Research for Prions

Ask questions about projects relating to: biology, biochemistry, genomics, microbiology, molecular biology, pharmacology/toxicology, zoology, human behavior, archeology, anthropology, political science, sociology, geology, environmental science, oceanography, seismology, weather, or atmosphere.

Moderators: MelissaB, kgudger, Ray Trent, Moderators

Research for Prions

Postby buzzingbee87 » Mon Sep 02, 2013 10:08 pm

Hi,

I sent a post earlier asking about prion research, but I am not sure if it went through, so I just want to repost it here.

I am a high school student in 11th Grade looking to enter the Science Fair in March 2014, and the topic that I want
to look more into is prions and their effects on the human or vertebrae brain, as well as possible
prevention options. I was wondering, do I need to do animal testing? Where can I get prions?
Do I need to use disabled prions?

Thank you!
buzzingbee87
 
Posts: 16
Joined: Mon Sep 02, 2013 9:34 pm
Occupation: Student: 11 Grade
Project Question: Hi! I am a high school student looking for assistance for my science fair research project. I want to look more into prions and their effects on the human or vertebrae brain, as well as prevention options, and I was wondering if I could have some help deciding the next step to take. Should I use animal testing? How can I get some prions? Do I need to use disabled prions? Thank you!
Project Due Date: March 2014
Project Status: I am just starting

Re: Research for Prions

Postby SciB » Tue Sep 03, 2013 6:43 pm

Hi bb87,

You have chosen a very interesting and exciting research area but one that is not going to be very easy to experiment with. If you live near a university where there is someone doing research on prions, you could approach them as a student volunteer to do a project in their lab. Prions can cause human diseases such as Kreutzfeldt-Jakob and these abnormal proteins are transmissible, so they are dangerous to work with. They have to be handled under Biosafety Level 2 conditions at a minimum and many labs use BSL3 procedures, which would be way beyond a high school’s budget. Also, the ISEF rules prohibit experiments on BSL3 agents (http://www.sciencebuddies.org/science-f ... ents.shtml).

So, if you want to pursue a study of prions, which I think you should since you are really interested in them--my suggestion would be to make your project a virtual one. This will require a fair amount of reading and searching the literature on prions to come up with a hypothesis that can be tested using available online data and software, but it is doable. Prions and their targets in humans have specific amino acid sequences and secondary structure, and there are molecular biology programs into which you can put an amino acid sequence and obtain data about the form of the protein (http://en.wikipedia.org/wiki/List_of_pr ... n_software).

I have read that there is some relation between the abnormal protein in Alzheimer’s disease, beta amyloid, and the way prions do damage to other brain proteins. Maybe you could work the two into a hypothesis and then test it by looking at structure virtually and seeing how changes in amino acid sequence might affect their interaction, folding and deposition in the brain.

Think about where you want to go with your prion project and get back with us and I will continue to help you. Good ideas can come from anyone and you may hit upon something to test that other scientists have overlooked because they all tend to think along the same lines.

Best wishes,

Scibee
SciB
Expert
 
Posts: 414
Joined: Fri Feb 01, 2013 7:00 am
Occupation: Teacher
Project Question: I wish to join Scibuddies to participate in the Ask an Expert program.
Project Due Date: n/a
Project Status: Not applicable

Re: Research for Prions

Postby buzzingbee87 » Tue Sep 03, 2013 9:44 pm

Hi SciB,

Thank you so much for your detailed and prompt reply! I am truly grateful for the project idea that
you have given me, and did not even think that I could take this project into a virtual direction,
which seems much more feasible than what I had originally thought of. I will discuss this with
my teacher tomorrow and see how I can build off of your suggestions.

I was also just curious, where have you read about the correlation between Alzheimer's disease and
prions damaging the brain proteins? That sounds like something I would definitely be
interested in further researching, and was wondering if you read this in a science journal
or other literary source, so I could start from there to begin my task.

Once again, thank you so much and I will not hesitate to contact you once I know more
about my intended project direction and if I come across any difficulties.
buzzingbee87
 
Posts: 16
Joined: Mon Sep 02, 2013 9:34 pm
Occupation: Student: 11 Grade
Project Question: Hi! I am a high school student looking for assistance for my science fair research project. I want to look more into prions and their effects on the human or vertebrae brain, as well as prevention options, and I was wondering if I could have some help deciding the next step to take. Should I use animal testing? How can I get some prions? Do I need to use disabled prions? Thank you!
Project Due Date: March 2014
Project Status: I am just starting

Re: Research for Prions

Postby SciB » Fri Sep 06, 2013 7:10 am

You are welcome! I'm happy to help get you going. I think this idea of an abnormal protein that can make humans sick and even kill them just by causing misfolding of normal proteins is a really scary thing!Scientists need to definitely do more research on them.

I looked up prions and Alzheimer's on PubMed and got over 450 papers, so there is a lot of interest in this. I have attached the review that I read where the idea of Alzheimer's being similar to prion disease is discussed [Soto et al.]. I also found a review that i had not seen published in July 2013 where the author says maybe prions CAN actually be transmitted by bacteria. After all, a prion is just a whacky protein and bacteria make all kinds of proteins.

Virtual projects can be really important to understanding science. Many times scientists are so busy with writing grants and papers, going to meetings, supervising grad students, etc. that they don't have time to look at the data that has been published and manipulate it using the molecular biology programs available free [usually] online.

The sequence of the PrP has been known for years but I have never heard of anyone suggesting that certain microbes might carry prions. There is a program called BLAST [http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome] that allows you to look for a particular sequence in a protein database of a group of organisms. That might be a place for you to start. It takes a little work to learn the software but it is worth the trouble. All scientists use these programs a lot.

I'm glad you are going to study this question and maybe you will discover something nobody else has seen. That's the exciting part of science--being the first to find out something new. Keep posting on this thread and we'll be here to steer you on your way.

Best wishes,

Scibee
Attachments
Soto et al - amyloid and prions - 2006.pdf
(166.08 KiB) Downloaded 63 times
SciB
Expert
 
Posts: 414
Joined: Fri Feb 01, 2013 7:00 am
Occupation: Teacher
Project Question: I wish to join Scibuddies to participate in the Ask an Expert program.
Project Due Date: n/a
Project Status: Not applicable

Re: Research for Prions

Postby SciB » Fri Sep 06, 2013 7:12 am

BB87,

Here's the second review. I can only attach one item at a time.

Scibee
Attachments
Manuelidis - prion review - 2013.pdf
(677.56 KiB) Downloaded 66 times
SciB
Expert
 
Posts: 414
Joined: Fri Feb 01, 2013 7:00 am
Occupation: Teacher
Project Question: I wish to join Scibuddies to participate in the Ask an Expert program.
Project Due Date: n/a
Project Status: Not applicable

Re: Research for Prions

Postby buzzingbee87 » Fri Sep 06, 2013 5:57 pm

Thank you so much once again! :)

I am looking into those links. I have worked with BLAST before but didn't realize that it can totally help out here! :D
I will also look more into PubMed to discover more scientific papers. It would be really cool to discover something
never before seen. :D

Thank you once again, and I will continue to post here if I need anything else! It looks like
I have lots to work with and get my project going. :D
buzzingbee87
 
Posts: 16
Joined: Mon Sep 02, 2013 9:34 pm
Occupation: Student: 11 Grade
Project Question: Hi! I am a high school student looking for assistance for my science fair research project. I want to look more into prions and their effects on the human or vertebrae brain, as well as prevention options, and I was wondering if I could have some help deciding the next step to take. Should I use animal testing? How can I get some prions? Do I need to use disabled prions? Thank you!
Project Due Date: March 2014
Project Status: I am just starting

Re: Research for Prions

Postby buzzingbee87 » Mon Oct 07, 2013 8:49 am

Hi,

I was looking more into the connection between prions
and Alzheimer's disease, and unfortunately there is already a plethora
of information on this topic, so I decided to slightly change my topic
to trying to change the structure of an infectious form of the prion
into the noninfectious (normal) form by using protein modeling software
and proposing several models using this software.

However, I have no idea how to use protein modeling software and
which ones are good, bad, useful for me, etc.

Is there anyway that I can find out more information about which
products are good, or even help using one? I tried Googling
but I ended up really confused on what I was finding
because there are so many and I have no experience
in computer science.

Thank you so much!
buzzingbee87
 
Posts: 16
Joined: Mon Sep 02, 2013 9:34 pm
Occupation: Student: 11 Grade
Project Question: Hi! I am a high school student looking for assistance for my science fair research project. I want to look more into prions and their effects on the human or vertebrae brain, as well as prevention options, and I was wondering if I could have some help deciding the next step to take. Should I use animal testing? How can I get some prions? Do I need to use disabled prions? Thank you!
Project Due Date: March 2014
Project Status: I am just starting

Re: Research for Prions

Postby megidi » Mon Oct 07, 2013 3:37 pm

Protein folding software is quite complex, and the more advanced systems actually require the rental of server space. There is an obscene amount of calculations that go into it. I have not looked at software, so I will try to do some digging for you and see if there is a good source. In the mean time I will shoot an e-mail off to an old professor of mine and see if he has any input.

The other thing to consider is how to adjust the structure or denature the protein. Heat, chemicals, etc can change protein shape. It may be worth looking into ways to damage the pathogenic protein while minimizing damage to the hosts proteins.
megidi
Expert
 
Posts: 24
Joined: Wed Aug 07, 2013 8:12 pm
Occupation: Student - University
Project Question: Volunteer
Project Due Date: n/a
Project Status: Not applicable

Re: Research for Prions

Postby buzzingbee87 » Mon Oct 07, 2013 5:36 pm

Thank you for your prompt reply!
I look forward to hearing from you soon.

For damaging the pathogenic protein,
can that be done virtually, or does that have to be
done manually? I do not believe that I can actually access
prions because they are at such a high biosafety hazard,
but if there is a way to do this virtually I am all for learning
how I can this.

Thank you so much for going through such lengths for me again!
buzzingbee87
 
Posts: 16
Joined: Mon Sep 02, 2013 9:34 pm
Occupation: Student: 11 Grade
Project Question: Hi! I am a high school student looking for assistance for my science fair research project. I want to look more into prions and their effects on the human or vertebrae brain, as well as prevention options, and I was wondering if I could have some help deciding the next step to take. Should I use animal testing? How can I get some prions? Do I need to use disabled prions? Thank you!
Project Due Date: March 2014
Project Status: I am just starting

Re: Research for Prions

Postby megidi » Mon Oct 07, 2013 10:25 pm

The virtual part is going to be up to you really. FInding places in the structure that are less bond dense and therefore easier to manipulate. Doing it in a practical sense would be impossible in your situation for the reason you already stated.

Here are some resources my professor wrote back with. Hope these help.

Here is a site with some references regarding treatment of pathogenic prions. http://www.ncbi.nlm.nih.gov/pubmed/24093082

Another good place to start http://www.ncbi.nlm.nih.gov/pubmed/21679685#


He also replied with the suggestion to use the program Raptor X. Here is a wikipedia link with some descriptions. I however are unfamiliar with this program, but the page gives some decent input.

May I also recommend you reach out to a local university that has a genetics program, or maybe even an infectious disease physician. There is always ongoing research going on at universities that may be related to what your doing.
megidi
Expert
 
Posts: 24
Joined: Wed Aug 07, 2013 8:12 pm
Occupation: Student - University
Project Question: Volunteer
Project Due Date: n/a
Project Status: Not applicable

Re: Research for Prions

Postby buzzingbee87 » Tue Oct 08, 2013 8:16 am

Thank you so much!

I will try working with Raptor X and see where I can go from there,
as well as try to reach out to a local university in my area to
work with a researcher regarding my project.

Thank you again, and I will post again if I need further help!
buzzingbee87
 
Posts: 16
Joined: Mon Sep 02, 2013 9:34 pm
Occupation: Student: 11 Grade
Project Question: Hi! I am a high school student looking for assistance for my science fair research project. I want to look more into prions and their effects on the human or vertebrae brain, as well as prevention options, and I was wondering if I could have some help deciding the next step to take. Should I use animal testing? How can I get some prions? Do I need to use disabled prions? Thank you!
Project Due Date: March 2014
Project Status: I am just starting

Re: Research for Prions

Postby connief » Sat Oct 12, 2013 2:58 pm

Hello there,

You've gotten lots of great advice from all the experts that have posted! I would like to offer one of my suggestions as well. I think that taking your project in a virtual direction is a great idea, considering how human prions are dangerous to work with, but if you are thinking about doing experiments with actual prions, I may suggest perhaps finding a lab that works on yeast prions. Budding yeast has been one of the most popular model organisms used to study eukaryotic cell biology, and recently, prions have been found in yeast and have been used as models to study how prions are formed. The knowledge obtained from these studies could provide important implications about how prions are formed in mammals! Also, I would think that it's probably not as dangerous to work with yeast prions than with actual mammalian prions (although I don't personally work with prions myself, so if anyone has the expertise and sees anything wrong with this comment, please correct me), and budding yeast is a a really easy organism to grow and work with. Attached to this comment is a short review article about yeast prions in case you were interested.

Let us know if you have anymore questions.

Connie
Attachments
Sherman - Yeast Prions.pdf
(124.4 KiB) Downloaded 39 times
connief
Expert
 
Posts: 173
Joined: Thu Apr 04, 2013 12:27 pm
Occupation: Graduate Student
Project Question: I am volunteering for the "Ask an Expert" program.
Project Due Date: I am volunteering for the "Ask an Expert" program.
Project Status: Not applicable

Re: Research for Prions

Postby buzzingbee87 » Sat Oct 12, 2013 3:22 pm

Hi Connie,

Thank you so much for your suggestion! I truly am
grateful for all of the great advice I have been given
on this forum, and I'm sure I would not be where I am
now, almost ready to begin my project, if it wasn't
for this forum. :D Actually, to refer back to an old suggestion,
I want to use Raptor X but I am so confused on how to use it,
so any suggestions would be very much appreciated! (I haven't
been able to find a "Raptor X for Dummies" unfortunately...)

I have never actually heard of yeast prions before, so I
think I will try to contact a local lab to see if I can get more
experience working with these organisms...they sound really cool!

Thank you again, and I will post again if I need anything else.
buzzingbee87
 
Posts: 16
Joined: Mon Sep 02, 2013 9:34 pm
Occupation: Student: 11 Grade
Project Question: Hi! I am a high school student looking for assistance for my science fair research project. I want to look more into prions and their effects on the human or vertebrae brain, as well as prevention options, and I was wondering if I could have some help deciding the next step to take. Should I use animal testing? How can I get some prions? Do I need to use disabled prions? Thank you!
Project Due Date: March 2014
Project Status: I am just starting

Re: Research for Prions

Postby buzzingbee87 » Wed Dec 25, 2013 1:46 am

Hi,

I was working on my project virtually,
but wanted some advice and where to search
for an amino acid sequence for the prion?
I have tried Googling, and so far have only
found one for mice...

Thanks for all the help I have received so far!
buzzingbee87
 
Posts: 16
Joined: Mon Sep 02, 2013 9:34 pm
Occupation: Student: 11 Grade
Project Question: Hi! I am a high school student looking for assistance for my science fair research project. I want to look more into prions and their effects on the human or vertebrae brain, as well as prevention options, and I was wondering if I could have some help deciding the next step to take. Should I use animal testing? How can I get some prions? Do I need to use disabled prions? Thank you!
Project Due Date: March 2014
Project Status: I am just starting

Re: Research for Prions

Postby JMP » Wed Dec 25, 2013 5:09 pm

Hi,

You can find sequences to any number of proteins at the NCBI protein database:
http://www.ncbi.nlm.nih.gov/protein/?term=prion
Just search for your protein of interest. Click on the link. Towards the bottom of the page on the protein, you will see an amino acid sequence. This sequence first has a number and then a bunch of letters. The letters are the amino acid sequence (we use a single letter code to represent different amino acids. If you are not already familiar with this code, it should be easy to find online).

Also, although I'm not particularly familiar with Raptor X, you can find a number of different protein structures at the RCSB PDB database: http://www.rcsb.org/pdb/results/results ... ow=Current
Oftentimes different protein modeling programs can open these files, and they often already have the protein sequence embedded in the file.

Hope this helps and good luck!
JMP
JMP
Expert
 
Posts: 114
Joined: Fri Aug 09, 2013 12:56 pm
Occupation: Postdoctoral Fellow
Project Question: Signing up to be an Expert
Project Due Date: n/a
Project Status: Not applicable

Next

Return to Grades 9-12: Life, Earth, and Social Sciences

Who is online

Users browsing this forum: No registered users and 1 guest