Saturday, August 16, 2008

tough decision - how to focus

Like any graduate students doing research, there are some tough times. This is what I am going through recently. --The balance between research and family; the requirements of department to meet; the struggling to focus on only one project.

Looking back, I have to admit that I have not been very focused on my research. As a result, I have worked on 4 or 5 different projects. They are all excited projects. And I have made reasonable progress in most of them. But now I realized that to graduate quickly, I have to focus on one thing and do something deep enough. So, which project to drop?? I am struggling between two projects. The one I have made most progress and have produced quite a publication is really risky to follow up and should definitely have big impact (this is like marketing). The other one is relatively straightforward (I have to say relative) and will very likely generate some small paper(s).

Plus, the department required me to teach for two semesters --one of them has to be some kind of lecturing (like lab courses). This will definitely eat out a lot of my time in research.

I wish I had 48hours a day to work!!!

I think I probably will go with the relatively easier one so that I can graduate by the end of next year. After graduation, if the risky one has not been published by other researchers, I could continue it. (Again, this is marketing!!!)

Wish me luck!

by Beyond Lab

Thursday, July 31, 2008

lab design

For most biology research (especially molecular biology), lab design is an art. Poorly designed labs will "effectively" limit your productivity, including moving around, organizing equipment, communication, storage, wasting space, etc. All these things must be considered. In order to do that, the actual researchers have to be actively involved.

Our lab has moved a few times in the last two years, either moving across states, or from one building to another building. The building I am currently in is brand new. But we've already seen a lot of design problems.

To name a few:
1. No storage space. Biology research utilizes a lot of tubes, dishes, and so on. It is impossible to buy new one every day or every week. So, you always buy in boxes, even in 10-20 boxes each time. Therefore you have to have space to store them. However there is absolutely no space designed for this purpose. As a result, our lab manager had to personally buy shelf material from Home Depot and ask carpenter to put shelves on the walls, which are not as stable of course, but is much better. Now, everytime our big boxes come, we have to unpack them and put the contents onto the shelves (obviously the boxes are too big for regular shelves).

2. curtain and emergency light for microscopy room. Modern microscopy mainly refers to fluorescent microscopy. This requires dim or no light while working --means dark room. This was designed badly with an emergency light right above the microscope. It is emergency light, you have to leave it on all the time -- how do you use the microscope then since darkness is needed? Also microscopy rooms usually have curtains to block lights out. Ironically they designed white curtain for dark room!

3. Conference room. You have to present your powerpoint slides - always with images - so you want the lights in the conference room adjustable. This was designed. However, the rooms have two big windows facing south. The regular blinds let lights in easily. Bad hah. This is worse -- the room is about 2 meters wide and 5 meters long with the screen installed at the long side. You know what I mean, when you want to see the presentation, you have to bend your whole body back. No one's neck likes that. If there are more than 5 people, you'll have to watch the presentation half meter in front of the screen. Like it?

There are more...

Who the hell designed the building???

by Beyond Lab

Wednesday, July 30, 2008

another stupid microsoft thing

Have you ever tried to set up two internet connections for your labtop? --Are you tired of changing between static IP address and DHCP?

Will, microsoft actually has this function. How to use it? -- This is the help page.

Follow this, can you find the "alternative configuration" tab??

If you are lucky, you will see it. But very likely you don't see it. --Why? Simple! It only shows up if you select DHCP (automatical). If you set a static IP etc., there is no alternative configuration tab.

Why? Ask Bill Gates. (Oh, I guess he's off the hook already. But sorry, we have to blame him.)

by Beyond Lab

Monday, July 28, 2008

better than others?

Something I am doing right now requires me to demonstrate that I am better than others with the ame levels of education. What thing I can do but others cannot?

While thinking about this question, I remember something like "if you cannot describe what you are doing in one sentense, stop doing it. you are wasting your time."

Sure I can do that. But my training has been a bit diverse, although always in life science -- from medical school gradually shifted toward basic pathology research to current biological research. I'll have to explain some basics before people really gets what I am doing. On the other hand, this really gives me something special than others. I will have to take advantage of my training background.

However, I understand that to succeed, it is necessary to be able to clearly explain to lay people my research in PLAIN language. So that people understand the importance of my research and therefore provide support. This is not just grant writing, which is for experts to review. This is for everyone else. I will post it here once I am done.

by Beyond Lab

Wednesday, July 23, 2008

DNA for dating??

by Beyond Lab

It has always been said that it is chemistry brings two people together. Probably it is right (lol) - check out this site: .

When doing transplant, you always need to match certain genes for example MHC, but in the future, before date someone, test his/her DNA first. --Or try to steal some of stuff he used on your first date to get the DNA tested.

This is a joke. --That's all I can say.

But will the company profit? probably. There are enough idiots in this world. Only marketing matters in business.

Friday, July 18, 2008

where is your saliva samples being analyzed?

by Beyond Lab

it is clear that 23andme uses Laboratory Corporation of America (LabCorp) as its genotyping service lab with Illumina chips (arrays). --Beyond lab is wondering how much 23andme will pay LabCorp for each sample, how much is the chip and how much can they get from what customres pay. --This market is huge but is absolutely quantity-dependent. The more customers, the more profit. What will the customres get and how will the information help the customres? --that's something else.

money, money

by Beyond Lab

Research is extremely expensive -- even more than drug development. NIH is throwing $8 million to epigenome and human disease studies, starting next year. Is this a big amount? No. absolutely not. it is just a few R01 grants. Epigenetic studies require a lot of new/expensive equipment and techniques, such as microarray, sequencing. in many cases, new methodologies have to be developed. Also, when focusing on human diseases, it needs more resource input.

More importantly, epigenetics is an expanding area with new markers appearing one by one. Which one of the epigenetic markers is more important? How could $8 million be balanced properly to all these markers?? WE NEED MORE!!!

Hopefully this is just the beginning.

Wednesday, June 25, 2008

summer vacation and protection

by Beyond Lab

There are a lot of reasons to avoid exposure to strong sunshine. This should be especially noticed during this summer travel time. -- Being tan might make you look good and feel good. But does your body feel good as well? -Most likely not.

There is clear scientific connection between heavy sunburn and melanoma (a kind of skin cancer) occurrence. People received multiple severe sunburns are at higher risk of developing melanoma. Children are at even higher risk.

Protect yourself and your family by doing necessary things, high SPF sunscreen (and reapply every 2 hours if in heavy sunshine), protective clothing and hats, and so on. What's the best solution? -- avoid the sun during peak hours -10am to 2pm.

Just my 2 cents.

Tuesday, June 24, 2008

A graduate student oath -- will it help?

by Beyond Lab

University of Toronto created a graduate student oath to let the students remember their social and moral responsibilities, in other words, to conduct research ethically. I think one of the reasons is to try to avoid so many scientific misconduct in the scientific research area. To name a few, the Korean tem cell scandal, the recent retract of an important paper by Linda Buck, a Nobel prize laureate. There are not only irreproducibility of their data, but also the way they put all responsibility to one of the co-first authors. All these are absolutely not normal and should not happen in the pursuit of science.

Will this oath help? I completely doubt it. -- The overall scientific environment is so competitive, mainly financially, that researchers have to publish before their competitors and have to publish in good journals to secure enough support for their continuing research, and their personal salary in many cases.

Is there any way out? Things have to be changed gradually. Higher NIH budget (in US) is definitely one of the first things to do.

Monday, June 16, 2008

what's wrong with those consumer genomics companies?

by Beyond Lab

After the action of New York state about 2 months ago, California is taking a similar approach to try to regulate consumer genomics (personal genomics) companies from offering genome services without prescription from doctors. With many posts in my blog talking about the current situation of personal genomics, you might understand that one of the basic reasons is that it is not ready yet. (Most) Consumers feel what they got from the services didn't worth the money. As many experts suggested, the current consumer genomics services should be considered as "recreational genomics" -- therefore whichever company marketing these services should not relate them to health or medical implications. Otherwise, you have to get physician's prescription. So, at this point, it is reasonable for New York and California two states to initiate some regulations.

This is a good thing!

Saturday, June 14, 2008

to make use of genome

by Beyond Lab

Human genome is huge. Individual variations are also extremely common. Most of these variations don't have any effect on any function. But some, either by itself or in combination with others, do. What, how, when, and where these variations matter is something we have to know before personal genomics really mean anything.

As one of my earlier posts indicated, some companies, in collaboration with research institutes, have projects on their target diseases or conditions. But that's obviously not enough. We have to know everything - eventually.

So, there is a "genome-wide association studies" from NIH which involves "rapidly scanning markers across the complete sets of DNA, or genomes, of many people to find genetic variations associated with a particular disease". Many diseases are under study now. This sort of "national" or global initiative, like the previous human genome project, is really the drive to our understanding of our genome and therefore could make use of genome information.
More detail information could be found here:

Wednesday, June 11, 2008

One gene, one disease??

by Beyond Lab

Obviously not. Life is so complicated that it is impossible for one gene to be solely responsible for one function and therefore one disease. Almost all genes identified have multiple domains (function units) with different "potential" function. So, mess up one gene would certainly have more than one consequences. This has been confirmed in many species, from bakers yeast to human.

So, it is almost impossible to predict the occurrence of one disease just by analyzing the function/structure of one gene or its product. It has to be a combination of various information. With that being said, is it helpful to analyze one gene if it is know that this particular gene (or its mutant formats) always associates with certain disease. Absolutely!. But how accurate is it? No one knows when it comes to one individual -- yes or no. Probability means nothing for one individual.

Why am I saying this? Because one company Orion Genomics just licensed JHU technology to analyze IGF2 gene (insulin-like growth factor 2) with the hope to be able to predict the outcome (progression) of colorectal cancer. -- Beyond Lab personally thinks this is not very wise. I don't know how they will promote their future product to analyze one single gene. --Most current genetic or genomic detection products for breast cancer all involve many genes. One gene? Unlikely mean anything.

Sunday, June 8, 2008

More on presentation

by Beyond Lab

Last month's Nature Methods had an editorial named "talking points".

The short list of advice is:
1. Plan for the allotted time.
2. Know your audience.
3. Define your goals.
4. Structure your talk.
5. Keep your slides simple (content).
6. Keep your slides simple (design).
7. Beware of animations and multimedia.
8. Watch your delivery.
9. Choose your words.
10. Rehearse!

One thing Beyond Lab wants to point out here is that it once again recommends serif font just as Tomjoe's comment to one of my earlier posts.

So, use it!!!

Big money on personalized medicine

by Beyond Lab

Luxembourg government decided to take the challenge to push personalized medicine researches with big money. In collaboration with three U.S. institutes, U. of Luxembourg will establish several research centers to build a BIOBANK which collects huge amounts of disease samples and genetic information. This proposed system will be used to promote translational research and systems biology and in the long run will build the basics for personalized medicine. Of course, this has to be helped with modern personal genomics studies.

To Beyond Lab, this initiative is an important step toward personalized medicine. With U.S. economy going slow and U.S.federal funding being flat, other countries like Luxembourg, Japan, Singapore, and even South Korea are putting big amount of money in life science. At this point, the whole thing is still at data/information collection stage. But very soon, really useful knowledge/technology will come out and some of them will bring money back to those countries who invested in the research. Although it is difficult to predict exactly a time frame, the fast growing technologies will sure prove this is the case.

Wednesday, June 4, 2008

Personal genomics -- not only cancers

by Beyond Lab

A significant part of personal genomics studies have been focusing on the relationship to cancers. But that's definitely not the whole case. Recent gene analysis showed the potential use of personal genomics in other diseases related to our everyday life such as metabolic disorders -- folate (a kind of vitamin) metabolism.

Sequencing of a vitamin-dependent enzyme (critical proteins which carry out most of the molecular reactions in our body) methylenetetrahydrofolate reductase (MTHFR) from about 600 persons' genomes found that there are some variations in the populations. Some of the variations actually affected the enzyme function. More importantly, increasing folate level could rescue its function to normal level. --This is really direct evidence that simply changing what we eat everyday could interact with personal genomes and therefore have obvious benefit.

How useful is your personal genomes? Studies like this will gradually prove it. - Some time in the future, sequencing your genome will be like buying a car. Of course, by then genomics counselors will be a good job :)

Monday, June 2, 2008

colorectal cancer and patient personal genomics

by Beyond Lab

Here, another example showed that colorectal cancer patients with normal K-RAS gene have better response to a FDA approved drug (an EGFR antibody if you are interested).

The study was a multi-center multinational prospective clinical trial (Phase II) of Cetuximab where about 600 colorectal cancer patients were examined for K-RAS gene mutations and related to response to drug treatment (in combination with standard chemotherapy). --More wild-type K-RAS carriers showed reduced cancer and decreased risk of cancer progression. The numbers are not dramatic, but are significant considering the number of patients studied.

This kind of study will gradually build the foundations of personalized medicine and the eventual application of personal genomes (genomics). As mentioned in one of my previous posts, those personal genomics companies should collaborate with researchers to expand this kind of correlation studies (especially with NIH funding is limited).

Friday, May 30, 2008

new marketing strategy: RESEARCH

by Beyond Lab

You have probably already heard that 23andme established a collaboration with Parkinson's Institute to work on a system to use computer and internet to assess the relationship between patients' medical information, genes and Parkinson's Disease. This is not only a completely new thing to everyone, but also a very clever way to promote the companies' personal genomics services. Research to promote business -- Hasn't this been going on for a long time except no involvement of computers and internet.

Because it is so new, a lot of ideas need to be developed by the collaborators. They need to prove the principle actually works. Just to name a few challenges: an internet based information collection, analysis and distribution system (which is far mor complicated than a conventional database); a way to use this information and personal genomes securely; how to expand to other disease models for example diabetes ...

Although Beyond Lab has no doubt of the potential success, it takes time to let both the academics and general community accept the concepts. Let's keep an eye on it.

Saturday, May 24, 2008

personal genome service in China

by Beyond Lab

Last year my brother had chances to interact with several personal genomics companies in China. From his first hand experience, I briefly describe the situation of industrialization of personal genomics services in China. There seem to be some success in terms of marketing in this premature market.

There are about 4~5 private companies promoting sequencing genome for individuals. The most success one was established by several marketing experts. Among those are an editor China Daily news paper press, a marketing specialist (who is the president), a graduate student of Peking University (this is the only “scientist”), a novel writer, a lawyer. What's obvious from this combination is that they are good at marketing. In fact, according to them, they've sell up to 300 million Chinese Yuan of personal microarray genomic services in about one year last year. Their "success" also relies on another factor -- China has 1.4 billion people and the rich have too money to consume. Those rich people are keen to try new technology even if they don't understand it at all. This is called "fashion".

Their marketing strategy is massive media broadcasting and training workshops. They take advantage of the fact that so many people are looking for chances to make money and so many people can be easily talked into new things. So, they recruit a lot of distributors, who have to pay them a certain amount of money to join,to do the actual person-to-person marketing in hospitals and health related business areas. They are quite successful so far.

Another company takes a different approach. They collaborate with one academic organization to promote personal genomic services to children. Since children are parents' future and main focus, people are willing to pay for this kind of new things such as a microarray analysis if breast cancer related genes etc.

Still one more company is trying a governmental approach. The company director established some relationship with Department of Health of central government and persuaded the Department to develop a suggestive medical protocol for genetic testing in favor of this companies' product (one of which is similar to above breast cancer microarray). Once this protocol is distributed to hospitals, there will be doctors prescribe these related tests. How good is this approach? There is not enough data yet. But it is certainly interesting to follow up.

I don't know any company is providing SNP personal service in China as of now.

You may find some of these are special to China. But this is still the beginning of the field. Marketing of personal genome service is a challenge around the world.

Friday, May 23, 2008

personal genomics and cancer treatment, another model

by Beyond Lab

A recent extensive study showed that different genetic mutations (personal genomics)of a single gene could result in different drug response.

The most common lung cancer - non-small cell lung cancer - is associated with mutations of a gene called EGFR. Using AstaZeneca’s cancer drug Iressa (gefitinib), this study found that patients' drug-response, to a large degree, depends on the specific mutations. Without going into the details, this study indeed support the potential application of personal genomics in medical practice. Once enough genetic, genomic and clinical information is accumulated, doctors could select treatment that will sure be effective based on patients' genome -- so called personalized medicine.

Tuesday, May 20, 2008

mourn the dead, join rescue efforts

by Beyond Lab

Help those people in Sichuan, China!!!!

An extended question, if all the dead in the earthquake had their personal genomes (or some cells) stored somewhere, do you agree to clone them? --Or even just the children?

Thursday, May 15, 2008

disease links and personal genomics

by Beyond Lab

"Most biology today is low input, high throughput, no output biology" --Sydney Brenner (on the conference to celebrate 25th anniversary of GenBank April 2008) commented on the current information crisis in biology.

This is exactly true for personal genomics. Modern high throughput biology research has generated so much data that exceed the capacity of data storage hardware many times. For example, new DNA sequencing technique easily generates gigabyte-level data. These new techniques will make the $1000 personal genome possible in a few years.

However what do the data tell us? Not so much. There are only a number of cases where the linkage between genes and diseases has been established, such as BRCA1 and breast cancer. We are still at the starting point now in terms of genome-wide association study. The complexity of our body, the complexity of genome regulation and epigenome regulation all make this a tough work. Plus new techniques and theories appear quickly and a lot of our knowledge has to be modified, even completely discarded. And a lot of current research is not solid enough to establish the clear links we need clinically. It is still a long way before we can comfortably say that we KNOW our genome!

Researchers have to be able to be patient enough to collect more data. Personal genomics customers have to be patient enough before your genome get decoded. Don't be too excited by personal genomics companies' marketing tricks.

Wednesday, May 14, 2008

Al Gore and personal genomics

by Beyond Lab

Do you know that Al Gore, former Vice President and Nobel Prize winner, has a close connection to personal genomics company Navigenics?

Here it is. Gore is a partner with the venture capital firm Kleiner Perkins, the lead investor in Navigenics. Navigenics co-founder David Agus is also his friend. He said at one occasion on Navigenics that "it's going to be a fantastic success." However if you think about it, how much does he know about gene, genome and diseases?? Probably not much. Because he is certainly not in the field.

But if he promotes this personal genomics service like he promoted his global warming film, Beyond Lab thinks that Navigenics could actually get some sort of success. --Just joking.

But this certainly could be one of Navigenics' marketing places.

Tuesday, May 13, 2008

Blood Matters, facing genetic mutations

by Beyond Lab

What will happen after having your personal genome mapped (or sequenced or SNP'ed)? Will your life be changed if there is an well-established disease causing mutation?

If you are wondering these questions, please check this book out.

Blood Matters From Inherited Illness to Designer Babies, How the World and I Found Ourselves in the Future of the Gene. By Masha Gessen.

Masha carries a known BRCA1 mutation which is known to be a cause of breast cancer and ovary cancer. She inherited this mutation from her mother who died of breast cancer. This book described how her life has been changed after knowing the positive mutation. She has several options: 1, ignore it and live a "normal" life; 2. have breasts removed; 3. have ovaries removed; 4. have both breasts and ovaries removed; 5. monitor closely (which you should do anyway); 6. try to improve physical/immune system and fight against potential cancer.

What's her choice?

Although I haven't read the book yet, it certainly is on my list.

Sunday, May 11, 2008

talks on consumer genomics or personal genome

by Beyond Lab

As noted in one of my earlier posts, there are a lot of issues surrounding consumer genomics (personal genome) services /products and talks between academic and industry are required. Well one such discussion just happened last week at Cold Spring Harbor Lab (CSHL).

At the Biology of Genomes meeting at CSHL, one section witnessed Dietrich Stephan, co-founder and CSO of Navigenics; Linda Avey, 23andMe co-founder; Kari Stefansson, deCodeme president, CEO, and director; Francis Collins, director of the National Human Genome Research Institute. Other participants included Kathy Hudson from Johns Hopkins University and Joseph McInerney from the National Coalition for Health Professional Education in Genetics. Eric Lander was also there.

A lot of "existing" issues were discussed, especially the usefulness of personal genome. If you want to know more about the discussions please visit Daniel Macarthur's blog. I really like the comments about "a 'wiki-style' catalog of genetic associations".

Thursday, May 8, 2008

moving week

by Beyond Lab

This week we are moving the lab to a new building. You can't imaging how much stuff you have until it is time to pack. Fortunately, the moving is just next door -- we don't have to pack every tube and every reagent. We can carry most of them on carts and move ourselves. But still there are a lot of work -- defrosting freezers, rearranging equipment and so on.

But still, this is much easier compared to two years ago when the whole lab relocated from New York to Florida. That was a one month down time.

Now, we hope the down time will be only one week. --Just hope, I am not confident. There are inevitably a lot of problems in a new building, for example we have discovered that there are not enough internet ports, weak wireless signal, lacking power outlets, tables, chairs etc. Most ridiculous is that my assigned cubicle doesn't have any power outlet. There are outlets on both sides but there is no way my lights or laptop power cord could reach them.

Well, as long as they can fix them quickly.

Wednesday, April 30, 2008

Powerpoint presentation tips

by Beyond Lab

Note: one slide was a picture taken on one of the annual national big decision-making meetings in China showing the audience was bored and felt asleep. This is not a result of bad powerpoint presentation though, -- the presenter (one of the leaders) was simply reading what everyone has in his/her hands.

Another funny one:

Want more:

How not to give a presentation: Richard Smith, editor; BMJ

Tuesday, April 29, 2008

on scientific language

by Beyond Lab

T. Ryan Gregory (an assistant professor of evolutionary biology and genome biology at the University of Guelph in Guelph, Ontario, Canada) tried to translate scientific expressions in papers to plain language in a humorous way. This is fine. But please don't take it seriously because it is absolutely not always true.

Maybe evolution people do that (for example to hand-draw a regression line), but not all other fields can do that. Especially, if you do microarray analysis where you have millions of data points, you are always asked to deposit your raw data to a public database at NCBI, which everyone can access and analyze. --If there's any manipulation, some body will find out. Then you will be doomed.

Plus, most scientific conclusions must be reproduced by different labs before being generally accepted.

However, still he has a good point that the scientific language in published papers should be more meaningful to lay people. --Maybe a short plain version of every paper should be included while being published.

Friday, April 25, 2008

personal genome discussion

by Beyond Lab

A discussion of the personal genome by a panel of "masters" from various fields. Although so far no video available, but this is a must see.

At Univ. of Washington, on Apr 23, Bill Gates, Eric Lander, Maynard Olson, Leena Peltonen, and George Church discussed many aspects of the personal genome: the science, the industry, and ethics etc.

Some interesting notes from above Sandra Porter's post.

"The panelists were asked if they had had their genomes sequenced. Only George Church answered yes. It was interesting though, even though Leena Peltonen and Eric Lander said that they weren't interested in having this done, both of them said they had been tested for certain genetic diseases, Eric, for Tay Sachs, and Leena for 40 diseases common in Finns. Bill Gates said that if the top 20 infectious diseases were to be cured, he would be happy to have his genome sequenced and make it public."

"Eric Lander playfully asked the other panelists if they thought presidential candidates disclose their genomes. He reminded us that we had a president with Alzheimer's disease and we would have found that potential if we had tested him. In the future, will we ask the older candidates to get tested for Alzheimer's?"

--I heard Eric Lander's talks. It is always very informative and amusing. :)

Here you are. I did a quick google and found a place to watch the discussion.
The beginning part is just music --weird. but drag to start from after 15min.


Thursday, April 24, 2008

GINA, proteome, and more

by Beyond Lab

GINA will very possibly be passed today and sent to George Bush. This is good in protecting your gene (personal genome) information from being misused by insurance companies etc. To know about GINA, this blog has the details.

Personal proteome? It might be too early but it eventually will come around. Researchers around the world are trying to start an ambitious project to map all the proteins in our body. It will definitely cost more than sequencing our genome because there are so many types of cells/tissues in our body and each type has characteristics proteins. Moreover, to understand protein is not just know their names and sequences -- the higher order structures (2,3, and 4-dimensioin) and the interactions among proteins are all critical. How should this be funded? Public money? Private support? Scientists would have to do some marketing to get enough support. Nonetheless, it is useful and must be done.

A step further, once this information is available some day, will there be many private companies to sell personal proteome service like the current personal genome companies? Let's see.

On another topic, since most of the genome or proteome research is done with public funding, should the information be used by private companies to earn money??? Should they be charged for using that information for profit. --Interesting to think about it. Your comments are welcome.

Wednesday, April 23, 2008

more on personal genomics

by Beyond Lab

Just something to back up what I wrote in yesterday's post about personal genomics.
Boston Globe has an article about this
Some doubt genome's value as health tool.

There have been a lot of this kind of reports some where, both in scientific journals and media. However the image is still not clear. It would be interesting to see how the companies promote their products and challenge the scientist's views. Will simple search engine optimization do the work??

Tuesday, April 22, 2008

It's Google, again!

by Beyond Lab

Just wondering, do you want to have your personal genome information go public like James Watson? Be careful if you pick 23andme or Navigenics to have your DNA sequenced. Google just invested a big lot of money to Navigenics. Eventually, Google will probably put everything up to the web including indexing your DNA.

Just kidding. What I don't really understand is to me (and certainly a lot of other scientists in the field), personal genome or consumer genomics is certainly not ready yet, but why so many people are jumping into this water??!! Is it fun?

Maybe Google will put ad links to every possible website and to promote eMarketing of this 'promising' new thing. One day, conversation will start like this, "Sequenced yet?"

Monday, April 21, 2008

consumer genomics, educational or medical

by Beyond Lab

New York State sent letters to companies offering consumer genomics tests (personal genomome) because the state considers these tests as "medical" test and should obtain a permit before being prescribed by physicians. The 23 companies include Navigenics, 23andMe, Affymetrix, Illumina, and HairDx etc. Some companies claim consumer genomics is educational, therefore should not require special permit. What on earth is this?

--This is a gray area. But considering the massive information (potentially informative at many aspects), I tend to think that consumer genomics belongs to those genetics tests which are not simply educational. Proper regulations are necessary. FDA probably should hold some kind of panel discussion before it really becomes a problem. Cold Spring Harbor Laboratory is holding such a symposium late this year on this topic (both technology and applications). It is a quickly expanding area involving a lot of deciplines, which makes this kind of discussion important.

I am exciting to see what other people say. So please leave your opinions here.

Sunday, April 20, 2008

personal genome, internet and eMarketing

by Beyond Lab

I did a simple experiment today --search the internet for "personal genome" using different search engines --just want to see what you get on the first page. Here are the results. Only 23andme, which is literally part of google, shows up in google search. Seems some of the companies need to do some search engine optimization (SEO) if they want to have better internet marketing.



MSN Live:

PS. There are too many terms with basically same meaning. For example, if you try "consumer genomcis" on these search engines, you will get different hits. But the fact is NO companies were on the first pages.

Friday, April 18, 2008

alcoholism connected to epigenetics

Epigenetics gets real!!!

A group from Chicago published a paper two weeks ago connecting chromatin remodeling (epigenetics) in brain to alcoholism. It is exciting because this is for the first clear evidence, as far as I know, humans' everyday activity could affect epigenetics.

Using laboratory rats as model, they found that acute anti-anxiety effects of alcohol are mediated by reduced histone (H3 and H4) acetylation in the amygdala region of the brain. What's more interesting is that increased anxiety accompanied with withdrawal from alcohol dependence is caused by a further increase in this process (acetylation). Neuropeptide Y, a known protein and mediator of anti-anxiety, is a potential target of the transcriptional regulation associated with this epigenetic mechanism. Inhibition of this process could indeed prevent anxiety. These data could potentially explain a lot of symptoms related to alcoholism and withdrawal anxiety. The clinical significance will have to be proved by further study.

When you drink next time, remind yourself that you are modifying your epigenome!

Thursday, April 17, 2008

cancer clinical research and Sydney Brenner

Nobel laureate Sydney Brenner called for a “bedside to bench” approach to researchers at the AACR meeting this month. Biological and medical researches have been following a way from lab bench to hospital bed all the time. Input from clinical professionals to basic research is limited. This actually could be one of the most important reasons that translational research is extremely slow.

However, it is easier to say it than do it. This could be a slow process with both parts having to be patient enough. It is like talk to evolution people about molecular biology - macro world and micro world have different languages.

But this should benefit us and should be promoted. Go for it!

Wednesday, April 16, 2008

Watson and Alzheimer’s disease

You must have heard that the "complete" sequencing of the genome of James D. Watson - the pioneer of molecular biology. The sequencing actually was finished about one year ago in two months and cost about 1 million. Now the results are out in Nature.

Here are some numbers:
7.4 - fold redundancy -- current sequencing technique requires redundant sequencing for assembly purposes;
3.3 million - single nucleotide polymorphisms (SNP) --these are single nucleotide variations to the reference sequences;
0.61 million - of those SNPs were previously unknown;
10,654 -- 10654 of those SNPs could cause amino-acid substitution within the coding sequence, that means that the protein sequences could be changed which could affect the protein function;
222,718 - small insertion and/or deletion polymorphisms, which affects local chromosomal regions;
345 - of above overlap gene coding sequences and could alter protein function;
1.5 million -new sequences;
49 - potential genes from above 1.5 million new sequences

Will Dr. Watson develop Alzheimer's disease? That's secret. The sequence of Apoliprotein E gene and neighboring regions was not disclosed.

How about breast cancer? --come on, not him. But his genome does contain a related mutation. He is not too concerned because he doesn't have any daughter.

Are you interested in his genome? (I am not :) ) But here is the link:

Is Dr. Watson the first one to have genome completely sequenced? -- No. The founder of J. Craig Vender Institute (Rockville, Maryland), Mr. Vender was the first one. However, the technology was different and it cost $100 million. 100 times more!

How useful the sequence is? --"it will be extremely difficult to extract medically, or even biologically, reliable inference from individual sequences" - Maynard Olson.

How useful will it be? -- Some day, it will be useful.

Tuesday, April 15, 2008

stem cell patent?

Steven Salzberg, a Professor of bioinformaticsat at the University of Maryland, raised the question of patenting stem cells by WARF - Wisconsin Alumni Research Foundation. Many aspects involved here, for example, is patent a good thing at all? Is patenting research a good thing? Is patenting research funded by public money a good thing? Look at people's comments. Interesting topic to discuss.

My point is simple: patent them but give them free (or almost free) to academic researches.

Saturday, April 12, 2008

Stem Cell meeting

The 6th ISSCR (International Society for Stem Cell Research) Annual Meeting will be held from June 11 to 14, 2008 in Pennsylvania.

Looking at the speaker list, you will regret if you are in this field but you will miss this conference.

Conformed speakers include:

Sir John Gurdon FRS, Wellcome Trust/Cancer Research UK Gurdon Institute, UK, Keynote Address
Rudolf Jaenisch, MD, Whitehead Institute for Biomedical Research, USA, Closing Address
Douglas A. Melton, PhD, Harvard University, USA
Shinya Yamanaka, MD, PhD, Kyoto University, Japan

and more...

Friday, April 11, 2008

Parkinson's disease - new information

Parkinson's disease has been thought to be a good disease model where cell replacement could actually help. It's caused by the damage of a particular kind of neural cells by an abnormally formated protein. Therefore anything replacing these damaged cells are thought to be effective. Stem cell researchers around the world are trying to make this kind of cells from embryonic stem cells for replacement. However it should be noted that earlier trials in 1990s already started injecting normal cells from aborted fetuses into the affected patients' brains to replace those cells destroyed. Although not exactly same as stem cells, these researches did offer some useful information. First, the injected cells did actually survive and incorporated to the patients' brain system. Second, these cells could offer some benefit (although not dramatic in most cases).

Now, some of the patients have died and postmortem examinations told us something surprising -- in some cases, some of the injected cells acquired similar damage as the original disease cells. Parkinson's disease usually only hits old people. However those injected cells are still relatively "young" (slightly over one decade), how did these cells got the dangerous protein? No one could answer yet. Although only 6 cases were analyzed, these findings indicate the complex of this disease. Will the same thing happen to stem cell derived cells in the future? How to get away with this problem?

Further research is necessary. problems will be solved eventually.

Thursday, April 10, 2008

What can be done will eventually be done

-- in time!

just put it up here.

another step toward regenerative medicine -- clonal precursor cells

A recently online paper from Regenerative Medicine (May 2008, Vol. 3, No. 3, Pages 281-302) entitled The ACTCellerate initiative: large-scale combinatorial cloning of novel human embryonic stem cell derivatives might offer something toward both basic research and clinical medicine.

Michael D. West (BioTime, Inc, Alameda, CA) et al. used a shotgun-like, or random induction/selection, approach to isolate 140 cell clones (hEP as they named them)from human embryonic stem (ES)cells. These cells are not ES cells anymore. They are differentiated toward various different lineages but not terminally differentiated either. What are they? Not sure yet as of now because further characterization and comparison to all known cell types in our body is required. Are they useful? Yes. 1) these cells are relibable sources because ES cells are extremely sensitive to all kinds of environment factors and too difficult to control in experiment. Therefore ES cells with the same name from different labs may actually be different things. These hEP clones, once properly characterized, could certainly provide a reliable source for research. 2) From these, further study may induce them into different cell types needed in medical research/practice. Currently, people can only induce ES cells into a limited number of final differentiated cells and they are not pure at all. These certainly limited the progress of research and regenerative medicine. They didn't say this --but I think it is very interesting and practical -- following the same shotgun approach, these hEP cells could be induced to further differentiate down the road to become more specified cell types (randomly). Certainly, some of them should be actual tissue cells and could be useful. These might actually bypass the difficult targeted induction approach.

Ethical problems? Of course. For example, what exactly are those hEP cells or the further differentiated cells as I proposed? New entity?? Questions like these certainly exist but the research should move on because humans will benefit eventually. A quote from a pioneer Sir John. Gurdon, "if something works well, ethical concerns will disappear."

Wednesday, April 9, 2008

MethodShare from Genome Technology

Genome Technology Online has launched another method/technology forum called MethodShare. ( or

There are a few articles and some discussion about various life science techniques. But so far, I don't see anything really interesting or different from other general forums such as protocol-online. It is also not necessarily good if you are particularly interested in something for example python in bioinformatics -- you'd better go to more focused places.

Anyway, it is certainly a good e-Marketing strategy. And keep an eye on it!

Tuesday, April 8, 2008

not necessarily new but useful tips

These tips might help you increase the yield and quality of your DNA sample from gel extraction.

Although the manufactures don't really put these in their manual, actual bench scientist always have good tips for improving the experiments. --Talk to them or visit these blogs. --Will help.

Monday, April 7, 2008

Blogging your thesis?!

This guy, a PhD candidate in microbiology and currently at Tulane University, is blogging his ongoing thesis writing online.

With his advisor's approval and several journal editors' positive feedback, he's posting part of his thesis, namely the introduction (which is a kind of review), and probably material and methods. As for the unpublished result part, I doubt that his advisor will allow him to do this before publication. Open science has not reached that level yet. You still have to publish your research somewhere to get noticed and get cited. I doubt Nature or any other journals will accept a paper with a blog article as one of the references.

-- Well, keep an eye on this. Certainly a brillant idea!

--Should I also blog my thesis when I write it? Maybe --

Friday, April 4, 2008

smoking leads to lung cancer??

Have you been told or been thinking that smoking causes lung cancer? Well, this is not exactly clear from recent studies.

An association between a genetic variation on chromosome 15 (15q24/15q25.1) and risk of lung cancer was found by three independent studies. But the link to smoking, or more scientifically nicotine dependence, is not clear. Some of the studies are still preliminary. So it is still possible that people with 'abnormal' chromosome 15 tend to be affected by environment - smoking - more easily and therefore are more likely to develop cancer in the long run.

We'll see if further studies with more - up to millions of - people can make it clear.

The papers mentioned here are:
  1. Hung, R. J. et al. Nature 452, 633–637 (2008).
  2. Thorgeirsson, T. E. et al. Nature 452, 638–641 (2008).
  3. Amos, C. I. et al. Nature Genet. doi:doi: 10.1038/ng.109 (2008).

Thursday, April 3, 2008

Dynamic "cold" genetic material

Two recent papers changed the concept of "cold" DNA, the so called heterochromatin.

1. Proliferation-dependent and cell cycle–regulated transcription of mouse pericentric heterochromatin
The Journal of Cell Biology, 2007; Vol. 179, No. 3, 411-421

Cell cycle control of centromeric repeat transcription and heterochromatin assembly

Genetic information resides in DNA in most organisms. DNA is packed into chromatin and stays in nucleus of a cell. There are two different package status: one loose and one tight. These are the original concepts of euchromatin and heterochromatin coined by German botanist Heitz 80 years ago. He proposed that heterochromatin reflects a functionally inactive state of the genome (all DNA information of an organism). Decades of research have generally been supportive to this idea. Heterochromatin is generally gene poor, highly packed, late replicating, and has a very low recombination rate. Modern molecular hallmarks of heterochromatin generally include heterochromatin protein 1 (HP1, swi6 in fission yeast) and methylation of histone H3 lysine 9 (H3K9) by histone methyltransferase (HMTase) (suv39, clr4). On the whole, Heitz’s original “inactive state” hypothesis still holds until recently.

The first paper demonstrated cell-cycle-specific transient disruption and transcription of mouse pericentric heterochromatin. It shows that mammalian pericentric heterochromatin is transcribed by RNA polymerase II twice during the cell cycle. A heterogeneous population of short RNAs (about 150 bp) is generated during mitosis, while a longer (mostly >1 kb) population is produced in late G1 and early S phase. Cell cycle regulation of pericentric transcription does not require Suv39h1,2-dependent chromatin modification, but it does require passage through "Start" in G1 phase. Future studies will determine whether these mammalian pericentric transcripts are important for heterochromatin formation as they are in fission yeast, as reported in the second paper.
in this paper, at regions serving as RNAi-dependent heterochromatin nucleation centers in fission yeast (in the pericentric, mating-type, and telomere regions), heterochromatin is abundant during G2 but greatly reduced during M, G1 and S phases. Heterochromatin reduction in M, G1 and S is correlated with phosphorylation of histone H3 on serine 10 (H3S10) and with binding of condensins. Genetic analyses show that condensin binding (in M and G1) and methylations of H3K36 (in S) and H3K9 (in G2) all contribute toward proper heterochromatin formation in G2 and toward proper regulation of transcription of the RNAi-dependent nucleation centers during S phase.

Because centromere /heterochromatin defect is almost the most common feature of cancers, this transcription could be the most basic factor during cancer formation. It might be that this transcription leads centromere structure problem, which leads to chromosome segregation defect which cause gene mutation etc. and cancer eventually.

Wednesday, April 2, 2008

Combining Genomic and Clinical Data for Cancer Therapy

This just came out today. So check it out.

An article entitled " Gene Expression Signatures, Clinicopathological Features, and Individualized Therapy in Breast Cancer" in the Journal of the American Medical Association, retrospectively studied traditional diagnostic standards of breast cancer outcomes — such as patient age, tumor size, and so on — and information about gene expression by modern genomic technology in a thousand breast cancer tumors. The conclusion is appealing: Gene expression patterns can, indeed, define subgroups of women with different prognoses and treatment responses.

“The combination of these two methods, one of which uses the clinical description of a patient’s breast cancer and the other which looks at gene expression at the molecular level in a patient’s tumor, may allow us to [match drugs with patients] with unprecedented accuracy,” senior author Anil Potti, an investigator at Duke University, said in a statement.

Traditionally, breast cancer evaluation is based on factors the so called TNM classification system, such as the patient’s age, tumor size, the level of lymph node involvement, and the degree of metastasis. These clinicopathological features could be employed to make predictions about clinical outcomes and help doctor’s to determine whether adjuvant cancer therapies such as chemotherapy or radiation therapy are warranted or necessary for different patients. However the estimation simply based on these factors are not always meaningful, e.g. it tends to overestimate cancer recurrence in younger patients.

To determine whether genomic data can provide additional information, the researchers studied women with early-stage breast cancer who had been followed for on average 11 years after initial assessment.
Indeed, the researchers did find that "molecular traits of patients in the poor prognostic clusters were highly specific and distinct from those of the good prognostic carriers”.

As the authors pointed out, identifying these subgroups may not only refine predictions about patient outcomes, it also provides information about patients’ underlying biology and the tumor microenvironment. That’s because gene expression patterns reveal different genetic pathways that are activated or silenced in different tumors during the long tumor formation progress.
For instance, low expression of cancer risk genes, chromosomal instability, and so on predict good outcome. However, high expression of genes associated with oncogenic pathway activation and wound healing etc. tend to be associated with poor outcome. Some genetic signatures also might indicate different responses to chemotherapy.

As wrote in an accompanying editorial in the same issue of JAMA, by Northwestern University researchers Chiang-Ching Huang and Markus Bredel, “This is one of the largest studies in human cancer showing the ability of gene expression profiles to improve risk stratification beyond established risk assessment algorithms that take into account clinicopathological variables”. This study “demonstrates the potential value of using microarray-based gene signatures to refine outcome predictions.”