genomics
evolgen | October 12, 2007Previous entries:
Part 1 - Introduction
Part 2 - The Backstory
Part 3 - Obtaining Sequences
Part 4 - Obtaining More Sequences
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 5 of this series (Examining the Outgroups) can be found below.
Examining the Outgroups
In the previous post I mentioned that the two outgroup species in our analysis, the mosquito Anopheles gambiae and the honeybee Apis mellifera, have only one copy of the aldolase gene. If that's the case, then it's likely that the gene was…
evolgen | October 10, 2007Please God, don't let it happen. Please don't let Franky Collins win this stupid award. I don't usually make pleas to you, but, given that this is a matter regarding a man of faithTM, I figured it's a good time to plea to the sky fairy. So, do whatever you can to prevent Congress from awarding Frank the medal.
As for my more terrestrial readers, here's the skinny. The Genetic Alliance is petitioning the US Congress to award Collins the Congressional Gold Medal. Why? Because he's in charge of the National Human Genome Research Institute (NHGRI). Now, the NHGRI has done a great job in promoting…
evolgen | October 5, 2007Previous entries:
Part 1 - Introduction
Part 2 - The Backstory
Part 3 - Obtaining Sequences
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 4 of this series (Obtaining More Sequences) can be found below.
Obtaining More Sequences
Last time we downloaded sequences for both aldolase genes from Drosophila melanogaster (see here). But, if we want to study the evolution of these genes, we need sequences from a few more species. There are now complete genome sequences available for 12 Drosophila species…
evolgen | October 3, 2007Previous entries:
Part 1 - Introduction
Part 2 - The Backstory
This post is part of a series exploring the evolution of a duplicated gene in the genus Drosophila. Links to the previous posts are above. Part 3 of this series (Obtaining Sequences) can be found below.
Obtaining Sequences
In the previous post I described the aldolase gene family, which encode proteins involved in cellular respiration. There are two aldolase genes in the Drosophila melanogaster genome. If we want to study the evolution of these genes, we can obtain the sequences from the 12 Drosophila species that have had their…
evolgen | September 28, 2007This is a repost (with some edits) of an introduction to publishing original research on blogs -- a series I am reintroducing. The original entry can be found here.
In April of last year, Bora pushed the idea of publishing original research (hypotheses, data, etc) on science blogs. As a responsible researcher, I would need to obtain permission from any collaborators (including my advisor) before publishing anything we have been working on together. But what about small side projects or minor findings that I don't expect to publish elsewhere? As it turns out, such a project has been laying…
evolgen | September 26, 2007The human genome is one big, bloated motherfucker. It's almost all non-protein-coding DNA. The same is true for many other eukaryotic genomes. Sure, some of it has a function. But a whole lot of it (and maybe most of it) is just junk.
There are some who point to a relationship between genome size and organismal completexity and argue that those large genomes are necessary to explain the compelexity they observe. There are other that disagree -- T.R. Gregory at Genomicron being one of the more vocal objectors in the geno-blogosphere. First off, how do you measure complexity? Second of all,…
evolgen | September 26, 2007Over a year ago I threatened to perform some original research and publish it on my blog. I got as far as writing an introduction to the project, but I never actually posted any data. I know, I suck.I had hoped to make the project simple enough that people could follow along. The problem was the available data were not in a form that would be accessible for most readers. So, I've held off until now. But the appropriate data have now been deposited in Genbank, so I can continue the series.
Over the next couple of days I'll post the previously published entries, and they will be followed by the…
sporte | September 6, 2007One of my readers asked: Why does genome sequencing cost so much?
My short answer is because it's big.
But I thought it would be fun to give a better answer to this question, especially since I'm sure many of you are wondering the same thing.
Okay, so let's do some math.
Don't worry, this math isn't very complicated and I'll explain where most of the numbers come from.
Estimating costs from salaries
First, we'll take the easy route. My experience with grant budgets has taught me that the greatest cost for any project comes from salaries. If we look at the PLoS paper with Craig Venter's…
sporte | September 5, 2007If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.)
You may be wondering, and rightly so: just what is a SNP?
Never fear, hopefully this post will answer some of those questions.
tags: DNA sequencing, DNA , SNPs, genetic testing
SNP stands for Single Nucleotide Polymorphism. That's a mouthful. It means some people, will have one base at a certain position, in a…
sporte | September 4, 2007
"Come quickly, Watson," said Sherlock Holmes, "I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend."
The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value.
Holmes gazed thoughtfully at the map, then slowly lifted his eyes and coldly surveyed his subject's beaming countenance. "You have an affinity for the ocean," said Holmes, "that you indulged to excess as a reckless youth. An experience as a medic in the military changed your life and gave you a reason to do more than…
evolgen | September 4, 2007Lookie here -- they've sequenced Craig Venter's genome. What did they learn about Craig? Well, he's European. He has 46 chromosomes. He's got some structural differences from the reference genome. Venter also differs from the reference genome by insertions and deletions.Like every other human, he's got a boat load of repetitive sequences in his genome. And he differs from that reference genome in coding sequences.
Levy et al. 2007. The diploid genome sequence of an individual human. PLoS Biol 5: e254 doi:10.1371/journal.pbio.0050254
evolgen | September 2, 2007
Remember when I said that the near future of eukaryotic genome sequence would involve sequencing EST libraries (collections of mRNA, or transcribed genes) rather than de novo sequencing of whole genomes? Well, I did, even if you don't remember. Anyway, a new paper in PLoS ONE puts that approach to the test for the purpose of generating sequence data to study mammalian evolution. Here is the last paragraph from the paper, summarizing why EST sequencing projects are useful in phylogenetics:
While complete genomes are the ultimate data sets for resolving phylogenetic and evolutionary issues of…
evolgen | August 31, 2007
Eukaryotic genomes are chimeras of sequences from many different sources. There are the genes responsible for the normal functioning of the host, but there are also transposable elements (TEs), sequences from mitochondria (numts), and endogenous retroviruses (ERVs). In addition to those examples, other symbionts also infect eukaryotes and leave traces of their presence in the genomes of the hosts. One such parasite of many invertebrates is Wolbachia, a bacteria that invades the germ cells of its host and inflicts odd behaviors such as male killing, feminization of males, and reproductive…
evolgen | August 31, 2007Genome rearrangements are fast becoming one of the most interesting aspects of comparative genomics (I may be slightly biased in my perspective). We have known for quite some time that genomes of different species (and even within species) differ by inversions of their chromosomes (this was first studied in Drosophila). In fact, some of the early work on the evolutionary relationships of species was done using chromosomal rearrangements. Additionally, there's a whole lot of important biological implications of rearrangements, including speciation, human disease, and the function of genes…
evolgen | August 30, 2007
A group of researchers from France and Italy have sequenced the genome of the finest grape varietal, Pinot Noir. The genome has hallmarks of ancient triploidization, shared by other dicotyledons, but there is no evidence for recent polyploidization. That meant sequencing and assembling this genome is easier than doing so for other agricultural plants that experienced genome doubling (and tripling) as a result of domestication.
Comparisons of gene content with Arabidopsis thaliana reveals an enrichment of various gene families responsible for protein products that produce favorable features…
evolgen | August 21, 2007Nautilus, Nature's blog for authors, has a guest post by Robin Rose on long author lists, entitled "What's an author?". The post is representative of a certain brand of curmudgeonliness mixed with a dash of either ignorance or naivete. Rose has seen author list with more than 20 authors, and he's confused. Did each author contribute equally? How could the manuscript possibly have gotten written? How do you evaluate each author's contribution? Should we cite these long author publications differently? These are all questions running through Dr. Rose's mind, and he has bothered to share them…
evolgen | July 8, 2007I've got far too many tabs open in my browser window, and I gotta blog them ASAP so that I can clean up the ol' computer. Here are a few things I've been meaning to blog, in list form:
Nature Genetics has published an issue devoted to structural variation in genomes. There appears to be a bias toward human genomes, but it's cool nonetheless. Also, I'm pretty sure all the articles are FREE ACCESS.
The most recent issue of Molecular Ecology has a bunch of articles on the genetics of speciation. There's also an article on the genetics of pigmentation variation in Drosophila melanogaster.
Peter…
evolgen | July 1, 2007It's not entirely obvious at first, but this article in the New York Times is about the problems with gene patents in a world where one gene does not equal one protein. Now, we've known that this model isn't entirely correct, what with alternative splicing and all. Additionally, the human genome also contains many "genes" which are only transcribed into RNAs, but not translated into proteins. All of this has been pretty much accepted by geneticists for a few years.
But rather than putting all of this in the appropriate context, Denise Caruso muddies the waters by overemphasizing the…
evolgen | June 22, 2007
Sensing and reacting to one's environment is necessary for survival. Different species have different expertise in regards to how they sense their environment. Humans, for example, have reduced olfactory abilities relative to other mammals, but excellent color vision. Cats have good night vision, but poor vision during day light. These proficiencies and deficiencies in sensory abilities hold for non-mammalian taxa as well.
Olfaction and taste have been well studied in a variety of taxa. Amongst the invertebrates, the genes responsible for olfaction and taste in Drosophila are one of the best…