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Basics

Category archives for 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.

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…

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…

“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 Part V: checking out the library We all know that sequencing a genome must…

Shotgun sequencing. Sounds like fun.

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…

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?

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…

The wind storms and heavy rains that hit Seattle recently, demonstrated why a bypass mechanism can be a helpful thing – for both bacteria and motorists. Under the bridge on Mercer, from the Seattle Times

This is the fifth part of a multipart series on antibiotic resistance in bacteria. The previous installments: 1. A primer on antibiotic resistance: an introduction to the question of antibiotic resistance. 2. Natural vs. synthetic drugs: what is the difference between an antibiotics and synthetic drugs. 3. How do antibiotics kill bacteria? a general discussion…