I posted a few days ago that I was going in to propose that I could help a local high school science teacher run an interactive genetics lab for her students during their upcoming genetics unit. I talked to her for several hours that day, having abandoned my original proposal of a strawberry DNA extraction for a human cheek cell DNA extraction followed by imaging of the student's samples with agarose gel electrophoresis.
This has been modified during the course of my research, and with the invaluable help of the contributors to the Diybio mailing list, which you all should most definitely join. Originally I was ignorantly going to try to run the electrophoresis on unbroken genomic DNA. What I didn't realize was that human chromosomes were entirely too long to be resolved by a gel except as a smear at the top of the gel where it gets stuck in the pores of the agarose.
Thanks to several online collaborators I've been able to figure out the specifics of the electrophoresis process (details of which are surprisingly vague online and in journal articles except for specific protocols, information which is pretty much useless except for the most basic information if you are running a different experiment), and more importantly, how to make a gel run which will have meaningful results that wont end with a smear of clumped and stuck DNA
I'll be publishing several articles here about what I've learned as soon as I get time. Right now I'm too busy doing the actual work of setting up the demo and getting organized to produce a digested record of what I've learned. In the mean time feel free to check out my threads on the Diybio mailing list (google groups) for a day to day reference and to see the process by which I got the information, and the other researchers who have helped me.
Showing posts with label plans. Show all posts
Showing posts with label plans. Show all posts
Friday, October 14, 2011
Tuesday, October 11, 2011
Onward and Upward, Challenges and Chances
Well guys, I've done a lot more research and have been talking (and asking copious questions) on the diybio mailing list(google groups). It looks like I have my work cut out for me, and I'm going to have to study a good deal, but the plans for the lab are starting to come together.
Budget wise, I'm looking at about a hundred dollars a month in financial resources. I'll post a work up on the money side in detail once more details are available to me, as I'm not sure what qualities of equipment I'm going to need, or what I'll be able to improvise. With that said, I should have a fully functioning neurobiology lab in a year on the outside. More on this later.
Right now the bulk of my time is spent catching up my knowledge of research methods to my theoretical understanding. I've decided there are a few main avenues I need to pursue in the short term.
One is general knowledge of neuroscience. My sources of information have primarily been books aimed at giving a practicing clinician background knowledge on the fine workings of the brain. This is because up until about a year ago I was planning on getting my M.D. in psychiatry and going into research from there. Now, I've obviously become absorbed in pure research. Because of this my knowledge of brain chemistry is quite advanced, but my electrophysiology and macro scale anatomy is quite lacking.
The next is a need to be able to understand complex biology protocols. I've done some basic labs in the little bit of college I've had so far but it wasn't at nearly the level that I need to be operating at.
Along with this is the need to get a grasp on the general research methods of biology and specifically those which apply to neuroscience. My focuses for right now are reading everything I can about advanced microscopy and the optics and electronic/physical principles behind them, electrical sensor arrays and the electrical engineering behind them and cell culturing and manipulation techniques such as microfluidics.
An interesting non-neuroscience development in that I am going to be proposing a diybio genetics demonstration to a high school science teacher co-worker of my mom. I heard in passing that the teacher was planning on doing a tissue collection on her students and sending it in to be sequenced and analyzed by the Human Genome Project. While this is a great and innovative idea, I thought it would also be cool for the kids to be able to tangibly see and manipulate DNA as well. To any biohacker this immediately screams a coarse strawberry DNA extraction. I've put together the materials list, protocol, and some interesting background information that can be presented during the demo in the hopes that she will at least use the material and, ideally, allow me to conduct the demo under her supervision. My meeting is set for tomorrow, and you can bet that I'll post more when I know more.
That's about it for this missive from the lab in potentia, so I'll leave you with a few more links, this time basic background and technique articles.
Principles of Microscopy, an article by a professor of cell biology and molecular genetics explaining the principles behind visible light, fluorescence, confocal, and phase contrast microscopy.
Basic Microfluidic Concepts, an article on the University of Washington faculty pages site about the basic concepts behind microfluidics, as well as some numeric analysis of those principles.
Bonus: The beginners Strawberry DNA Extraction, from the University of Utah. Not really a protocol so much as a recipe (there's even meat tenderizer!), it's a great way to show kids and your friends the wonders of science.
Budget wise, I'm looking at about a hundred dollars a month in financial resources. I'll post a work up on the money side in detail once more details are available to me, as I'm not sure what qualities of equipment I'm going to need, or what I'll be able to improvise. With that said, I should have a fully functioning neurobiology lab in a year on the outside. More on this later.
Right now the bulk of my time is spent catching up my knowledge of research methods to my theoretical understanding. I've decided there are a few main avenues I need to pursue in the short term.
One is general knowledge of neuroscience. My sources of information have primarily been books aimed at giving a practicing clinician background knowledge on the fine workings of the brain. This is because up until about a year ago I was planning on getting my M.D. in psychiatry and going into research from there. Now, I've obviously become absorbed in pure research. Because of this my knowledge of brain chemistry is quite advanced, but my electrophysiology and macro scale anatomy is quite lacking.
The next is a need to be able to understand complex biology protocols. I've done some basic labs in the little bit of college I've had so far but it wasn't at nearly the level that I need to be operating at.
Along with this is the need to get a grasp on the general research methods of biology and specifically those which apply to neuroscience. My focuses for right now are reading everything I can about advanced microscopy and the optics and electronic/physical principles behind them, electrical sensor arrays and the electrical engineering behind them and cell culturing and manipulation techniques such as microfluidics.
An interesting non-neuroscience development in that I am going to be proposing a diybio genetics demonstration to a high school science teacher co-worker of my mom. I heard in passing that the teacher was planning on doing a tissue collection on her students and sending it in to be sequenced and analyzed by the Human Genome Project. While this is a great and innovative idea, I thought it would also be cool for the kids to be able to tangibly see and manipulate DNA as well. To any biohacker this immediately screams a coarse strawberry DNA extraction. I've put together the materials list, protocol, and some interesting background information that can be presented during the demo in the hopes that she will at least use the material and, ideally, allow me to conduct the demo under her supervision. My meeting is set for tomorrow, and you can bet that I'll post more when I know more.
That's about it for this missive from the lab in potentia, so I'll leave you with a few more links, this time basic background and technique articles.
Principles of Microscopy, an article by a professor of cell biology and molecular genetics explaining the principles behind visible light, fluorescence, confocal, and phase contrast microscopy.
Basic Microfluidic Concepts, an article on the University of Washington faculty pages site about the basic concepts behind microfluidics, as well as some numeric analysis of those principles.
Bonus: The beginners Strawberry DNA Extraction, from the University of Utah. Not really a protocol so much as a recipe (there's even meat tenderizer!), it's a great way to show kids and your friends the wonders of science.
Monday, October 10, 2011
What is this? ...or... The fouding of a blog.
You may find yourself on this page wondering why in the world there is only one post. What is the purpose of this person sending text out into the internet, what do they want, what do they do? I created this blog as a way to chronicle my work on several projects I'm getting started, as well as a platform to post articles online.
And what is this work you ask? I'm into diybio and neuroscience. Really into it. I think a fun afternoon is reading about fMRI and the creation of a culture of cells of C. elegans from embryonic stem cells so that I can research how their neurons work (if you can't tell, thats been my afternoon). Furthermore, I'm so much of a mad man that I not only want to read about these procedures and wait patiently until I'm able to go back to college and work in a professional lab, I want to be able to do this in my home. Obviously I'm not going to be shelling mouse brains into tupperware or some other sort of frankenstein nightmare, I have a code of ethics and a mind for safety. But, my goal is to find a way to, while following standard ethical guidelines and safety regulations, create a lab environment in my home where I can do these sort of things.
That will probably be the first formal post on here, an article detailing my plan to make this happen. As anybody with half a brain will be able to tell, this isn't going to happen overnight and a lot of planning, preparation, leg work and experimentation is going to have to go into this. I've been thinking about this specifically for a couple of months now, and I think I've developed some good ideas as to how to make this happen.
Depending on how often I find myself itching to publish over the next few weeks, you can expect to be able to find anything from posts of links I've found interesting, thoughts and ideas I want to get on record, or background on myself and what I'm planning to do.
To start you off with some actual content instead of this meta-content I've written so far, here's some of the articles I've read in the past few days:
Circuit Neuroscience, The Road Ahead(pdf)
Neural Circuits (preview page of a book on Neuroscience on the NLM site)
Abstract of a Nature article on a novel way to use florescent attached proteins to detect voltage levels in a neuron
WormBook A novel way of culturing nematode worm neurons to facilitate their study. (I could see this being paired with the florescent work above to make an observation setup)
As well as a slew of wikipedia articles branching off of the Neuroscience category.
I don't have a large presence on the internet but you can contact me by commenting here or by emailing me at the link provided in the "About Me" section. I'm also trying to start posting to the diybio global mailing list, available on google groups or linked to by the Diybio local page.
And what is this work you ask? I'm into diybio and neuroscience. Really into it. I think a fun afternoon is reading about fMRI and the creation of a culture of cells of C. elegans from embryonic stem cells so that I can research how their neurons work (if you can't tell, thats been my afternoon). Furthermore, I'm so much of a mad man that I not only want to read about these procedures and wait patiently until I'm able to go back to college and work in a professional lab, I want to be able to do this in my home. Obviously I'm not going to be shelling mouse brains into tupperware or some other sort of frankenstein nightmare, I have a code of ethics and a mind for safety. But, my goal is to find a way to, while following standard ethical guidelines and safety regulations, create a lab environment in my home where I can do these sort of things.
That will probably be the first formal post on here, an article detailing my plan to make this happen. As anybody with half a brain will be able to tell, this isn't going to happen overnight and a lot of planning, preparation, leg work and experimentation is going to have to go into this. I've been thinking about this specifically for a couple of months now, and I think I've developed some good ideas as to how to make this happen.
Depending on how often I find myself itching to publish over the next few weeks, you can expect to be able to find anything from posts of links I've found interesting, thoughts and ideas I want to get on record, or background on myself and what I'm planning to do.
To start you off with some actual content instead of this meta-content I've written so far, here's some of the articles I've read in the past few days:
Circuit Neuroscience, The Road Ahead(pdf)
Neural Circuits (preview page of a book on Neuroscience on the NLM site)
Abstract of a Nature article on a novel way to use florescent attached proteins to detect voltage levels in a neuron
WormBook A novel way of culturing nematode worm neurons to facilitate their study. (I could see this being paired with the florescent work above to make an observation setup)
As well as a slew of wikipedia articles branching off of the Neuroscience category.
I don't have a large presence on the internet but you can contact me by commenting here or by emailing me at the link provided in the "About Me" section. I'm also trying to start posting to the diybio global mailing list, available on google groups or linked to by the Diybio local page.
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