Genetics & Molecular Biology
sporte | March 24, 2009For the past few months, the shake-up that began with Next Generation DNA Sequencing has been forcing me to adjust to a whole new view of things going on inside of a cell. We've been learning things these past two years that are completely changing our understanding of the genome and how it works and it's clear we're never going back to the simple view we had before.
What's changed? The two most striking changes, to me at least, are the new views of the way the genome is put together and what the cell does with the information.
They just don't assemble chromosomes like they used to.
I used to…
sporte | March 22, 2009What do the missing Romanov children, genetically engineered humans, financial risk taking, and poop have in common?
You can read about all these topics from this month's Gene Genie carnival at Mary Meets Dolly.
Who would have thought that mutations could be so much fun?
sporte | February 2, 2009A long-sought goal in genetics has been to develop therapies that can use correctly functioning genes to replace genes with defects. If we had the technology to predictably modify our genomes, we would have the ability to cure many diseases instead of having to place people on medications for their entire lives.
For a long time, gene therapy has remained an elusive dream. But, in the past few years the dream has come closer to reality, especially in the case of ten children, who live because of researchers who kept that dream in sight (1).
Figure 1. Random children
Technorati Tags:…
sporte | January 6, 2009My garden at home is looking a bit bleak after all the snow, Mendel's Garden is blooming wonderfully at Jeremy Cherfas' blog Another Blasted Weblog.
Jeremy has prepared a nice collection of perennial favorites. I especially like the story about pea breeding and, if you view the post, there are several interesting pictures of peas. These peas are far more diverse than the kind you'd normally see in a genetics text. Not all peas are shrunken or waxy.
genetics, Mendel's garden, blog carnival
sporte | January 2, 2009The New York Times had a great article a couple of days ago on the need for personalized medicine to become more than a catchy phrase.
As we're learning more about the interaction between genes and drug metabolism, we're also learning that large numbers of people are either taking the wrong drug or taking drugs that won't work.
tags: personal genomics,
pharmacogenomics
Researchers have known for some time that genetic variants determine how well drugs work. Some versions of a gene cause a drug to be metabolized faster, some slower, and when combined, at an intermediate rate. In the…
sporte | January 2, 2009Mosquito-borne diseases, like Dengue and Malaria, are serious problems in many parts of the world. While some people are working on treatments for mosquito-carried disease, others are looking at ways to treat the mosquitoes.
Figure 1. Image of Aedes aegypti from the Public Health Library
tags: tropical disease, yellow fever, dengue, insect control,
malaria
Controlling insect activities by messing with their genomes isn't a new idea. In many parts of the world, screwworms are controlled by damaging their genomes on a large scale by treating the flies with X-rays and releasing the…
sporte | November 14, 2008Masha Gessen was faced with a terrifying choice: cut off her breasts, and possibly save herself from cancer, or use them to feed her child.
It was late at night when I walked back to my empty dorm room at the conference. Shivering, I stood on the narrow bed, quickly shut the windows, tore the blankets off the other bed, and wrapped myself up, trying to get warm. Too cold to sleep, I picked up my copy of Masha Gessen's "Blood Matters: From Inherited Illness to Designer Babies, How the World and I Found Ourselves in the Future of the Gene," expecting boredom to lull me into unconsiousness…
sporte | October 25, 2008Why should professional scientists have all the fun?
Researchers have been engineering glowing cats, and selling glowing fish at pet stores. High school kids can do genetic engineering too, if they have the right equipment. And you can help them get the equipment by contributing to our DonorsChoose fund drive.
If you're willing to help students, they'll be able to do biotechnology in the class room and learn about DNA. They'll put genes for green fluorescent protein into bacteria and see how that bit of invisible liquid in a test tube gets used to make a glowing protein.
Even better,…
sporte | October 21, 2008Maybe you did it for the extra cash. Maybe you wanted to be part of the sperm cube public art project. Whatever the reason, it's possible, just possible, your sperm took on a life of it's own, once you left it.
And now that a genome is no longer an entirely personal bit of information, you may be in for a surprise meeting someday, with the end result.
That's right.
Male adoptees are getting their DNA tested and getting information about their possible surnames.
According to the BBC news:
At least 30 men registered with US consumer genetic testing firm Family Tree DNA have found their…
sporte | September 27, 2008One of the holy grails of modern medicine is the development of a vaccine against HIV, the virus that causes AIDs. An obstacle to attaining this goal has been the difficulty in stimulating the immune system to make it produce the right kinds of antibodies. A recent finding in Science describes a gene that controls production of these antibodies and may provide insights to the development of an effective vaccine. (1).
Antibodies are special kinds of proteins that bind to things, often very tightly. If they bind to the right molecules, they can prevent viruses from infecting cells and target…
sporte | September 25, 2008Lots of bloggers in the DNA network have been busy these past few days writing about Google's co-founder Sergey Brin, his blog, his wife's company (23andme), and his mutation in the LRRK2 gene.
I was a little surprised to see that while other bloggers (here, here, here, and here) have been arguing about whether or not the mutation really increases the risk to the degree (20-80%) mentioned by Brin, no one has really looked into the structure and biochemistry of the LRRK2 protein to see if there's a biochemical explanation for Parkinson's risk. I guess that task is up to me.
Let's begin at…
sporte | August 21, 2008One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that sometimes this reconciliation may never happen.
One of the projects that I've been working on during the past couple of years has involved developing educational materials that use bioinformatics tools to look at the isozymes that metabolize alcohol. As part of this project, I've been…
sporte | August 12, 2008Ancestry tests aren't just for humans anymore. We went to Petco this weekend to buy dog food and found brochures for doggy DNA testing. Now, those of you with dogs of uncertain parentage need puzzle no longer. According to Petco, their SNP test (what is a SNP?) can identify over 100 different breeds and they'll tell you which breeds are represented in your dog and whether your dog's breeding is mixed (or pure).
The brochure from Petco also claims that knowing something about your puppy's parentage could be helpful in understanding their behavior and potential health risks. That's probably…
sporte | August 6, 2008This the third part of case study where we see what happens when high school students clone and sequence genomic plant DNA. In this last part, we use the results from an automated comparison program to determine if the students cloned any genes at all and, if so, which genes were cloned. (You can also read part I and part II.)
Did they clone or not clone? That is the question.
But first, we have to answer a different question about which parts of their reads are usable and which parts are not. (A read is the sequence of bases obtained from a chromatogram file.)
How does our data get…
sporte | August 5, 2008This the second part of three part case study where we see what happens when high school students clone and sequence genomic plant DNA. In this part, we do a bit of forensics to see how well their sequencing worked and to see if we can anything that could help them improve their results the next time they sequence.
How well did the sequencing work?
Anyone who sequences DNA needs to be aware of two kinds of problems that afflict their results. We can divide these into two categories: technical and biological.
Technical problems are identified using quality values and the number of bases…
sporte | August 4, 2008What happens when high school students clone and sequence genomic DNA?
Background
DNA sequencing is a wonderful tool for discovery and a great technique for getting students involved in molecular science. This fall, Bio-Rad will officially begin selling their DNA cloning and sequencing kit. Now, students across the country will have the tools in hand to begin their own projects cloning and sequencing plant genes.
Of course, without bioinformatics there's no way to know what's been cloned or sequenced.
This is where we come in. As part of an agreement with Bio-Rad, we adapted a version of…
sporte | June 20, 2008It's pretty common these days to pick up an issue of Science or Nature and see people ranting about GenBank (1). Many of the rants are triggered, at least in part, by a wide-spread misunderstanding of what GenBank is and how it works. Perhaps this can be solved through education, but I don't think that's likely. People from the NCBI can explain over and over again that some of the sequence databases in GenBank are meant to be an archival resource (2), and define the term "archive," but that's not going to help.
Confusion about database content and oversight is widespread in this…
sporte | June 19, 2008Right or wrong, the word "dopamine" always conjures up images in my head of rats pushing levers over and over again, working desperately hard to send shots of dopamine into their tiny little rodent brains.
Dopamine, like many other neurotransmitters (chemicals that send signals in the brain), works by binding to proteins on the surface of brain cells and sending a signal to the cell. There are five different subtypes of receptors for dopamine (D1-D5) with somewhat different activities (1) and drugs that bind to these receptors are known to have potent effects on brain activity and behavior (…
sporte | June 18, 2008In a recent post, I wrote about an article that I read in Science magazine on the genetics of learning.
One of things about the article that surprised me quite a bit was a mistake the authors made in placing the polymorphism in the wrong gene. I wrote about that yesterday. The other thing that surprised me was something that I found at the NCBI.
The article that I wrote about definitely made a mistake and I don't understand why it wasn't caught by the reviewers. I found it pretty quickly by searching OMIM and I was only trying to find information about dopamine, not verify results.…
sporte | June 17, 2008In its simplest sense, we imagine that learning occurs through a series of positive and negative rewards. Some actions lead to pleasure, others to pain, and it seems reasonable to expect that people will repeat the actions with pleasurable results and avoid those that ended in pain. Yet, we all know people who aren't deterred by the idea of punishment. We all know people who never seem to learn.
Could there be a physical reason, hidden in their genes?
In December 2007, Science published a study by Klein et. al. (1) where they asked if a specific genotype at a location called "DRD2-TAQ-IA"…