DNA Sequencing!

I'd like to apologize in advance for this long-winded post, but I thought a breakdown of genetic sequencing was necessary before I begin to talk about the more interesting stories and aspects of genome sequencing.

The human genome has about 3 billion base pairs, making up around 20000 genes, which then make op our 24 chromosomes.  The base pairs are made up of four nucleotides, represented by the letters A, C, G,  & T.  So how do we accurately obtain the sequence of 3 billion of these letters? The method used today is called the termination method, and will be explained below.

First, chromosomes are cut into lengths around 150000 base pairs long, using a restriction enzyme.  These enzymes cut the DNA whenever they encounter a specific sequence of letters.  Next, the DNA fragments are separated from each other and are introduced to DNA vectors, in order to make clones.  DNA vectors are DNA strand of known sequence, which form into a circle.  The circles are split open chemically, and allow the human DNA fragment to insert, see illustration.  To clone these vectors, bacteria are introduced.  When the bacteria takes a vector into its cell, the vector will be duplicated when the bacteria duplicates.  These bacteria are then cultured until millions of copies of one DNA fragment are obtained!

Now the sequencing process can begin.  Heat is added to separate the double strand DNA into single strand.  Then, three materials are added to the copies of the DNA fragment & vector.  First, a primer is added, which has a sequence matching the end of the vector strand, so the beginning of the human DNA can be found.  A mixture of regular nucleotides, A, C, T & G is added, and new double strands begin to form onto the separated single strands.  This process would go on until the whole human DNA fragment is duplicated, but special terminator nucleotides are added to the mixture to stop the process at random points.

Since the ratio of regular to terminator nucleotides is very high, duplicated strands will be anywhere from 2 base pairs long to hundreds of base pairs long before a terminator happens to stop the process.

Now we have millions of DNA strands of varying length, with special terminator nucleotides on the end of each one.  These terminators are extra special because each one of the four has the ability to reflect light when a laser is shown on it! The colors reflected can be seen in the illustration just above.

Illustrations courtesy of pbs.org: NOVA online

The final process in sequencing is involves separating the new strands based on length, and reading the terminator nucleotide reflection of each length.  But how can these be separated by length, when the a base pair is only the size of a molecule?  The batch of DNA is placed at the end of a capillary tube with a gel inside.  The gel allows shorter lengths to travel faster than longer ones, which puts them in order by length!  Finally the laser is projected onto the other end of the capillary, and reads the terminator nucleotide of each length of DNA.  A DNA sequence can finally be put together! To the laser detector, the sequence show in the illustration to the right will read green, blue, green, green, yellow, red, which translates to ACAAGT.

This process of sequencing is repeated for all of the cut chromosome fragments and different vectors until the entire sequence is obtained!

The Future of Genomics and You

From Nature Feb. 2011

Someday in the future, it may be standard procedure for a human's genome to be mapped right after birth.  Each person may be provided with a genetic information card (like a credit card).  This can act as a method of identification and could potentially revolutionize pharmaceuticals.  Provided with your genome, a pharmacy may be able to alter a drug so it is taylor-made for you.  This could eliminate side effects and increase effectiveness of medicine.

The scenario presented above is just a snap-shot of where some scientists believe genomics will take us in the future, although we may never see this in our lifetimes.  A recent article in the journal Nature entitled "Charting a course for genomic medicine from base pairs to bedside" by Green & Guyer outlined their take on the future of and associated challenges that genomics will face.

The field of genomics has been one of the fastest growing in science in the last few decades.  Many species' genomes have been mapped, and links have been found between many diseases and genetic coding.  The current technology is improving, but costs too much and can take too much time to catalog a given specimen's genome. 

The article states the focus of genomics is to understand human biology and the diagnosis, prevention, and treatment of human disease (genomics in agriculture are outside the scope of their work).  A great opportunity that arises is the ability to treat a disease without a thorough understanding of it.  For example, different cancer therapies may be selected based on the genomic profile of the tumor in question, without a full understand of how the tumor works.  To gain the full benefits that genomics will someday provide, Green & Guyer believe the next step must be the genome cataloging of tens (even hundreds) of thousands of different people.  With this, diseases may be correlated to genetic variations in humans that either create the disease or make the human more susceptible to the disease.

The largest step in creating this huge database of human genomes is the development of cheaper and faster equipment.  Once a genome can be analyzed quickly and economically, the amount of genetic information available will skyrocket.  Legal issues will be associated with the availability of this personal information, but they probably will be handled in a similar fashion as medical records are handled today.

In sum, a community effort is needed to make technology better and to create a large database of genetic information.  Once available, individual scientists will be able to take this information and pursue hypothesis-driven research to advance the field of medicine and better the health of millions.

Dr. Oz's take on GMO = terrible science communication

Browsing other blogs, I found one called Tomorrow's Table by Dr. Pamela Ronald, a respected plant pathologist.  In December 2010, she appeared on a panel of experts to discuss GMO food safety on the Dr. Oz show.  I'll give a summary, but the segment can be found here. 

First, I just want to say how frustrating it was watching this.  Frustrating not for the fact that I'm pro GMO food (I'm not necessarily), but rather because the science was presented so poorly by Oz and his producers.  Dr. Ronald was also frustrated, if you check out her blog.  The show starts out with a video overview of GMOs.  The background music is dramatic and fearful, and he uses words like "franken foods."  This is followed by Oz questioning the three experts about GMOs, and the general conclusion (among Oz and two of them) is that they are unsafe.  The whole segment they team up on Dr. Ronald, and it seems the only reason she is there is so they can claim they represented both sides.  The segment is framed very well for someone trying to scare viewers of GMOs, focusing on human health and children's health.  Both sides were not represented properly, and Oz's communication used the deficit model.

Through the last few weeks I've research these crops, and human health is the least of our worries for the current GM crops out there.  They've been in the food supply about 15 years with no health concerns to show for it.  The companies engineering these plants check that the new protein is safe, and they check if the new crop is otherwise identical to the original.  Then, the plant still has to meet FDA standards for a normal crop, there are not yet special guidelines for GM crops.  There are other risks, if you view my earlier posts.

Oz also tries to make the argument that 6 European countries have banned GMOs, therefore they should be considered unsafe.  Ronald counters that the scientific community in Europe is generally in favor of GMOs, but the reason they are banned is a political and social one.  Based on how politics work, I'm going to have to side with Dr. Ronald on that one.  Media, religious, and political leaders can get people to believe anything.  For example, a NPR report recently showed that over half of Republican primary voters still believe Obama was not born in the United States.  One that I find particularly offensive as a geologist is that many still think the Earth is 6000 years old, despite the overwhelming amount of scientific knowledge that shows it is over 4 billion years old. 

I'd like to conclude by saying that it is unfortunate that someone with a TV show can potentially influence millions in a 15 minute segment through misleading and improper science communication.  The truth is though, most people receive all of their knowledge about current issues through television media (often times very biased).  Dr. Ronald pressed the audience to visit specific science websites that would show peer-reviewed work supporting that GM crops are not harmful to human health.  But c'mon, you know 99% of the viewing audience would never do that.  Why did Oz and his producers present GM crops this way? Because they wanted the shock effect and wanted the fantastic and frightful news that would boost their ratings.

Banana Vaccine

There is some research and experimentation into genetically engineering vaccines within plants, like bananas and tomatoes.  Vaccines today are very expensive to produce and sometimes have poor shelf lives, but by putting vaccines in foods those problems may be fixed.  

Most likely these vaccines would be "grown" in a controlled environment where cross-pollination and adverse effects on other species would not be possible.  But, considering what would be the widespread use and disposal of these foods, there is potential that the gene could enter the domestic food supply.  Ingestion in large quantities and ingestion by certain people with health conditions may be very harmful.  There also is the primary issue of the effectiveness of the modified foods as a vaccine.

It seems unlikely (and unsafe) at this point, but someday instead of a painful shot we may be immunized by a tasty banana.

Controversy: The Pros and Cons of Genetically Modified Crops

Genetically modified (GM) crops are a hot topic right now amongst farmers and environmentalists.  Here are some Pros and Cons, adopted from this PBS report.   After reading these I'd love to hear your opinions.  Do you think they are safe to humans? Even if they are safe, are they necessary considering environment risk? Also would like to hear any additional benefits or risks you may think of.  

Pros:

• GM crops may provide more nutrients, vitamins, and reduced saturated fats than traditional varieties.  
• Crops can be resistant to disease and insects, potentially cutting farming costs on insect/herbicides.
• Crops can be engineered to have a longer shelf life.
• Some believe GM crops may help fight world hunger.
• GM crops are already ingested in high quantities in the U.S. with no health concerns to show for it, and testing of new GM crops is very thorough (based on many sources I've seen).

Cons:

• Some studies show crop yields are not increased.
• There is the potential of "super weeds" and "super insect" evolution.
• Not all the effects may be possibly known, and the corporations pushing GM crops are profit-driven, leading some to believe they are overstated benefits and overlooking risks.
• Further travel down the road of monoculture.  Currently 15 species of crops account for 90% of world energy consumption (PBS.org).  A diversity of crops may be considered natural and provides insurance against drought and disease.
• These crops may hurt small farmers, as they will become reliant on seeds from corporations producing GM crop.  They may also hurt foreign farming if modification allows more tropical crops to be grown in more temperate climates.
• The EU and some other nations will not consume GM crops exported by other nations, so adopting them domestically could hurt U.S. export numbers.

Regulations on Sugar Beets

Sugar beets account for about 50% of sugar production in the U.S, and genetically modified sugar beets made up 95% of the total sugar beet crop in 2010.  From NPR,  The modified beets are "Roundup Ready", so the herbicide Roundup can be sprayed onto the beet fields, killing all weeds, but leaving the beets unharmed.

On Feb. 4th the USDA lifted a temporary ban on the planting of genetically modified sugar beets.  In late 2010 a Federal judge ruled that the beets cannot be planted until a full environment impact study is completed. The USDA lifted the ban due to the upcoming planting season, and due to their fear that U.S. sugar beet yields would severely drop if GM sugar beets are not planted.

Opponents feel the USDA broke the law, as they disputed a federal court ruling.

Self Interview and 1st Evaluation

What is the purpose of this blog?

 - The purpose of this blog is to inform people about genetics and new advances in the field.  It also focuses on presented the information in an understanding and entertaining way.

Who is the imagined audience(s) of this blog?

- My classmates and also the general public.

Better science communication, throw a party!

A reading for my class from Investigating Science Communication showed that many times, even when dialogue is attempted, scientists feed their knowledge/research to people and questions are encouraged afterward.  This can be very similar to the feared deficit approach.  

In the reading, Davies proposed that scientific dialogue should aim to have an impact on individuals; large scale impacts on science and policy are not always necessary.  To do this, I thought, a more social event should take place.  Scientists may come, give a very brief talk about their work, then they should mingle with the invited and interested public.

There is no need for a stage and auditorium seating; tables, chairs, and a comfortable atmosphere is the proper setting to encourage conversation.  Drinks and appetizers should be available (I recommend a cash bar, as an open bar may get out of hand).  This way people will be able to jump from scientist to scientist, express their views and ask questions, and enjoy their martinis.  When science is communicated in a more personal and conversational way, as Alan Alda related in the video we watched, it is better received and understood.  I think better understanding between scientists and the public may be achieved at an event like this compared to a talk and Q & A session.

Just a thought!