Basics

Vizzini: He didn't fall? Inconceivable! Inigio: You keep using that word. I do not think it means what you think it means. - William Goldman, The Princess Bride
Excuse me while I temporarily interrupt the genome sequencing series to define a word. Artifacts in the classroom It's disorienting. You learn a word in certain context. You're sure of it's meaning and then you end up in a situation where people use the word in ... Read more
To the ancient Greeks, a chimera was a kind of monster, with the body of a goat, the tail of a dragon, and a lion's head. To geneticists, a chimera can be an animal that's derived from two embryos, such as a transgenic mouse. Or if the organism is a plant, it can be a plant with a graft. We have a chimeric cherry tree in our back yard with branches from Rainier cherries, Bing cherries, and Van cherries. And you should see the chimeras that hang out at evolgen. Naturally, the DNA cloning and ... Read more
The general steps in genome sequencing were presented in the earlier installments ( there are links at the bottom of the page), but it's worth repeating them again since each of the earlier steps has a bearing on the outcome of those that come later. These are:
  • Break the genome into lots of small pieces at random positions.
  • Determine the sequence of each small piece of DNA.
  • Use an assembly program to figure out which pieces fit together.
That first step, making a collection of DNA fragments (a library), with breakpoints at random positions is of ... Read more
"How much do I love you? I'll tell you no lie. How deep is the ocean? How high is the sky?" - Irving Berlin The other installments are here: Part I: Introduction Part II: Sequencing strategies Part III: Reads and chromats ... Read more

Shotgun sequencing. Sounds like fun. Speculations on the origin of the phrase I think that this term came from shotgun cloning. In the early days of gene cloning before cDNA, PCR, or electroporation; molecular biologists would break genomic DNA up into lots of smaller pieces, package DNA in lambda phage, transduce E. coli, and hope for the best. Consistent with the shotgun metaphor, we even used to store our microfuge tubes in plastic bullet boxes that my boss found at the sporting goods store. (Apparently this practice was unique ... Read more

Considering that several genomes that have been sequenced in the past decade, it seems amazing in retrospect, that the first complete bacterial genome sequence was only published 12 years ago (1). Now, the Genome database at the NCBI lists 450 complete microbial genomes (procaryotes and archea), 1476 genomes from eucaryotes, 2145 viruses, and genome sequences from ... Read more
About a week ago, I offered to answer questions about subjects that I've either worked with, studied or taught. I haven't had many questions yet, but I can certainly answer the ones I've had so far. Today, I'll answer the first question: How do you sequence a genome? Before we get into the technical details, there are some other genomic questions that you might like answered. How much does it cost to sequence a genome? I remember in 2002, when we were at the ... Read more
In the effort to help us define a few basic concepts, PZ started out by giving us a nice simple definition of a gene, but as he, rightly noted:
I tell you right now that if I asked a half dozen different biologists to help me out with this, they'd rip into it and add a thousand qualifiers, and it would never get done.
Well, okay, technically speaking he didn't ask me for help. But, since I'm a ... Read more

The wind storms and heavy rains that hit Seattle a few years ago, and flooded the Battery Street tunnel, demonstrated why a bypass mechanism can be a helpful thing - for both bacteria and motorists.

When the weather is nice, I bike to work. But when the weather gets bad, (I consider rain and 69 mph winds to be BAD), I take the easy way out. On the day of the big windstorm, driving home was not so easy. A mudslide covered one of my usual paths, blocked two lanes on a very busy street, and stopped traffic well into the depths of the city. Since we had to get to a soccer ... Read more

There are five ways that I know of that allow bacteria to escape death. I call these the five paths to antibiotic resistance

1. Persistence is resistance: Most antibiotics kill by acting on the metabolic pathways needed for bacteria growth. Ironically, bacteria can survive by not growing. Read more about it.
2. The Star Wars Strategy: Destroy (or modify) the antibiotic before it destroys you.
3. Pump it out. ... Read more

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