Wednesday, March 23, 2011

2nd Evaluation

Personal blog posts: 15
  • Time spent on my posts: 1-2 hrs each
I'm active in the blogging community that is our classroom by commenting on others blogs.  There's a few blogs I follow closely and try to comment on most every post (Nuclear Option).  I've also responded to every comment on any of my blogs, interacting with classmates comments.  Also, when someone comments on one of mine, I try to return the favor on their blog.

Monday, March 21, 2011

Nanopore Sequencing

It has been said that the goal in the genetic sequencing industry is to develop a sequencing method within the next five years that will bring the cost of a human genome to $1000.  Crazy cheap considering it was 10 million dollars five years ago.  Many believe the technology that will get us there is nanopore sequencing.

With this method of sequencing, single strands of DNA will be forced through a membrane with extremely tiny holes in it, or nanopores.  These would be a width small enough to only let one strand of DNA through at a time, about one billionth of a meter!

In the image, the yellow zipper looking object is a DNA strand.  It is forced through the membrane due to an electric force.  This force is obtained by a positive and negative ionic solution on either side of the membrane.  Also, there is a voltage difference across the small pore in the membrane, so electrons will pass from one side of the pore to the other.

To reiterate an earlier post, DNA consists of four nucleotide bases, represented by the letters A, C, G, and T.  These four bases are the building blocks of life, or the blueprint if you will.  As the DNA strand moves through the membrane, electrons will experience a current change based on the nucleotide base that is passing through, either A, C, G, or T.  A device measuring current will allow a computer to determine the exact sequence of bases as they pass through the membrane, and once all of the DNA has passed through, a whole genome will be obtained.

It is anticipated that this technology is likely to succeed and bring the cost of sequencing down significantly.  It's really only a matter of time! Check out this link for a 3 minute video explaining nanopore sequencing technology in a slightly more in depth manner.

Monday, March 7, 2011

Cost of Genome Sequencing Dropping like a Rock

Check out this graph from

Note the logarithmic scale on the vertical axis!  Something else you may not recognize is Moore's Law, which is a long-term trend in the computer hardware industry that involves the doubling of computing power, a decent comparison to show the great progress of sequencing technology.  Five years ago it cost over $10 million, but today it costs only $20,000 to sequence an entire human genome.

In the sequencing technology industry, the big goal is to develop a $1000 genome sequence in the next 5 years.  If (more like when) this happens,  I believe many things will change in medicine, and I bet many of you reading this may get your DNA sequenced by such a machine within the next decade.

For my next post I'll talk about nanopore sequencing, a cool technology that may get us to this 1000 dollar mark!

Friday, March 4, 2011

Human DNA similarities to chimps and bananas, what does it mean?

When I was a child I remember hearing humans came from monkeys.  I asked myself, "Then why are monkeys still around?" A valid question.  The problem with the initial statement though is that we did not come from monkeys, but rather we share a common ancestor.  When it comes to common ancestors and evolution, genetic sequencing has provided a great understanding.

I'm sure you've heard it before; humans and chimpanzees are about 98.8% similar.  What does that really mean though? This number refers to comparing single nucleotide changes in the DNA, or changes in the sequence of the A,C,G,T code.

Comparing genetic duplications in genes, the number lowers to 96%.  What's a duplication? As Even Eichler of University of Washington says, if we consider the genetic code as a book, entire pages will be repeated in one species but not the other.  So conservatively, we are 96% alike with out closest cousin.  Here's some other common animals and our genetic similarites (these numbers are consistent across all reliable sources):

Cat: 90%
Cow: 80%
Mouse: 75%
Fruit Fly: 60%
Banana: 50%

 Interesting to look at.  What I find most fascinating is the 50% match to bananas! Animal and plant life share so much ancient DNA coding from way back when plant and animal life diverged approximately 1.5 billion years ago.

The sequencing technology allowing for genetic comparison has been huge for anthropologists and evolutionary biologists.  Anthropologists have used comparisons of genes between humans and our closest cousins to better understand when and how genetic variations occurred.  Evolution was already well established before this technology existed with fossil records, embryology, comparisons of skeletal systems, study of vestigal appendages, and finally the understanding of the driver of evolution: natural selection.  Genetic sequencing confirmed our understanding of species divergence and evolution, and also allowed scientists to better understand and build the the fascinating "tree of life."

Tuesday, March 1, 2011

Hot off the Press: Genetics in the News

 Some recent genetics news:

  • Genetically modified crop growing increased by 10% worldwide in area last year, up to 148 million hectares.  This is equivalent to about 10% of the world's total cropland area.  The article, found here, also states several new GM crops will be approved for commercialization by 2015.  These include potatoes resistant to the disease causing the Irish famine in 1845, disease-resistant bananas, and insect resistant tomatoes, broccoli, and cabbage.

  • This article raises ethical questions about genetic predictors of disease and introduces a survivor of breast cancer.  About 10 years ago a genetic test had revealed her mother carried a mutation signaling a heightened risk for the disease.  Since learning of her high risk, she decided to be vigilant and opted for frequent mammograms.  Eventually she did develop breast cancer, but due to the frequent mammograms, it was diagnosed very early and was treatable.  Knowing in advance helped this patient, but some patients don't want to know about their susceptibility to diseases, as they feel it is "future-robbing" news.

  • Genetically modified fungus could be used to combat malaria carried by mosquitoes.  Instead of genetically modifying a new breed of mosquitoes, researchers at the University of Maryland have modified a fungus that usually attacks the mosquitoes.  Now, the fungus only delivers compounds that target the malaria parasite.  They believe that malaria transmission to humans could be reduced five-fold.  This is significant, as malaria deaths each year are estimated to be about 780,000 in the world.  The article may be found here.