Help with suggestions and ideas :P

[coolboydrummer]

Hello and thank you in advance for your help ,

I have been looking at genomic project suggestions and I am interested in comparing protein sequences or possibly mRNA in different diseases and their relations and effects on humans/eukaryotes or just to possibly find a cure or find why these sequences are related. Any project ideas related to this or any interesting project ideas in this field would be GREATLY appreciated as I am very interested in this field, and I would like to learn much more about it. If this makes completely no sense, then maybe some suggestions for interesting ideas in the field of genomics, microbiology, or biochemistry would also be appreciated

Thank You for your time,
Mason

[tdaly]

Mason,

Out of curiosity, how old are you? If you are in high school, there is a high chance that your school posseses the equipment to do what you want to do! Anyway, it looks like what you want to do is look at how protien structure is related to function. THe first thing to do is decide which diseases you want to work with. Once you have decided this, the next step is to investigate the process for determining which proteins make up the diseases you have chosen. Then investigate what the best techniques are for determining the protein conformation of these diseases. I know a person who workes in the biochem field. I will have her contact you. (It might be a while, becuase she is out of town at the moment) I also have a couple books you may be interested in. One deals with microbiology, the other on protiens. I would be more than happy to tell you wnere to find these books if you are interested.

Post Script: What school do you attend? I have serveral contacts who may be willing to mentor you with your project. Mr. DeSouza is an expert in the methods of biotechnogy, and also teaches at a local high school. If you can give me more details on your project, I will talk to him about it, and see what he thinks.

Good Luck! Let me know if I can be of any more help!

[coolboydrummer]

Hello Terik,

Im 15 and in high school, i have already completed high school bio, right now i am currently taking high school chemistry and next year i will be taking AP bio. Sigh, im an IB student, if you know what IB is, you probably pity me. My school is very old, and the totally oh-so-wonderful school board of palm beach county loves to cut the budgets of magnet schools, so I do not think my school will have the equipment but I will definitely ask when i return to school! Sadly altho thank you very much for the offer, i don't think Mr. DeSouza will be able to help me because i live in Florida and i go to atlantic high school Im assuming he is probably somewhere in California...if u know someone in my area who could mentor me, though, that would be great! I live in west palm beach, Florida.

Please tell me the books you have and other information as I am very interested in this subject, and i could possibly use them for my experiment!

As for my project, I researched T and B cells and i found that CD3 is the major protein involved with T-cell activation. Possibly i could take this information, find more information on B-cells, and then maybe compare this with some proteins or mRNA from the HIV virus, since AIDS attacks T-cells and the immune system. Maybe this could possibly show why AIDS attacks T-cells and immune system or similarities and differences in their functions? If u could please help speed me along on this topic, i know there is probably something really cool that i could do with this information, but i am currently having a brain lapse . If this information can not go anywhere then maybe u could suggest a protein for a disease that could? Im not exactly sure what i should do at this point for my experiment.

My friend's dad is a biochemist and he is currently researching a cure for AIDS...only problem is hes Hindu and he speaks VERY little english, and then the english he does speak is very hard to understand. If the person you know who is working in the biochem field could contact me that would be awesome! She could help me once i get my project started and i would like to talk to her about her career as i am very interested in it myself. She could contact me on the forums or email me at

THANK YOU VERY MUCH for the help you have given and for whatever help you will give!!!!

Mason

[coolboydrummer]

Also just wanted to say, i would definitely like to contact the person you know who is involved in biochemistry, even if she is out of town and will not be back for awhile. I am not totally pressed for time, but I need to have like the purpose, some research, hypothesis and all that good stuff in about a month and a half or so.

Any help you could donate as quickly as is convenient for you would once again be appreciated!

Mason

[tdaly]

Mason,

It was wrong of me to assume that you lived in the Bay Area. It is good to know that you are dedicated. Congratulations on being an IB student. I wanted to enroll in the IB program, but was unable to due to distance. You are priveleged. I know that your school has some of the equipment nesseacary, because some of the AP Bio labs require some of the same equipment. The HIV field is a good choice, because there is a lot being done research wise in that area at the moment. I think that the inference that there is some relationship between the structure of the T cell and the HIV virus. If you remember from bio, many scientists believe that viruses evolved from the cells they infect. You should do some more research into the function and structure of the CD3 protien, including where in the cell it is synthesized, etc. Be sure to look at all four levels of the protein structure. A possible question regarding the CD3 protein may be something like "Do HIV viruses posess a protein that denatures the CD3 protein in cells?" As you learn more, you will be able to refine your question. I think (notice the word THINK) that a good source of investigation may be to look into whether or not the HIV virus affects the CD3 protien. But first, research! I cannot empasize enough the importance of research.

Anyway, as far as equipment goes, you will most likely need a way to assay the CD3 protein. (if you decide to study it specifically) I'll ask around.

I will ask Erika Ebbel, a recent MIT graduate in biochem, to look at your ideas and give3 yoiu advice. If you want to e-mail her directly, the best thing to do is to e-mail. She porbably wont get back to you until after the 18th. Please feel free to ask her any questions.

There are two books I reccomend. I can photocopy the sections out of them and send them to you. One deals with bioplogy in general, but gives a good overview of protiens, structure and function, viruses, etc. The other book deals with the techniques of microbiology, protein synthesis, etc.

I reccomend that you formulate your questions NOW. It will make it much eaier to do research, because you can rule out the irrelevant. The sooner you define your question, the better. I think that the CD3 protien and its role in the T-cell/HIV exchange is the basis of an excellent research project.

Let me know if you need anything else. if you want the pages from the books, let me know. Do not post your address here, as anyone on Science Buddies can see it!

[coolboydrummer]

Hey,
Sorry that it took me so long to respond, I've been very busy lately. I emailed Erika Ebbel but i have not received a response. Some bad news is that I can work with the protein CD3 but that would require tons of paperwork and my chemistry teacher is not up to it. I cannot work with any protein for the HIV virus even with a professional at a research institution. Very stupid of me to even consider that the science board would let me do that.
Can I still do my project? I went on the website with the search engine for proteins but i wasnt sure how to use this information to compare CD3 with proteins from HIV virus. What exactly should I look for in the two proteins when I'm getting the information on them? I'm not completely sure what to do next. It looks like all that I will be able to do with this project is use internet resources or MAYBE work with just the CD3 protein . If anyone has any suggestions on what to do next, please help!
I would definitely like those pages, you can email me at and ill reply to you. Also, if you could please tell Erika that I would like some help in the areas of my project, it would be greatly appreciated, as I think she might have some sort of spam-filtering and she may not have received my e-mail.
If you or anyone who happens to be browsing through has any ideas or pointers on my project area, please help!! I do not want to give up this project!

Thanks a bunch!!!
Mason

[tdaly]

Mason,

The reason that Eirka has not responded to your query is that she just got back from a trip. I will make sure that she knows about your project. Is your fair ISEF affiliated? If si, the best thing to do is to talk to the director of your Fair's SRC board. It was NOT stupid of you to try your project. Do not give up!!! I can guarentee that there is someone out there who is willing to work with you. If your chem teacher wont do the paperwork for you, ask the AP bio teacher. If s/he says no, ask someone else. Get the idea? YOU CAN DO YOUR PROJECT!!! Erika will be a great resource. Your project WILL work!

About research: I will send you the pages. Read them. Then, pick up a copy of "Painless Science Fair Projects" If you go to http://www.science-fair.org, you can pick up a copy. This book is awesome. It has an awesome section on research. Then look at the "How to do a science project" section on this site. There is a section on formulating research strategies that may be helpful. Go to your library. See if they have a copy of the "McGraw-Hill Encyclopedia of Science and Technology." This is an exellent reference. Look up protiens, amino acids, CD3 proteins.

As to comparing the proteins, when you have read the material I will send you, you will have a decent idea about how protiens are built/made. You can then compare the proteins based upon four levels of protein comformation. Check out some of the Cutting Edge projects, whiuch are located on this site. They might have some good info/techniques. They might also have some good references. If you have more questions, please ask. I will send the pages shortly.