is working to create a clump of tissue that is acting like a brain that is developing. Another cool thing is that if the cells are stained with using antibody stains (use one antibody to tag a specific protein found on a specific cell and use another antibody with a fluorescent protein attached to tag the first antibody) scientists can see that the cells have also started to differentiate and even form layers that approximately look like the forebrain, midbrain, and hindbrain along with the meninges and many other structures.
The lab could not get either of the three procedures to work as well as they were hoping. They combined the three ways of producing the cerebral organoids and created a new protocol. From what I understand, my job is to slice these organoids like a loaf of bread with the width of each slide ranging from 4 to 10 microns. I then use antibody staining to see if the cells have aged, developed, and/or differentiated at all.
If I get positive results, the lab will start doing their actual experiment. I will write more about the experiment on another day.
I spent the day learning about what they have been doing in the lab since January. Today's entry will be about the lab in general and what I read today. In the beginning, it took me 30 minutes to get through 5 sentences and I was just reading the Abstract! As I spent more time reading the articles, I was able to better understand the project. Dr. Corbo has given me a lot of good articles to read. This should help me understand the basic science behind my project in his lab.
Humans don't want to conduct experiments on other human beings without testing first on cell culture and animal models. However, brain development studies are hitting a wall currently with using mice and other animals as models for the nervous system. Human brains are not fully represented by animal brains. Recently three separate groups of scientists have found a way to use pluripotent stem cells to create a cerebral organoid.
Pluripotent cells have been a huge breakthrough for many scientists interested in various fields. A term that you may be more familiar to is stem cells. While stem cells are actually taken from a fetus, pluripotent stem cells (the official name) are, most of the time, altered skin cells that have reverted back to a stem cell-like state. Scientists have then been able to change the pluripotent stem cell (abbreviated in scientific literature as PSC) into any cell in the body with the right chemical concoction added to the medium in which the PSC reside. The concoction is determined by trial and error.
There are a couple of problems the three groups had to address. First, this process has never been done before with the goal to create neuronal cells. Each group had a slightly different way of attacking the issue. Second, when the process worked, the cells obtained were not good enough to actually do any scientific work on. This was fixed by using a scaffolding material. The most successful choice was Matrigel. Matrigel is a hydrogel that contains extracellular proteins. The proteins act as an anchor to allow cells to grow and spread out more. Third, the normal method of creating these cells only created a flat sheet of tissue. While that is a little interesting, it's not very useful for the scientists who want to study a three-dimensional organ. So, they "agitate" the solution. That basically means that they gently and continuously swirl the solution of cells around. This creates a 3-D shape resembling a sphere (really just looks more like a blob). What's even more cool is the fact that cells on the inside are starting to die and leave cavities. That sentence sounds weird because scientists want live cells. Brain actually has cavities called ventricles that are extremely important to the structure and function of the brain. So, noticing that the core cells are dying is a really good sign that the process is working to create a clump of tissue that is acting like a brain that is developing. Another cool thing is that if the cells are stained with using antibody stains (use one antibody to tag a specific protein found on a specific cell and use another antibody with a fluorescent protein attached to tag the first antibody) scientists can see that the cells have also started to differentiate and even form layers that approximately look like the forebrain, midbrain, and hindbrain along with the meninges and many other structures.
The lab could not get either of the three procedures to work as well as they were hoping. They combined the three ways of producing the cerebral organoids and created a new protocol. From what I understand, my job is to slice these organoids like a loaf of bread with the width of each slide ranging from 4 to 10 microns. I then use antibody staining to see if the cells have aged, developed, and/or differentiated at all.
If I get positive results, the lab will start doing their actual experiment. I will write more about the experiment on another day.
Friday, May 6, 2016
First Couple of Days
My first couple of days at May Project have been fruitful!
I am working in the Clinical Research Science Building at the Wash U Medical School. (I get my own desk!) I am programming in Java to model cancerous cell growth and proliferation. So far, I have been able to simulate a single cell's progression through the cell cycle (given certain time parameters, such as time in each phase of the cycle), though there are many more nuances to cell growth that I hope to add later to my model, such as cell size, which increases at an exponential rate, according to some articles I have read.
As of now, my program outputs which phase of the cell cycle that the cell is currently in, given a time point and a start time.
Soon, I will be trying to increase the number of cells in this simulation and hopefully adding a visual representation of this model instead of having just numerical outputs. I am thinking of implementing a Monte Carlo simulation that will give the number of cells in each cell cycle phase (G1, S, G2, or M) at a given time point. I would represent this as a bar graph, though I still have to figure out how to do that in Java...
It would also be interesting if I could visually represent the spatial development of a mass of cancerous cells. It would be a cool Java applet!
I am working in the Clinical Research Science Building at the Wash U Medical School. (I get my own desk!) I am programming in Java to model cancerous cell growth and proliferation. So far, I have been able to simulate a single cell's progression through the cell cycle (given certain time parameters, such as time in each phase of the cycle), though there are many more nuances to cell growth that I hope to add later to my model, such as cell size, which increases at an exponential rate, according to some articles I have read.
As of now, my program outputs which phase of the cell cycle that the cell is currently in, given a time point and a start time.
Soon, I will be trying to increase the number of cells in this simulation and hopefully adding a visual representation of this model instead of having just numerical outputs. I am thinking of implementing a Monte Carlo simulation that will give the number of cells in each cell cycle phase (G1, S, G2, or M) at a given time point. I would represent this as a bar graph, though I still have to figure out how to do that in Java...
It would also be interesting if I could visually represent the spatial development of a mass of cancerous cells. It would be a cool Java applet!
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