Finding tools for your project

[Sareena Avadhany]

Hi Experts,

I am currently working on a project that involves curcumin and how it aids in the prevention of diseases. I am just getting started on my project, and found a research scientist, Dr. Bhaya at Stanford University who is willing to help me through the scientific method at first. She works with cynobacteria, so she is now trying to find a mentor which does work that is similar to what I'm interested in.

My first assignment from Dr. Bhaya is to start researching about curcumin, and think about what equipment I would need to do my project. I haven't the slightest clue what instruments I would need, as I am just starting my research. As for now, I am a bit in the middle because I have to mentor to refer to, as Dr. Bhaya is a very busy person.

Thank you for your help.

Sincerely,
Sareena

[Sareena Avadhany]

Hi Experts,

I am currently working on a project that involves curcumin and how it aids in the prevention of diseases. I am just getting started on my project, and found a research scientist, Dr. Bhaya at Stanford University who is willing to help me through the scientific method at first. She works with cynobacteria, so she is now trying to find a mentor which does work that is similar to what I'm interested in.

My first assignment from Dr. Bhaya is to start researching about curcumin, and think about what equipment I would need to do my project. I haven't the slightest clue what instruments I would need, as I am just starting my research. As for now, I am a bit in the middle because I have no mentor to refer to, as Dr. Bhaya is a very busy person.

Thank you for your help.

Sincerely,
Sareena

[Sareena Avadhany]

Hello Experts,

Winterbreak has just started for me, and I want to take opportunity of this time to start researching my project. I had mentioned my previous concerns in the post above. Any suggestions would be really helpful.

Sareena

[deleted-71490]

Saranna:

http://www.ncbi.nlm.nih.gov/entrez/quer ... t=Citation

http://www.hort.purdue.edu/newcrop/Crops/Tumeric.html

http://www.mult-sclerosis.org/tumeric.html

These sites should get you started in devfeloping a reading list.

Matt Mulanax

[phamlinh]

Hi Sareena,

I understand how overwhelming this process can be. Like I posted elsewhere, if you want some help getting in touch with a cancer biology or immunology professor at Stanford, let me know. It sounds like a mentor closer to San Jose may be better for you.

The list of references are a good starting point, but I can understand how it's difficult to understand exactly what you need for an experiment.

Here's a suggestion for now. Take one of the papers that looks promising. Look at the first figure and try to understand what's going on. If you don't understand, don't feel discouraged! This is something scientists don't learn how to do until graduate school, much less high school. Post a link and ask for help.

In the meantime, figure out what methods were used to generate the figure. Then go to the material and methods section and read over the methods. Try to read it like a "how to" section. In all likelihood, there's not going to be enough information for you to understand exactly how one would go about doing the experiment. Post the steps as you understand them to this bulletin board, and then someone can help you fill in the gaps.

I hope this was helpful.

Best of luck,

Linh

[Sareena Avadhany]

Thank you Linh,

I am still conducting my research at the same time looking for a mentor. I've contacted an outreach program coordinator at the Carnegie, a board of director for my regional science fair and a professor at SJSU, but have had no luck so far. I'm still waiting for a reponse.

In terms of vicinity, I would prefer to have an advisor at SJSU, but it would of course be amazing to work at Stanford. Do you happen to know anyone at either of these universities who might be willing to advise me on my project?

Thank you.

Sincerely,
Sareena

[Sareena Avadhany]

Hi Experts,

Today I was researching for my topic on PubMed, and I found an article that I thought would help me. It only showed me the abstract though. I would like to get the full text, but don't know how to.

http://www.ncbi.nlm.nih.gov/entrez/quer ... med_docsum

How do you research on PubMed? I typed in something on the search bar, and the drop down list next to the search bar had so many different options...PMC, PubMed, Journals...etc.

Thanks for your help.

Sincerely,
Sareena

[carolinethorn]

Hi Sareena

Usually to get to the full text of the articles you (or your university) needs a subscription to the journal. If the logo of the journal shows up nest to the title you can click there or there is another place on the far right where it says "Links" and hit link out.
There are some journals that have free access but not the paper you are interested in.
If you find a mentor at a university they will probably let you use their subscription to get the journals.

One way to try and get around this block is to search for the professor who is the last author on the paper. Most of the abstracts on pubmed show the name of the university or hospital the research was done at. You may be able to find information about their work on their website. Or you could email them and ask for a copy of their paper.

As a separate subject -
I have worked with circumin and its effects. Unfortunately I work in a dry lab now (computers only) so cannot offer you space to work but I can talk to you about my previous experiments and some of the background you need for your research if you like. I was testing drugs and molecules that effected a gene involved in the body's response to injury or infection. I used circumin to block the actions of a transcription factor, a switch that turns on the gene. The transcription factor is called NF-kappa B.

good luck,

Caroline

[Sareena Avadhany]

Hi Caroline,

Thank you! I would really appreciate if you could give me some information on what you did in your research. I'm eager to learn as much as possible about my interests.

"Curcumin and how it aids in the prevention of diseases" is a very vast topic. I'm looking to narrow it down to one specific disease. I'm trying to see what interests me the most as of right now.

Any information would be very much appreciated.

Sincerely,
Sareena

[carolinethorn]

There has been a lot of work on circumin and cancer. Aggarwal at MD Anderson in Texas has done studies looking at how circumin can inhibit cancer cells from growing.

http://www.eurekalert.org/pub_releases/ ... 071105.php

My work was on a gene called SAA1 that is switched on in response to infection or injury. It is switched on by pro-inflammatory molecules called cytokines. I looked at it in a human liver cell line and a human epithelial cell line. I wasn't looking at all of the possible effects of circumin, i needed something that was anti-inflammatory and might block the pro-inflammatory substances i was using. so i was looking at a very specific activity of circumin blocking the NF-kappaB pathway by blocking the IKK protein.

Were you planning on doing experiments with mammalian cell lines? I think from other postings that this can be difficult to get permission for.
There is a similar pathway to the NF-kappa B pathway in Drosophila flies that is also involved in response to infection. Its also involved in development. There is a homologue for IKK. Limh would be able to help with this. Perhaps circumin acts on the drosophila protein as well? Then you could have a model system .

best of luck,
Caroline

[phamlinh]

Hi Sareena,


I'm away for the holidays, so my postings will be more intermittent.
However, through Stanford I do have access to the journal in
question. If you want, post your email address in the experts only
forum, and I'll send you the file as a .pdf. I think this should be
okay, and I definitely DON'T want you posting your email address in
this general forum.


With regards to research, I know from personal experience that it IS
possible to conduct research with vertebrate animals at ISEF. You
just have to get permission first. In high school, I did experiments
with both mice and mammalian cell lines. As you can imagine, the
experiments with cell lines took much less time to get approval than
the mice. But it is doable. Better yet, you could work with insect-based cell lines, and then approval would not be required because it is an invertebrate.

My lab works with Drosophila immunity, but I'm not certain if we're accepting high school students right now. I'll ask my advisor and see. There are a number of labs at Stanford, however, that do take high school students, particularly over the summer. In fact, there's a high school mentorship program that sounds right up your alley. Here is the link:

http://ccis.stanford.edu/

I also found a list of the faculty directors.

http://ccis.stanford.edu/people.html

Anyone on this list has definitely hosted summer high school students in the past and has a strong interest in mentorship. I know a few of these professors and can give you some specific recommendations. Keep in mind, though, that there are also other professors not listed that have also mentored high school students. I would try to network as much as possible.

Ron Levy is a really nice professor that works in cancer immunology. Based on Caroline's work with circumin, it sounds like it may inhibit NF kappa B, a transcription factor that is involved in a number of signaling pathways. I'm willing to bet that Ron Levy's work has some involvement with NF kappa B.

PJ Utz is another awesome mentor that works in autoimmune diseases like lupus.

Steve Galli is very nice and has a great work environment. He works with animal models of asthma.

There are a few other professors that I don't see on this list. Tim Stearns works with yeast and often hosts undergraduates. In fact, he designed an undergraduate class that is built around research. I'm sure that he's hosted high school students in the past.

If I think of anyone else, I'll be sure to post it. In the meantime, I would strongly suggest that you poke around the CCIS website. I know the program doesn't start until the summer, but it gives you and idea of what type of research a high school student can do. Even better, you may be able to start your research now and continue it during the summer.

Congrats on really taking initiative on your project. I'm very impressed! I'll make sure to speak with my mentor.

By the way, here is a list of all of the faculty in the cancer biology program:

http://www.stanford.edu/group/cancerbio ... groups.htm

If you want any advice on any of the faculty, ask me and I can network with other graduate students to see what they think.

Best of luck,
Linh

[Sareena Avadhany]

Hi Linh and Caroline,

Thank you very much for the information. Looking into circumin and cancer looks very very interesting.

Thank you Linh for the contacts you provided. I am a little familiar with the scholarship program CCIS. I'm not sure, but I think the last time I read it, it was only given to going-to-be-seniors or graduated seniors. I'll recheck.

Is it possible to conduct an experiment involving cancer without injecting the cancer cells into mice?

Sincerely,
Sareena

[carolinethorn]

Hi Sareena,

Yes, it is possible to do a project about cancer without injecting cancer cells into mice!

Because one of the main features of cancer is that cells grow out of control compared to normal cells, people often study some of the aspects of how cell growth is controlled in many types of cells including yeast cells. Yeast cells have very similar genes and proteins that control when cells divide compared to human cells, so sometimes people use yeast as a model system for the "cell cycle". They could use other types of cells as well -cells that were isolated from a tumor from a mouse or a human, or fly cells, but one of the simplist models would be yeast. They grow the cells in a culture and measure how fast they grow and other markers for cell reproduction and division.

Another way that cancer cells are different from normal cells is that they ignore signals to die. Because the genes and proteins for dying are similar between worms and human cells, people often study "apoptosis" or cell suicide in c.elegans worms. Normal cells that have damaged DNA have a protective mechanism that causes them to commit suicide. There are proteins that start to digest the cell, the cell membranes make lots of folds called blebs, the DNA breaks into pieces and eventually the cell breaks into little pieces that are eaten up by the white blood cells. There are ways to measure the proteins and the DNA breaking up.

So you have lots of choices of model systems without the difficulty of getting approval to work with mice, or even mammalian cells. You could do experiments with insect, worm or yeast cells that wouldn't need approval. You would need to define which feature that is cancer-like that you want to look at and how the circumin might act. For example, you might look at insect cells and measure how fast they grow normally, then you could add a cancer promoting drug or chemical, carcinogen, and measure how fast the cells grow then. Then you could do the experiment with the carcinogen and the curcumin and see if it prevents the increase in cell growth.

I think you can come up with some great experiments.
good luck,
caroline

[phamlinh]

Hi Sareena,

I think the CCIS grade requirement is mostly a maturity requirement. You've already demonstrated on this message board that you're quite mature and committed to performing some research. I would still strongly suggest that you try contacting the CCIS personnel and find out if they're willing to make an exception. And even if they're not, I'm sure one of those labs would be willing to host you. They've already shown a strong committment to mentoring high school students, and advisors *love* students that are interested in a long-term project. It's hard to complete a project in 3 months, or even 6 months. But doing something substantial over the course of 2 years is definitely doable. I'm very impressed that you're thinking this far ahead, and I'm sure some professor will be just as impressed.

Regarding your question, it is definitely possible to do cancer experiments on cell lines without having to perform experiments on mice. There are a couple of different cell lines out there. A primary cell line is one cultured directly from tissue and only has a certain number of cell divisions left. For example, I know a few labs that work with keratinocytes from fish scales. They pluck a scale off a fish and allow the cells to migrate into a culture disc. These cells are fully differentiated, so they are only going to divide a few times.

In contrast, the more interesting type of cell line for your purposes is called an immortalized cell line. These are cell lines that have been transformedi n some way such that they will divide an infinite number of times. If you think about it, this sounds a lot like cancer. These types of cell lines have been transformed so that they closely resemble cells in malignant tumors. In fact, some of the cell lines actually come from tumor samples and have been cultured in vitro for a number of years.

So it's perfectly doable to look at anticancer drugs dealing only with a cell line. I think that's a very good project for you. You can look to see whether a number of factors are altered in the cell line. For example, if you find some drug that stops cell division, then you've got a potentially good anticancer drug (as long as it isn't toxic). Cancers do a wide variety of other things as well though. For example, they migrate to other sites of the body, the undergo angiogenesis (the process by which a large tumor recruits blood vessels in place where they normally wouldn't occur. This is a critical difference between benign and malignant tumors), etc.

I hope this was helpful.

Best of luck,
Linh

[Sareena Avadhany]

Thank you Linh and Caroline,

I was planning on competing in my regional science fair in 2007, which gives me a year to prepare my project.

I recall that the ISEF rules, since my fair is affiliated, says that for a 2007 science project, research can only be done from January to March (or May) of 2007 and for only 12 consecutive months.

So suppose I do want to experiment with mice or another vertebrate animal and I want to start in the summer or something that requires SRC/IRB approval. How would I have my experiment approved before I conduct it in the summer? I remember applications were only sent out in the August/September time.

Thank you.

Sincerely,
Sareena

[phamlinh]

Hi Sareena,

Unfortunately, it's been many years since I competed in ISEF, and the reuls weren't as rigorous as they may be now. I got approval from my local SRC board during August/September and renewed it every year. However, for your situation, I would get in touch with a mentor lab first. Get an experimental design plan in mind, and think about how you're going to submit it to SRC. In the meantime, any university that you work at should require you to take a safety class; this should teach you the basics of what you need to know. I think you can start to learn how to do the experiments, but not necessarily conduct experiments until after you get approval. If you ask, maybe you can get approval for an interim period.

With regards to the time frame, it is true that you can only present primary data for the period you specified. However, this does *NOT* mean that you can't start working in a lab beforehand. Especially as a sophomore, it will take a while to get aquainted with setting up experiments in a lab setting. you can put your summer work in a different background binder, and present only the data derived from the current period. The stipulations for continuation projects is that you ask new questions, address new hypotheses, and set up knew experimental design. Any scientist will tell you that after 3 months, their experimental plan has changed slightly, and in a year, it will have changed significantly.

This was how I tackled these problems when I was in high school. Talk it over with your teacher though and find out if it sounds like a workable plan.

Linh

[Sareena Avadhany]

Hi Caroline and Linh,

I did some research on NF-kappa B and the gene SAA1. I am a little confused because the websites that I was looking at were pretty advanced for my limited knowledge about genes and proteins.

I will try explain what I understood what I read, and hopefully I got the right idea!

So the IKK protein is part of the SAA1 gene. So the NF-kappaB transcription factor turns on the IKK protein that is pro-inflammatory/anti-inflammatory?

I am confused on what cytokines are and how it works with the SAA1 gene, as well as the pro-inflammatory and anti-inflammatory. Is there a certain website that can explain my questions?

Thank you!

Sareena

[Sareena Avadhany]

Hi Experts,

I recently met a biophysicist doing his Ph.D, and asked him questions about my project. He had told me that while doing my research, I must figure out the difference between a good and a bad journal. How can you tell if the journal is credible or not?

Thanks!

Sincerely,
Sareena

[deleted-71557]

Hi Sareena,

one way that people tell whether a journal is good or bad is by it's "impact factor". It measures how many times articles in a journal are refered to by other articles in different journals. If it's higher, then the articles in that journal are having more "impact" on their field. You can find a longer description here:

http://scientific.thomson.com/free/essa ... actfactor/

Unfortunately, impact factors are not freely available, but you may be able to get access to them at a library.

Good luck ! It's great you are seeking help from experts in the area.

[phamlinh]

Hi Sareena,

At this stage in the game, I would not worry as much about what is a "good" or "bad" journal. There are things known as impact factors, but all of these websites require subscriptions and are not freely available. Moreover, what defines a good journal is somewhat ambiguous. It involves subjective things like readability, how important the work is considered to be at that particular time, etc. At this stage in the game, I would focus on reading review articles rather than primary literature. This means articles that are written as an overview of the field rather than individual research articles that present a particular series of experiments. You can do pubmed searches limited to review articles, and that should help you get an idea of the general picture of the field. Then, if you're interested, you can read the specific articles referenced in the review and get an idea of how the individual experiments are performed.

Here is the website on Pubmed where you can affect the Limits:

http://www.ncbi.nlm.nih.gov/entrez/quer ... &DB=pubmed

Under publication type, choose review articles. This should give you some hits that are more general overviews for your topic of choice. If you need help getting a particular review article, post me in the experts forum as before, and I should be able to email you the attachment.

As a general arbitrary rule for which journals are reputable, the simpler the name, the better. The "big 3" journals include Science, Nature, and Cell. PLoS is a new journal that may be really great for you since all of the articles are freely available online. Each article also has a box inset that explains the relevance of the research in plain English. PLoS can be found at http://www.plos.org.

For cancer biology/immunology, Immunity and Nature Medicine/Nature Immunology may also be good journals for you.

I hope this was helpful.

Linh

[phamlinh]

Hi Sareena,

You're asking some fairly complicated about immunology, so I'll try my best to answer them here. However, it would be very useful to find an immunology textbook to read over and expand on what I have written here. Kuby immunology or Janeway immunology are both good textbooks to try. Janeway is available on Pubmed in a searchable format. Here's a link to the chapter on cytokines:

http://www.ncbi.nlm.nih.gov/entrez/quer ... .1062#1072

Try exploring around that website by using the search function. But I'll try to give you an overview here:

NF kappa B is a transcription factor that is broadly conserved among all animals. A transcription factor is a protein that is required to turn on certain classes of genes. So, NF kappa B will get induced by certain stimuli (such as immune stimuli), NF kappa B will get activated, travel to the nucleus of the cell, and turn on certain genes. This general sort of scheme is called a signal transduction pathway. Signal transduction pathways are subject to positive and negative regulation. In other words, there are ways to turn the pathway on and to shut it down.

As you can imagine by the word "pathway", there are upstream and downstream components in a pathway. In other words, proteins are activated in a certain order like stepping stones. If any part of the pathway is missing, you can't jump to the next stone, and the pathway is interrupted.

Okay...so NF kappa B is a transcription factor that works in the nucleus. This means it's a very downstream component. There have to be upstream components that can turn it on. The cell has receptors on its surface that get activated, this turns on a downstream component, and the cascade continues until ultimately, NF kappa B is turned on.

To imagine this visually (sort of), here's a general schematic going from the cell surface to the nucleus:

Receptor activated -> protein 1 -> protein 2-> NF kappa B travelling to the nucleus to activate transcription.

IKK stands for inhibitor of kappa kinase. It is part of the signaling pathway that regulates NF kappa B. It's actually a negative regulator (hence the word inhibitor in its name). Normally, IKK is inhibiting NF kappa B activation by keeping it in the cytoplasm. However, once the signal transduction pathway is activated, the activity of IKK is nullified. (in other words, inhibiting the inhibitor allows the pathway to be activated. It's a little confusing, but I hope that you understand. If not, ask and I'll try to explain it more clearly). Without IKK present, NF kappa B is allowed to be activated, and it can travel to the nucleus to activate transcription.

There are a wide variety of genes that are activated by NF kappa B. Some of those things may include cytokines and the SAA1 gene that you're talking about. However, cytokines may also activate NF kappa B. This is called a positive autofeedback loop.

cytokine -> activate NF kappa B -> transcription of more cytokines

Eventually, this feedback loop is turned off again.

Okay...now on to cytokines. Cytokines are signaling molecules secreted by cells that activate other signaling pathways. There are a wide variety of cytokines that you can read about in that link posted above. In general, there are two classes of cytokines: proinflammatory and antiinflammatory.

Proinflammatory cytokines will activate NF kappa B and promote an immune response. This means cells involved in the immune system will be activated, and you've turned on the response. (If you don't turn off the response, you can develop autoimmune diseases where the immune system attacks itself (like arthritis or type I diabetes). If you can't turn on the immune response, then you have an immunodeficiency (like AIDS patients).

Other kinds of cytokines are involved in turning off the immune response. These are called antiinflammatory cytokines.

As I mentioned above, these sorts of pathways have to be tightly regulated. You have to have a means of turning the pathway on for a while, and then turning it off again. This is why a particularly stimulus will usually turn on a proinflammatory response for a while, and then later on turn on an antiinflammatory response.

As for SAA1, as far as I can tell from Pubmed, it does not encode IKK. I believe that it is a type of serum amyloid protein. If I'm wrong about this, let me know or send me a link to the reference and I can clarify.

SAA1 is called an acute phase response protein. When you have a very strong bacterial response, cytokines are produced. This turns on many signaling pathways (including one that activates NF kappa B). This in turn causes release of other cytokines that are proinflammatory. These have multiple effects, but once site of action is the liver. During proinflammatory situations, the liver gets activated and starts producing acute phase response proteins. One of these is SAA1. From what I skimmed, SAA1 is produced during inflammatory situations. However, it is also turned on during chronic inflammation. This is the situation where the immune response has been turned on, but it hasn't been turned off appropriately and is starting to damage the host.

I know this is a lengthy response, but I hope that it clarifies some of your questions. If it's still confusing (and it probably is since you're asking very advanced questions), please let me know and I'll try to explain it again. Basic questions (like what is inflammation good for?) are particularly useful because it will let me know how much of you're reading you've been able to understand.

I think review articles and textbooks will be very useful at this stage of the game. But I think speaking one on one with a mentor will be the most useful because you're dealing with very complex questions. I hope that search is going well, and if there's anything I can do to help, let me know.

Best of luck,
Linh

[carolinethorn]

Hi Sareena,

Sorry i have been away on vacation and missed some of this.

As Linh described SAA1 is a gene that is switched on by NF kappa B. NF kappa B can be switched on by various different cytokines, in the experiments I did with the SAA1 gene I used Interleukin-1 (IL-1).

Curcumin seems to block the switching on of the SAA1 gene by blocking NF kappa B. I only looked at adding curcumin and IL-1 together and measuring the SAA1 gene and seeing that it was no longer switched on. I did not ever look at how the curcumin blocked the NF kappa B but i think other people have looked at this. There are a couple of different ways that the curcumin could block NF kappa B. It might bind directly to the NF kappa B and stop it being able to interact with genes and switch them on, or it mgith stop the NF kappa B from getting into the nucleus. Or another way is that the curcumin works on the IKK, the inhibitor of NF kappa B to make the inhibitor work more strongly.

But as Linh also said, SAA1 is just one gene out of hundreds that NF kappa B switches on. I just mentioned that because you had asked what my project was. There are plenty of other genes that are much more famous, some that are well known for being part of cancer pathways which might be more appropriate to look at.

best of luck,
Caroline

[Sareena Avadhany]

Hi Linh and Dr. Thorn,

Thank you very much for the amount of information and knowledge you've given me. I am very interested in your work Dr. Thorn, and will borrow the textbooks Linh had mentioned in a previous post.

I am still in the process of looking for a mentor, but after corresponding with a friend who is also into science fairs, he suggested that I come up with a research plan so being able to approach professors would be much easier. Any suggestions would be very much appreciated.

Sareena

[deleted-2131]

Sareena,

If you have any further ISEF rule questions, let me know. I know the insides and out of SRC, IRB, forms 1-7, etc. I am more than happy to guide you through the paperwork.!

Good Luck,

[carolinethorn]

Hi Sareena,

I think its a good idea to get your research plan together - to do some background reading and come up with the aspects of cancer that you are interested and the types of experiments you would like to try with the curcumin. Try not to get too specific though because most mentors will want you to use techniques that they already have running in their labs - because then there will be someone who has done it and can teach you, they already have the equipment and the chemicals or cells and it might be covered by their grant money.

I am happy to help you bounce ideas around for your plan,

-Caroline