Molecular Biology

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Category archives for Molecular Biology

New York Times Cracks

Let’s go through the basics again. Cracking the genetic code refers to figuring out how DNA encodes the information to make proteins — that was done decades ago. Sequencing a genome does not mean that you have decoded the genome; presumably, decoding a genome would mean you’ve figured out the function of every part of…

Troubleshooting with the Hive Mind

Late last week, my PCRs stopped working. One day I was able to amplify DNA from multiple different templates using different primers, and the next day I couldn’t. This is a major setback for me — a huge chunk of the remaining work I need to complete for my PhD involves doing PCR. If I…

Junk in the Media

The recent Scientific American article on junk DNA (discussed here) has instigated a quite a furor in the bioblogosphere. Here is a collection of links: ERV linked with a tone of disgust. I restated my frustration with the term junk DNA. JR Minkel, the author of the Scientific American article, responded to my criticisms. Ryan…

Junk DNA in Scientific American

Would I write about junk DNA? No. Never. Not me. Not even when Scientific American publishes sub par articles on junk DNA. Well, they’re at it again. The most recent junk DNA article describes a study by Gill Bejerano of Stanford University which I can’t find published anywhere (neither can ERV). Is Scientific American describing…

If it’s not human, it’s crap!

Those of us who work on non-human systems often grumble about the total disregard human geneticists (that’s geneticists who study humans, not humans who are geneticists) have toward non-human research (that’s research on non-humans, not non-humans doing research). I get the feeling that plant biologists have the same attitude toward non-plant researchers, and I imagine…

On Human Genes and Silent Mutations

Both Carl Zimmer and Larry Moran have posts on the gene content in the human genome. Carl points out that the estimate of the total number of genes in the human genome is decreasing, but we still don’t know what a whole bunch of those genes do (according to the one database he searched). Larry’s…

Junk DNA, Revisited

Some bio-bloggers are atwitter over an article by Wojciech Makalowski on Scientific American’s website about Junk DNA. I’m a little late to the game because, well, I’ve been really busy looking at sequences to determine if they are junk DNA. Is it irony? Is it coincidence? Who cares? It’s an opportunity to discuss semantics, and…

A Question about Retroposition

Duplicated genes can arise via various mechanisms — polyploidization, chromosomal duplication, segmental duplication, and retroposition — and we can usually distinguish the various mechanisms as each has distinct signatures. For example, retroposed duplicates arise when an RNA transcript is reverse transcribed back into DNA and re-inserted into the genome. This is how many transposable elements…

Shotgun Sequencing a Eukaryotic Genome

Shotgun sequencing refers to the process whereby a genome is sequenced and assembled with no prior information regarding the genomic location of any of the DNA we sequence. There are quite a few steps that you have to go through before you have an assembled genome sequence. We’re going to cover isolating DNA, putting the…

Mutation

Where the variation comes from. Evolution proceeds by the action of many different evolutionary forces on heritable variation. Natural selection leads to the increase in frequency of variation that allows individuals to produce more offspring who, themselves, produce offspring. Genetic drift changes the frequency of variation through random sampling of individuals from one generation to…