Molecular Biology

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Category archives for Molecular Biology

Of Genes and Species

I straddle the line between being a population biologist and a molecular geneticist. That’s a self-congratulatory way of saying that I am an expert in neither field. But existing in the state I do allows me to observe commonalities shared by both. For example, both fields have terminology (or what the uninitiated would call jargon)…

Gregg Easterbrook — good sportswriter, crappy at pretty much everything else he does — likes to take pot-shots at scientific research in his ESPN column “Tuesday Morning Quarterback” (TMQ). In this week’s edition he tells us how he doesn’t think scientific papers should have multiple authors and how he doesn’t like the advertisements in the…

Chromosome Number and Chromosomal Fusions

To the uninitiated, chromosome number may appear to reflect genome size — more chromosomes would mean a larger genome. This is not necessarily the case if we measure genome size by the number of base pairs in a genome. There are two primary ways to change chromosome number: chromosomal duplications and chromosomal fusions/fissions. Chromosomal duplications…

Ploidy and Sex Determination

There are a lot of different ways for animals to determine which individuals develop into boys and which ones become girls. You’re probably most familiar with the form of chromosomal sex determination that utilizes X and Y chromosomes — males are XY and females are XX. There are others, including ZW (males are ZZ, females…

Mutations are the fuel that drives the engine of evolution. Without mutations there would be no variation upon which natural selection and other evolutionary forces could act. Furthermore, much of the theoretical results regarding evolutionary genetics depend on estimates of mutation rates. For example, Kimura showed that the rate of fixation of neutral mutations is…

Phenotypic differences between populations, species, or any other taxonomic classification can be attributed to genetic and environmental causes. The genetic differences can be divided into sequence divergence of transcribed regions, copy number divergence, and expression divergence. These categories are hardly independent — expression divergence results from the evolution of the protein coding sequences of transcription…

Tissue Specific tRNA Expression

In light of the recent post on translational selection, I give you this paper from PLoS Genetics on tissue specific differences in tRNA expression from humans. From the abstract: We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue…

A Sequence Like Poison

New Scientist reports on research to identify DNA sequences that cannot be found in any nucleotide database. These sequences are short — so as to decrease the probability that they are missing due to chance alone — and the researchers from the Boise State University have identified over 60,000 15 nucleotide stretches of DNA that…

Silent Mutations Continue to Speak Up

Pim van Meurs has a blog post at The Panda’s Thumb about the recent paper on translational selection on a synonymous polymorphic site in a eukaryotic gene (DOI link). He points out that this was predicted in a paper from 1987. In short, the rate of translation depends on the tRNA pool — amino acids…

Not-so Silent Sites

As we all know, the genetic code is redundant. Within protein coding regions, substitutions at silent sites do not affect the amino acid sequence of the encoded protein. Because of this property, these synonymous substitutions (so-called because they result in the same amino acid) are often used to estimate the neutral rate of evolution —…